From b9c781a0a71a2803959926ce3027decfeb1db1ed Mon Sep 17 00:00:00 2001 From: flaviomoc <81574057+flaviomoc@users.noreply.github.com> Date: Mon, 20 May 2024 01:35:23 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20flaviomo?= =?UTF-8?q?c/divraster@79525362c3f82ca5d51ad1d3237bec7927f0341d=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/divraster-vignette.html | 2 +- pkgdown.yml | 2 +- reference/index.html | 5 ++ reference/spat.alpha2.html | 124 +++++++++++++++++++++++++++++++ search.json | 2 +- sitemap.xml | 3 + 6 files changed, 135 insertions(+), 3 deletions(-) create mode 100644 reference/spat.alpha2.html diff --git a/articles/divraster-vignette.html b/articles/divraster-vignette.html index dbb90b4..d910375 100644 --- a/articles/divraster-vignette.html +++ b/articles/divraster-vignette.html @@ -82,7 +82,7 @@

Flávio M. M. Mota, Neander M. Heming, and Gabriela Alves-Ferreira

-

2024-05-19

+

2024-05-20

Source: vignettes/divraster-vignette.Rmd
divraster-vignette.Rmd
diff --git a/pkgdown.yml b/pkgdown.yml index 1949245..07d941b 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.0.9 pkgdown_sha: ~ articles: divraster-vignette: divraster-vignette.html -last_built: 2024-05-19T20:12Z +last_built: 2024-05-20T01:32Z urls: reference: https://flaviomoc.github.io/divraster/reference article: https://flaviomoc.github.io/divraster/articles diff --git a/reference/index.html b/reference/index.html index 6e4d819..89356a9 100644 --- a/reference/index.html +++ b/reference/index.html @@ -97,6 +97,11 @@

All functionsspat.alpha2() + +
Alternative method to calculate alpha taxonomic diversity
+
+ spat.beta()
Spatial beta diversity for raster
diff --git a/reference/spat.alpha2.html b/reference/spat.alpha2.html new file mode 100644 index 0000000..02d6f72 --- /dev/null +++ b/reference/spat.alpha2.html @@ -0,0 +1,124 @@ + +Alternative method to calculate alpha taxonomic diversity — spat.alpha2 • divraster + Skip to contents + + +
+
+
+

Alternative method to calculate alpha taxonomic diversity

+ Source: R/alpha2.R +
spat.alpha2.Rd
+
+ +
+

Alternative method to calculate alpha taxonomic diversity

+
+ +
+

Usage

+ 
spat.alpha2(bin, cores = 1, filename = "")
+
+ +
+

Arguments

+
bin
+

A SpatRaster with presence-absence data (0 or 1) for +a set of species.

+ + +
cores
+

A positive integer. If cores > 1, a 'parallel' +package cluster with that many cores is created and used.

+ + +
filename
+

Character. Save results if a name is provided.

+ +
+
+

Value

+ + +

A SpatRaster object with richness.

+
+ +
+

Examples

+ 
# \donttest{
+library(terra)
+bin1 <- terra::rast(system.file("extdata", "ref.tif",
+package = "divraster"))
+spat.alpha2(bin1)
+#> class       : SpatRaster 
+#> dimensions  : 8, 8, 1  (nrow, ncol, nlyr)
+#> resolution  : 0.125, 0.125  (x, y)
+#> extent      : 0, 1, 0, 1  (xmin, xmax, ymin, ymax)
+#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
+#> source(s)   : memory
+#> name        : Richness 
+#> min value   :        2 
+#> max value   :        8 
+# }
+
+
+
+ + +
+

Developed by Flávio M. M. Mota, Neander Marcel Heming, Gabriela Alves-Ferreira.

+
+ +
+

Site built with pkgdown 2.0.9.

+
+ +
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This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"intro","dir":"Articles","previous_headings":"","what":"1 Introduction","title":"divraster-vignette","text":"Macroecological studies increasingly utilized context climate change, necessitating use tools analyze large datasets. examine comprehend intricate mechanisms underlie species distributions structure biological communities, diverse array metrics developed. metrics encompass alpha beta diversity patterns across taxonomic (TD), functional (FD), phylogenetic (PD) dimensions. package divraster addresses current gap field offering functions calculate diversity metrics directly rasters, eliminating need matrix transformations. capability especially valuable dealing extensive datasets, matrices often impose memory constraints.","code":""},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"alpha","dir":"Articles","previous_headings":"","what":"2 Alpha calculations","title":"divraster-vignette","text":"Alpha diversity calculations use tree-based approach taxonomic (TD), functional (FD), phylogenetic (PD) diversity. FD calculation, species traits matrix converted distance matrix clustered produce regional dendrogram (.e. dendrogram species raster stack) total branch length calculated. calculating FD community (.e. raster cell), regional dendrogram subsetted local dendrogram containing species present local community, branch lengths connecting summed represent functional relationships species locally present. Similarly, PD, sum branch lengths connecting species within community represents shared phylogenetic relationships cumulative evolutionary history. Alpha TD can also visualized using tree diagram, species directly connected root edge unit length, reflecting number different taxa community (.e. species richness) since taxa level.","code":""},{"path":[]},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"alpha-td","dir":"Articles","previous_headings":"","what":"2.1.1 Alpha TD","title":"divraster-vignette","text":"alpha taxonomic diversity first scenario ranges 0 67, second scenario, ranges 0 65, higher values concentrated towards north cases. comparing two scenarios, subtracting second first reveals greater species losses (n = 18) towards south.","code":"# Loading data # Presence-absence SpatRaster bin1 <- terra::rast(system.file(\"extdata\", \"ref_frugivor.tif\", package = \"divraster\")) bin2 <- terra::rast(system.file(\"extdata\", \"fut_frugivor.tif\", package = \"divraster\")) # Change extension to process faster terra::ext(bin1) #> SpatExtent : -41.875, -38.75, -21.375, -13 (xmin, xmax, ymin, ymax) e <- c(-41, -39, -15, -13) bin1 <- terra::crop(bin1, e) bin2 <- terra::crop(bin2, e) # Species traits traits <- read.csv(system.file(\"extdata\", \"traits_frugivor.csv\", package = \"divraster\"), sep = \";\", row.names = 1) # Phylogenetic tree tree <- ape::read.tree(system.file(\"extdata\", \"tree_frugivor.tre\", package = \"divraster\")) # Alpha TD calculation for scenario 1 alpha.td <- divraster::spat.alpha(bin1) alpha.td #> class : SpatRaster #> dimensions : 16, 16, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Alpha_TD #> min value : 0 #> max value : 67 terra::plot(alpha.td, main = paste0(names(alpha.td), \"_sce1\")) # Alpha TD calculation for scenario 2 alpha.td2 <- divraster::spat.alpha(bin2) alpha.td2 #> class : SpatRaster #> dimensions : 16, 16, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Alpha_TD #> min value : 0 #> max value : 65 terra::plot(alpha.td2, main = paste0(names(alpha.td2), \"_sce2\")) # Difference in Alpha TD between scenarios alpha.td2-alpha.td #> class : SpatRaster #> dimensions : 16, 16, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Alpha_TD #> min value : -18 #> max value : 0 terra::plot(alpha.td2-alpha.td, main = \"Delta Alpha TD\")"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"alpha-fd","dir":"Articles","previous_headings":"","what":"2.1.2 Alpha FD","title":"divraster-vignette","text":"alpha functional diversity first scenario ranges 3.7 4.4, higher values concentrated towards north, indicating greater functional diversity.","code":"alpha.fd <- divraster::spat.alpha(bin1, traits) alpha.fd #> class : SpatRaster #> dimensions : 16, 16, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Alpha_FD #> min value : 3.723151 #> max value : 4.378846 terra::plot(alpha.fd, main = names(alpha.fd))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"alpha-pd","dir":"Articles","previous_headings":"","what":"2.1.3 Alpha PD","title":"divraster-vignette","text":"alpha phylogenetic diversity first scenario ranges 1524 1860, higher values concentrated towards north, indicating greater phylogenetic diversity.","code":"# Alpha PD calculation alpha.pd <- divraster::spat.alpha(bin1, tree) alpha.pd #> class : SpatRaster #> dimensions : 16, 16, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Alpha_PD #> min value : 1523.921 #> max value : 1859.668 terra::plot(alpha.pd, main = names(alpha.pd))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"ses","dir":"Articles","previous_headings":"","what":"3 Standardized effect size (SES)","title":"divraster-vignette","text":"SES often used ecological studies measure magnitude difference observed randomized patterns generated null models, expressed standard deviation units. calculate SES using SESraster package, currently offers six community randomization methods. basic randomization methods include: keeping richness constant randomizing position species within raster cell (site), keeping range size constant randomizing position species presences space (species), randomizing site species simultaneously (). positive SES indicates observed functional/phylogenetic diversity higher expected solely based species richness (taxonomic diversity), whereas negative SES indicates opposite.","code":""},{"path":[]},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"ses-fd","dir":"Articles","previous_headings":"","what":"3.1.1 SES FD","title":"divraster-vignette","text":"SES indicates majority areas values close 0, suggesting functional diversity significantly differ expected change. However, one community projected functionally dispersed (SES_FD = 31), another community projected functionally clustered (SES_FD = -39). indicates increase decrease functional diversity within communities scenarios 1 2, respectively.","code":"# SES FD calculation ses.fd <- divraster::spat.rand(x = bin1, tree = traits, aleats = 3, random = \"site\") ses.fd #> class : SpatRaster #> dimensions : 16, 16, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Mean_FD, SD_FD, Observed_FD, SES_FD #> min values : 3.711791, 0.002639008, 3.723151, -18.594535 #> max values : 4.424008, 0.166680920, 4.378846, 4.860787 terra::plot(ses.fd, main = names(ses.fd))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"ses-pd","dir":"Articles","previous_headings":"","what":"3.1.2 SES PD","title":"divraster-vignette","text":"Similarly, SES phylogenetic diversity differ expected chance, communities presenting values close 0. However, one community projected phylogenetically dispersed (SES_PD = 10), another community projected phylogenetically clustered (SES_FD = -15). indicates increase decrease phylogenetic diversity within communities scenarios 1 2, respectively.","code":"# SES PD calculation ses.pd <- divraster::spat.rand(x = bin1, tree = tree, aleats = 3, random = \"site\") ses.pd #> class : SpatRaster #> dimensions : 16, 16, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Mean_PD, SD_PD, Observed_PD, SES_PD #> min values : 1617.695, 1.585962, 1623.451, -4.664356 #> max values : 1875.081, 97.284872, 1880.676, 11.069075 terra::plot(ses.pd, main = names(ses.pd))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"beta","dir":"Articles","previous_headings":"","what":"4 Beta diversity","title":"divraster-vignette","text":"Beta diversity captures variations species composition different communities. examining community comparison neighboring ones, referred spatial beta diversity. hand, assessing changes within community different time periods, termed temporal beta diversity. Beta diversity can partitioned two components: “replacement” “richness differences”. former accounts substitution one species another, latter encompasses discrepancies total number species (e.g. species gain loss). addition, since Btotal represents sum Brepl Brich components, proportion Brepl/Btotal (Bratio) can calculated, values close 0 indicating predominance Brich values close 1 indicating predominance Brepl. Moreover, concept beta diversity extends functional (FD) phylogenetic diversity (PD), using framework taxonomic diversity (TD). context TD, higher beta diversity represents higher dissimilarities species composition communities. contrast, FD, indicates higher dissimilarities functional traits, PD, reflects higher dissimilarities phylogenetic relationships species communities.","code":""},{"path":[]},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"betaspat-td","dir":"Articles","previous_headings":"","what":"4.1.1 Beta spatial TD","title":"divraster-vignette","text":"Spatial beta diversity TD indicates slight change species composition towards south, evidenced small values Btotal (~0.1). predominant component contributing change richness difference (Brich), suggesting dissimilarities community (.e. pixel) neighbors primarily due loss gain species. Bratio also indicates predominance Birch component communities.","code":"# Beta spatial TD calculation beta.td <- divraster::spat.beta(bin1) beta.td #> class : SpatRaster #> dimensions : 16, 16, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_TD, Brepl_TD, Brich_TD, Bratio_TD #> min values : 0.006060606, 0.00000000, 0.004264392, 0.0000000 #> max values : 0.109409606, 0.03638009, 0.103181683, 0.7259259 terra::plot(beta.td, main = names(beta.td))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"betaspat-fd","dir":"Articles","previous_headings":"","what":"4.1.2 Beta spatial FD","title":"divraster-vignette","text":"Similarly, spatial beta diversity FD indicates slight change functional traits composition towards south, evidenced small values Btotal (~0.08). predominant component contributing little change richness difference (Brich), suggesting dissimilarities community (.e. pixel) neighbors primarily due loss gain functional traits. Bratio also indicates predominance Birch component communities.","code":"# Beta spatial FD calculation beta.fd <- divraster::spat.beta(bin1, traits) beta.fd #> class : SpatRaster #> dimensions : 16, 16, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_FD, Brepl_FD, Brich_FD, Bratio_FD #> min values : 0.0004245858, 0.00000000, 0.0004245858, 0.000000 #> max values : 0.0793045655, 0.01846139, 0.0793045655, 0.756675 terra::plot(beta.fd, main = names(beta.fd))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"betaspat-pd","dir":"Articles","previous_headings":"","what":"4.1.3 Beta spatial PD","title":"divraster-vignette","text":"spatial beta diversity PD indicates slight change evolutionary history communities towards south. However change even lower compared TD FD, evidenced smallest values Btotal (~0.06). predominant component contributing little change also richness difference (Brich), suggesting dissimilarities community (.e. pixel) neighbors due loss gain evolutionary history. Bratio also indicates predominance Birch component communities.","code":"# Beta spatial PD calculation beta.pd <- divraster::spat.beta(bin1, tree) beta.pd #> class : SpatRaster #> dimensions : 16, 16, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_PD, Brepl_PD, Brich_PD, Bratio_PD #> min values : 0.002851805, 0.000000000, 0.001618621, 0.0000000 #> max values : 0.059656685, 0.008026876, 0.059656685, 0.8250616 terra::plot(beta.pd, main = names(beta.pd))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"betatemp-td","dir":"Articles","previous_headings":"","what":"4.1.4 Beta temporal TD","title":"divraster-vignette","text":"temporal beta diversity TD indicates future communities expected experience changes species composition, predominantly towards south, Btotal reaching approximately 0.3. predominance Brich component suggests dissimilarities attributed gains losses species. Bratio also indicates predominance Birch component communities.","code":"# Beta temporal TD calculation betatemp.td <- divraster::temp.beta(bin1, bin2) betatemp.td #> class : SpatRaster #> dimensions : 16, 16, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_TD, Brepl_TD, Brich_TD, Bratio_TD #> min values : 0.02985075, 0.00000000, 0.02985075, 0.0000000 #> max values : 0.31578947, 0.09836066, 0.31578947, 0.6666667 terra::plot(betatemp.td, main = names(betatemp.td))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"betatemp-fd","dir":"Articles","previous_headings":"","what":"4.1.5 Beta temporal FD","title":"divraster-vignette","text":"temporal beta diversity FD indicates less pronounced pattern compared TD, smaller values Btotal, reaching maximum 0.17. Brich component also predominant, suggesting small dissimilarities can attributed gains losses functional traits. Bratio also indicates predominance Birch component communities.","code":"# Beta temporal FD calculation betatemp.fd <- divraster::temp.beta(bin1, bin2, traits) betatemp.fd #> class : SpatRaster #> dimensions : 16, 16, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_FD, Brepl_FD, Brich_FD, Bratio_FD #> min values : 0.01733908, 0.00000000, 0.01012696, 0.0000000 #> max values : 0.17193290, 0.03741327, 0.17193290, 0.6872465 terra::plot(betatemp.fd, main = names(betatemp.fd))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"betatemp-pd","dir":"Articles","previous_headings":"","what":"4.1.6 Beta temporal PD","title":"divraster-vignette","text":"Likewise, temporal beta diversity PD indicates less pronounced pattern compared TD, smaller values Btotal, reaching maximum 0.18. Brich component also predominant, suggesting small dissimilarities can attributed gains losses evolutionary history. Bratio also indicates predominance Birch component communities.","code":"# Beta temporal PD calculation betatemp.pd <- divraster::temp.beta(bin1, bin2, tree) betatemp.pd #> class : SpatRaster #> dimensions : 16, 16, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_PD, Brepl_PD, Brich_PD, Bratio_PD #> min values : 0.0120217, 0.0000000, 0.009533166, 0.0000000 #> max values : 0.1792291, 0.0394096, 0.179229119, 0.7759122 terra::plot(betatemp.pd, main = names(betatemp.pd))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"traits-avg","dir":"Articles","previous_headings":"","what":"5 Traits average","title":"divraster-vignette","text":"Calculating average traits species climate scenario enables evaluation species traits contribute loss suitable habitat. Unlike functional diversity, combines functional traits index, approach provides direct insight spatial variations average traits. information can complement data necessary delineating conservation priority areas, shifts average traits—whether increasing decreasing—indicate potential loss species specific features. particular significance given functional traits closely tied ecological services provided species.","code":""},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"traits-ex","dir":"Articles","previous_headings":"","what":"5.1 Traits average examples","title":"divraster-vignette","text":"average beak depth first scenario ranges 8.5 9.6, second scenario, ranges 8.8 9.9. Beak depth increased 13.5% southern region decreased 4.5% central region. earlier analysis indicated prevalence species loss, implying rise average beak depth second scenario can attributed decline species smaller beak depths. Conversely, reduction beak size can attributed decline species larger beak depths.","code":"# Average traits calculation # Scenario 1 avg.traits1 <- divraster::spat.trait(bin1, traits) avg.traits1[[4]] #> class : SpatRaster #> dimensions : 16, 16, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Beak.Depth #> min value : 8.526923 #> max value : 9.601515 terra::plot(avg.traits1[[4]], main = paste0(names(avg.traits1[[4]]), \"_sce1\")) # Scenario 2 avg.traits2 <- divraster::spat.trait(bin2, traits) avg.traits2[[4]] #> class : SpatRaster #> dimensions : 16, 16, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Beak.Depth #> min value : 8.786792 #> max value : 9.942308 terra::plot(avg.traits2[[4]], main = paste0(names(avg.traits2[[4]]), \"_sce2\")) # Percentage of change change.traits <- (avg.traits2 - avg.traits1) / avg.traits1 * 100 change.traits[[4]] #> class : SpatRaster #> dimensions : 16, 16, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Beak.Depth #> min value : -4.495893 #> max value : 13.541296 terra::plot(change.traits[[4]], main = paste0(names(change.traits[[4]]), \"_%\"))"},{"path":"https://flaviomoc.github.io/divraster/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Flávio M. M. Mota. Author, maintainer, copyright holder. Neander Marcel Heming. Author. Gabriela Alves-Ferreira. Author.","code":""},{"path":"https://flaviomoc.github.io/divraster/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Mota FMM, Alves-Ferreira G, Talora DC, Heming NM (2023). “divraster: R package calculate taxonomic, functional phylogenetic diversity rasters.” Ecography, e06905. doi:10.1111/ecog.06905. Cardoso P, Rigal F, Carvalho J (2015). “BAT – Biodiversity Assessment Tools, R package measurement estimation alpha beta taxon, phylogenetic functional diversity.” Methods Ecology Evolution, 6, 232–236. doi:10.1111/2041-210X.12310.","code":"@Article{, title = {divraster: an R package to calculate taxonomic, functional and phylogenetic diversity from rasters}, author = {F. M. M. Mota and G. Alves-Ferreira and D. C. Talora and N. M. Heming}, journal = {Ecography}, year = {2023}, pages = {e06905}, doi = {10.1111/ecog.06905}, } @Article{, title = {BAT -- Biodiversity Assessment Tools, an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity}, author = {P. Cardoso and F. Rigal and J. Carvalho}, journal = {Methods in Ecology and Evolution}, year = {2015}, volume = {6}, pages = {232--236}, doi = {10.1111/2041-210X.12310}, }"},{"path":"https://flaviomoc.github.io/divraster/index.html","id":"divraster","dir":"","previous_headings":"","what":"Diversity Metrics Calculations for Rasterized Data","title":"Diversity Metrics Calculations for Rasterized Data","text":"Alpha beta calculations using rasters taxonomic (TD), functional (FD), phylogenetic (PD) dimensions. Spatial temporal beta diversity can partitioned replacement richness difference components. Functions calculate standardized effect size functional phylogenetic alpha diversity average traits available.","code":""},{"path":"https://flaviomoc.github.io/divraster/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Diversity Metrics Calculations for Rasterized Data","text":"CRAN version divraster can installed using: development version divraster can installed Github using:","code":"install.packages(\"divraster\") devtools::install_github(\"flaviomoc/divraster\")"},{"path":"https://flaviomoc.github.io/divraster/index.html","id":"divraster-basics","dir":"","previous_headings":"","what":"divraster basics","title":"Diversity Metrics Calculations for Rasterized Data","text":"Basic information divraster can found package’s webpage vignette:","code":"vignette(\"divraster-vignette\")"},{"path":"https://flaviomoc.github.io/divraster/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Diversity Metrics Calculations for Rasterized Data","text":"use R package, please cite publications: Mota FMM, Alves-Ferreira G, Talora DC, Heming NM (2023). divraster: R package calculate taxonomic, functional phylogenetic diversity rasters. – Ecography, e06905. information:","code":"citation(\"divraster\")"},{"path":"https://flaviomoc.github.io/divraster/index.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Diversity Metrics Calculations for Rasterized Data","text":"question find bug, let us know topic Issues.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/area.calc.html","id":null,"dir":"Reference","previous_headings":"","what":"Area calculation — area.calc","title":"Area calculation — area.calc","text":"Area calculation","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/area.calc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Area calculation — area.calc","text":"","code":"area.calc(r1, unit = \"km\", r2 = NULL, r3 = NULL, filename = \"\")"},{"path":"https://flaviomoc.github.io/divraster/reference/area.calc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Area calculation — area.calc","text":"r1 SpatRaster list multiple SpatRasters. unit Character. Default \"km\", \"m\" \"ha\" also available. r2 SpatRaster resolution extent \"r1\". r3 SpatRaster resolution extent \"r1\". filename Character. Save results name provided.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/area.calc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Area calculation — area.calc","text":"vector data.frame area values chosen unit.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/area.calc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Area calculation — area.calc","text":"","code":"# \\donttest{ library(terra) #> terra 1.7.71 bin1 <- terra::rast(system.file(\"extdata\", \"ref.tif\", package = \"divraster\")) my.list <- list(bin1 = bin1[[1:2]]) area.calc(my.list) #> sp scenario total.area #> 1 A bin1 6154.240 #> 2 B bin1 6346.524 # }"},{"path":"https://flaviomoc.github.io/divraster/reference/inputs_chk.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if objects are valid — inputs_chk","title":"Check if objects are valid — inputs_chk","text":"Check objects valid","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/inputs_chk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if objects are valid — inputs_chk","text":"","code":"inputs_chk(bin1, bin2, tree)"},{"path":"https://flaviomoc.github.io/divraster/reference/inputs_chk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if objects are valid — inputs_chk","text":"bin1 SpatRaster presence-absence data (0 1) set species. bin2 SpatRaster presence-absence data (0 1) set species. Species names 'bin2' 'bin1' must match! tree can 'data.frame' species traits 'phylo' rooted phylogenetic tree. Species names 'tree', 'bin1', 'bin2' must match!","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/inputs_chk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if objects are valid — inputs_chk","text":"Either success message error.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/load.data.html","id":null,"dir":"Reference","previous_headings":"","what":"Load data adapted from Mota et al. (2022), Tobias et al. (2022), and Jetz et al. (2014) — load.data","title":"Load data adapted from Mota et al. (2022), Tobias et al. (2022), and Jetz et al. (2014) — load.data","text":"Load data adapted Mota et al. (2022), Tobias et al. (2022), Jetz et al. (2014)","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/load.data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load data adapted from Mota et al. (2022), Tobias et al. (2022), and Jetz et al. (2014) — load.data","text":"","code":"load.data()"},{"path":"https://flaviomoc.github.io/divraster/reference/load.data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load data adapted from Mota et al. (2022), Tobias et al. (2022), and Jetz et al. (2014) — load.data","text":"list binary maps species reference future climate scenarios, species traits, rooted phylogenetic tree species. species names across objects must match!","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/load.data.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Load data adapted from Mota et al. (2022), Tobias et al. (2022), and Jetz et al. (2014) — load.data","text":"Mota, F. M. M. et al. 2022. Climate change expected restructure forest frugivorous bird communities biodiversity hot-point within Atlantic Forest. - Diversity Distributions 28: 2886–2897. Tobias, J. . et al. 2022. AVONET: morphological, ecological geographical data birds. - Ecology Letters 25: 581–597. Jetz, W. et al. 2014. Global Distribution Conservation Evolutionary Distinctness Birds. - Current Biology 24: 919–930.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/load.data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load data adapted from Mota et al. (2022), Tobias et al. (2022), and Jetz et al. (2014) — load.data","text":"","code":"data <- load.data() data #> $ref #> class : SpatRaster #> dimensions : 67, 25, 68 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41.875, -38.75, -21.375, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source : ref_frugivor.tif #> names : Amazo~inosa, Amazo~rytha, Amazo~nacea, Arrem~uatus, Arrem~urnus, Ptero~lloni, ... #> min values : 0, 0, 0, 0, 1, 0, ... #> max values : 1, 1, 1, 1, 1, 1, ... #> #> $fut #> class : SpatRaster #> dimensions : 67, 25, 68 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41.875, -38.75, -21.375, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source : fut_frugivor.tif #> names : Amazo~inosa, Amazo~rytha, Amazo~nacea, Arrem~uatus, Arrem~urnus, Ptero~lloni, ... #> min values : 0, 1, 0, 0, 0, 0, ... #> max values : 1, 1, 1, 1, 1, 1, ... #> #> $traits #> Beak.Length_Culmen Beak.Length_Nares Beak.Width #> Amazona_farinosa 42.3 35.6 20.5 #> Amazona_rhodocorytha 37.6 29.4 18.0 #> Amazona_vinacea 33.5 24.6 16.2 #> Arremon_semitorquatus 15.2 9.4 5.7 #> Arremon_taciturnus 14.6 10.0 5.5 #> Pteroglossus_bailloni 70.2 62.2 20.9 #> Cacicus_cela 33.7 24.0 7.9 #> Carpornis_cucullata 18.3 9.2 5.6 #> Caryothraustes_canadensis 17.4 11.8 8.5 #> Chiroxiphia_caudata 13.8 7.3 4.0 #> Chiroxiphia_pareola 11.4 6.5 4.4 #> Chlorophanes_spiza 15.9 11.4 4.5 #> Patagioenas_speciosa 24.5 12.3 4.8 #> Cotinga_maculata 17.4 9.8 5.9 #> Crax_blumenbachii 45.7 23.4 15.3 #> Crypturellus_soui 24.2 8.0 4.2 #> Crypturellus_variegatus 33.6 13.7 5.3 #> Cyanerpes_cyaneus 19.4 12.8 3.8 #> Elaenia_mesoleuca 12.5 7.1 4.1 #> Euphonia_cyanocephala 9.4 5.4 4.1 #> Euphonia_pectoralis 10.9 7.6 4.7 #> Euphonia_xanthogaster 10.7 6.0 4.8 #> Ilicura_militaris 9.4 5.2 2.8 #> Iodopleura_pipra 8.2 4.5 3.6 #> Laniisoma_elegans 20.3 13.2 5.4 #> Legatus_leucophaius 13.0 8.3 6.3 #> Lipaugus_lanioides 26.1 16.0 8.0 #> Lipaugus_vociferans 26.9 13.8 8.0 #> Machaeropterus_regulus 9.9 5.6 3.3 #> Manacus_manacus 11.5 6.8 4.4 #> Melanerpes_flavifrons 27.2 20.9 6.5 #> Mionectes_oleagineus 11.8 8.2 4.2 #> Mionectes_rufiventris 14.1 9.3 4.3 #> Neopelma_aurifrons 12.7 8.3 4.2 #> Odontophorus_capueira 21.3 11.7 7.6 #> Oxyruncus_cristatus 17.9 11.3 5.5 #> Pachyramphus_marginatus 14.7 10.1 6.9 #> Patagioenas_plumbea 23.1 12.9 4.3 #> Penelope_obscura 34.5 16.6 10.2 #> Penelope_superciliaris 34.8 16.3 9.9 #> Phibalura_flavirostris 13.8 9.5 6.5 #> Phyllomyias_burmeisteri 11.4 6.9 3.5 #> Pionopsitta_pileata 25.3 19.0 11.6 #> Pipra_pipra 12.0 6.6 4.4 #> Pipra_rubrocapilla 10.4 6.0 3.8 #> Pipraeidea_melanonota 12.6 7.4 4.8 #> Turdus_flavipes 21.7 11.0 5.0 #> Procnias_nudicollis 27.0 10.9 7.1 #> Psarocolius_decumanus 51.8 34.1 11.2 #> Pteroglossus_aracari 99.1 93.4 27.7 #> Pyroderus_scutatus 42.5 26.3 13.8 #> Pyrrhura_cruentata 22.8 19.1 12.1 #> Ramphastos_dicolorus 104.3 100.0 30.1 #> Schiffornis_turdina 17.0 9.7 4.9 #> Schiffornis_virescens 13.9 8.6 3.8 #> Selenidera_maculirostris 55.0 47.8 19.3 #> Stephanophorus_diadematus 14.1 8.7 6.4 #> Tachyphonus_cristatus 15.9 11.1 5.6 #> Tangara_cyanocephala 10.9 8.0 4.0 #> Tangara_cyanoventris 12.0 7.7 4.0 #> Tangara_desmaresti 12.6 7.9 4.3 #> Tangara_seledon 11.8 7.7 5.1 #> Thraupis_cyanoptera 17.9 10.0 6.4 #> Tinamus_solitarius 37.9 11.4 5.8 #> Touit_melanonotus 18.9 14.3 8.8 #> Trogon_viridis 25.2 15.0 10.1 #> Turdus_fumigatus 24.2 13.8 5.0 #> Xipholena_atropurpurea 18.3 10.2 5.2 #> Beak.Depth Tarsus.Length Wing.Length Kipps.Distance #> Amazona_farinosa 35.4 26.6 244.9 68.7 #> Amazona_rhodocorytha 31.0 22.3 210.0 62.6 #> Amazona_vinacea 26.7 21.5 214.2 67.3 #> Arremon_semitorquatus 7.7 25.2 70.0 4.2 #> Arremon_taciturnus 7.3 23.8 72.0 7.9 #> Pteroglossus_bailloni 26.0 33.0 129.0 18.9 #> Cacicus_cela 11.8 29.8 145.3 39.5 #> Carpornis_cucullata 6.8 23.3 113.6 22.4 #> Caryothraustes_canadensis 11.2 20.5 90.8 15.8 #> Chiroxiphia_caudata 4.6 19.8 75.9 13.4 #> Chiroxiphia_pareola 4.9 17.8 69.4 8.2 #> Chlorophanes_spiza 4.6 18.9 68.3 16.7 #> Patagioenas_speciosa 6.0 23.7 184.7 65.5 #> Cotinga_maculata 5.3 22.5 114.2 29.7 #> Crax_blumenbachii 23.3 110.0 384.0 33.9 #> Crypturellus_soui 3.9 36.4 127.5 32.9 #> Crypturellus_variegatus 5.0 41.1 155.4 50.1 #> Cyanerpes_cyaneus 3.6 13.7 60.9 15.7 #> Elaenia_mesoleuca 3.8 16.0 80.0 17.7 #> Euphonia_cyanocephala 4.1 14.5 64.2 18.6 #> Euphonia_pectoralis 5.3 15.9 61.1 13.6 #> Euphonia_xanthogaster 4.8 16.4 61.4 13.7 #> Ilicura_militaris 3.1 17.8 61.2 13.8 #> Iodopleura_pipra 3.5 13.9 56.6 13.7 #> Laniisoma_elegans 6.1 22.5 103.5 26.9 #> Legatus_leucophaius 4.6 15.1 78.5 20.1 #> Lipaugus_lanioides 8.3 24.6 133.8 22.8 #> Lipaugus_vociferans 7.3 21.4 123.1 20.9 #> Machaeropterus_regulus 3.1 13.9 52.9 12.5 #> Manacus_manacus 4.2 20.9 52.2 8.4 #> Melanerpes_flavifrons 6.7 18.8 117.0 31.2 #> Mionectes_oleagineus 3.4 16.0 60.5 10.5 #> Mionectes_rufiventris 3.8 16.2 68.4 9.2 #> Neopelma_aurifrons 4.3 15.7 71.0 15.1 #> Odontophorus_capueira 13.1 37.8 146.8 15.2 #> Oxyruncus_cristatus 5.6 20.7 92.2 24.0 #> Pachyramphus_marginatus 5.2 18.5 67.7 15.0 #> Patagioenas_plumbea 5.1 23.1 177.8 61.9 #> Penelope_obscura 12.0 70.6 309.4 14.6 #> Penelope_superciliaris 11.0 71.8 248.6 34.1 #> Phibalura_flavirostris 6.0 19.3 99.0 32.9 #> Phyllomyias_burmeisteri 3.4 15.3 63.9 14.9 #> Pionopsitta_pileata 17.5 14.5 140.0 49.8 #> Pipra_pipra 4.1 14.1 62.0 10.6 #> Pipra_rubrocapilla 4.1 12.6 61.2 11.5 #> Pipraeidea_melanonota 5.0 17.9 80.1 21.4 #> Turdus_flavipes 5.7 25.7 110.6 28.6 #> Procnias_nudicollis 5.9 29.4 148.4 35.1 #> Psarocolius_decumanus 17.8 46.5 198.6 49.1 #> Pteroglossus_aracari 32.6 34.5 143.1 22.4 #> Pyroderus_scutatus 15.5 38.0 231.0 41.0 #> Pyrrhura_cruentata 22.7 15.7 147.4 59.5 #> Ramphastos_dicolorus 33.4 46.1 191.8 26.9 #> Schiffornis_turdina 6.0 22.1 92.1 14.1 #> Schiffornis_virescens 4.5 21.4 80.2 12.5 #> Selenidera_maculirostris 22.4 31.8 130.7 19.4 #> Stephanophorus_diadematus 7.5 23.2 98.2 20.4 #> Tachyphonus_cristatus 6.9 18.2 76.2 14.2 #> Tangara_cyanocephala 4.9 16.4 61.5 13.6 #> Tangara_cyanoventris 4.7 18.1 67.0 12.7 #> Tangara_desmaresti 4.7 18.9 71.0 14.2 #> Tangara_seledon 5.2 15.9 64.2 14.4 #> Thraupis_cyanoptera 7.8 20.8 96.1 24.0 #> Tinamus_solitarius 6.0 73.1 261.5 35.1 #> Touit_melanonotus 13.3 10.2 107.5 45.1 #> Trogon_viridis 11.7 14.2 146.1 50.6 #> Turdus_fumigatus 6.7 31.0 113.5 23.9 #> Xipholena_atropurpurea 5.4 20.3 110.2 24.0 #> Secondary1 Hand.Wing.Index Tail.Length Mass #> Amazona_farinosa 177.2 27.9 135.0 625.99 #> Amazona_rhodocorytha 146.7 29.9 115.0 474.34 #> Amazona_vinacea 145.0 31.6 121.8 254.00 #> Arremon_semitorquatus 65.8 6.1 70.5 25.00 #> Arremon_taciturnus 64.5 10.9 61.3 24.80 #> Pteroglossus_bailloni 110.4 14.5 169.0 146.00 #> Cacicus_cela 104.1 27.2 97.8 85.45 #> Carpornis_cucullata 90.9 19.8 101.8 74.19 #> Caryothraustes_canadensis 72.5 17.8 71.2 34.50 #> Chiroxiphia_caudata 63.0 17.6 57.8 25.60 #> Chiroxiphia_pareola 59.1 12.2 34.4 16.84 #> Chlorophanes_spiza 50.9 24.7 48.2 19.00 #> Patagioenas_speciosa 114.0 36.5 98.3 258.47 #> Cotinga_maculata 84.5 26.0 71.5 65.00 #> Crax_blumenbachii 307.1 9.7 333.8 3500.00 #> Crypturellus_soui 96.4 25.4 47.9 216.16 #> Crypturellus_variegatus 105.5 32.2 44.6 378.00 #> Cyanerpes_cyaneus 44.5 26.0 34.8 14.00 #> Elaenia_mesoleuca 62.2 22.1 66.4 17.60 #> Euphonia_cyanocephala 45.6 28.9 37.8 14.00 #> Euphonia_pectoralis 48.8 21.8 33.9 14.40 #> Euphonia_xanthogaster 47.7 22.4 36.0 13.00 #> Ilicura_militaris 46.9 22.6 50.8 12.70 #> Iodopleura_pipra 43.0 24.1 32.0 10.03 #> Laniisoma_elegans 76.6 26.0 61.0 47.40 #> Legatus_leucophaius 59.2 25.5 55.2 22.20 #> Lipaugus_lanioides 111.0 17.0 116.0 94.80 #> Lipaugus_vociferans 102.1 16.9 110.2 75.42 #> Machaeropterus_regulus 40.2 23.7 22.6 9.34 #> Manacus_manacus 44.5 15.9 32.8 16.70 #> Melanerpes_flavifrons 85.8 26.6 69.5 57.78 #> Mionectes_oleagineus 50.8 17.1 48.2 11.17 #> Mionectes_rufiventris 60.0 13.3 55.0 13.30 #> Neopelma_aurifrons 55.9 21.3 50.0 14.00 #> Odontophorus_capueira 130.1 10.5 75.0 425.40 #> Oxyruncus_cristatus 67.2 26.3 64.3 42.00 #> Pachyramphus_marginatus 53.7 21.8 50.4 18.40 #> Patagioenas_plumbea 115.7 34.9 141.6 178.77 #> Penelope_obscura 286.3 4.9 313.5 1770.00 #> Penelope_superciliaris 217.8 13.5 286.8 894.99 #> Phibalura_flavirostris 66.2 33.2 104.8 46.50 #> Phyllomyias_burmeisteri 48.8 23.3 48.1 11.10 #> Pionopsitta_pileata 89.8 35.8 70.2 119.00 #> Pipra_pipra 51.0 17.3 26.6 11.11 #> Pipra_rubrocapilla 47.0 19.7 31.4 12.00 #> Pipraeidea_melanonota 59.3 26.5 57.8 21.00 #> Turdus_flavipes 81.9 25.9 84.1 65.14 #> Procnias_nudicollis 111.6 24.0 82.6 172.04 #> Psarocolius_decumanus 146.2 24.8 170.3 206.30 #> Pteroglossus_aracari 120.8 15.6 147.0 250.16 #> Pyroderus_scutatus 183.8 18.2 152.2 357.00 #> Pyrrhura_cruentata 88.5 40.2 130.6 75.90 #> Ramphastos_dicolorus 164.9 14.0 181.2 331.00 #> Schiffornis_turdina 74.5 15.9 67.7 31.70 #> Schiffornis_virescens 67.0 15.7 64.2 25.60 #> Selenidera_maculirostris 111.2 14.8 111.3 164.00 #> Stephanophorus_diadematus 77.4 20.8 81.2 35.40 #> Tachyphonus_cristatus 60.0 19.2 70.4 18.80 #> Tangara_cyanocephala 50.4 21.3 44.7 18.00 #> Tangara_cyanoventris 54.0 19.1 48.4 16.50 #> Tangara_desmaresti 56.8 20.0 52.8 20.40 #> Tangara_seledon 49.9 22.4 47.5 18.70 #> Thraupis_cyanoptera 72.1 25.0 66.5 43.30 #> Tinamus_solitarius 223.7 13.7 156.2 1386.41 #> Touit_melanonotus 62.4 42.0 41.8 66.51 #> Trogon_viridis 95.6 34.6 158.4 89.69 #> Turdus_fumigatus 89.6 21.1 90.8 75.70 #> Xipholena_atropurpurea 86.0 21.8 65.1 61.32 #> Habitat Trophic.Niche Range.Size #> Amazona_farinosa Forest Omnivore 6793599.57 #> Amazona_rhodocorytha Forest Frugivore 2672.56 #> Amazona_vinacea Forest Omnivore 105992.85 #> Arremon_semitorquatus Forest Omnivore 215137.21 #> Arremon_taciturnus Forest Omnivore 6755484.62 #> Pteroglossus_bailloni Forest Frugivore 657171.58 #> Cacicus_cela Forest Omnivore 8569297.31 #> Carpornis_cucullata Forest Frugivore 251722.97 #> Caryothraustes_canadensis Shrubland Omnivore 2650244.99 #> Chiroxiphia_caudata Forest Omnivore 1459549.86 #> Chiroxiphia_pareola Forest Frugivore 5040298.89 #> Chlorophanes_spiza Forest Frugivore 7921066.07 #> Patagioenas_speciosa Forest Frugivore 7713359.51 #> Cotinga_maculata Forest Frugivore 30327.88 #> Crax_blumenbachii Forest Frugivore 1149.72 #> Crypturellus_soui Forest Omnivore 11151222.76 #> Crypturellus_variegatus Forest Omnivore 5436849.92 #> Cyanerpes_cyaneus Forest Omnivore 8340306.15 #> Elaenia_mesoleuca Forest Invertivore 2216525.02 #> Euphonia_cyanocephala Forest Frugivore 2711347.81 #> Euphonia_pectoralis Forest Frugivore 1361244.46 #> Euphonia_xanthogaster Forest Frugivore 3715684.50 #> Ilicura_militaris Forest Frugivore 840759.23 #> Iodopleura_pipra Forest Frugivore 130157.72 #> Laniisoma_elegans Forest Omnivore 172527.96 #> Legatus_leucophaius Forest Frugivore 11371457.31 #> Lipaugus_lanioides Forest Frugivore 201153.30 #> Lipaugus_vociferans Forest Frugivore 7063057.92 #> Machaeropterus_regulus Forest Frugivore 125343.35 #> Manacus_manacus Forest Frugivore 7524946.19 #> Melanerpes_flavifrons Forest Omnivore 1557771.44 #> Mionectes_oleagineus Forest Frugivore 8947569.12 #> Mionectes_rufiventris Forest Invertivore 1057487.40 #> Neopelma_aurifrons Forest Frugivore 5071.66 #> Odontophorus_capueira Forest Omnivore 1724256.70 #> Oxyruncus_cristatus Forest Frugivore 1872045.95 #> Pachyramphus_marginatus Forest Omnivore 6344951.42 #> Patagioenas_plumbea Forest Frugivore 6564806.47 #> Penelope_obscura Forest Frugivore 1012773.03 #> Penelope_superciliaris Forest Frugivore 5614395.75 #> Phibalura_flavirostris Forest Frugivore 1084489.75 #> Phyllomyias_burmeisteri Forest Invertivore 971005.03 #> Pionopsitta_pileata Forest Omnivore 728878.23 #> Pipra_pipra Forest Frugivore 4953783.66 #> Pipra_rubrocapilla Forest Frugivore 3391760.24 #> Pipraeidea_melanonota Forest Omnivore 2111740.74 #> Turdus_flavipes Forest Frugivore 940921.44 #> Procnias_nudicollis Forest Frugivore 1467436.56 #> Psarocolius_decumanus Forest Omnivore 10475235.80 #> Pteroglossus_aracari Forest Frugivore 3319977.82 #> Pyroderus_scutatus Forest Frugivore 2116677.80 #> Pyrrhura_cruentata Forest Omnivore 10274.69 #> Ramphastos_dicolorus Forest Frugivore 1394133.06 #> Schiffornis_turdina Forest Omnivore 5587673.67 #> Schiffornis_virescens Forest Omnivore 1662556.58 #> Selenidera_maculirostris Forest Frugivore 930797.49 #> Stephanophorus_diadematus Forest Frugivore 1088996.67 #> Tachyphonus_cristatus Forest Omnivore 6338485.76 #> Tangara_cyanocephala Forest Frugivore 444844.92 #> Tangara_cyanoventris Forest Frugivore 475625.93 #> Tangara_desmaresti Forest Frugivore 260465.02 #> Tangara_seledon Forest Frugivore 672563.84 #> Thraupis_cyanoptera Forest Frugivore 224069.57 #> Tinamus_solitarius Forest Omnivore 1069608.94 #> Touit_melanonotus Forest Frugivore 14296.54 #> Trogon_viridis Forest Frugivore 7907953.76 #> Turdus_fumigatus Forest Invertivore 4070825.39 #> Xipholena_atropurpurea Forest Frugivore 1836.59 #> #> $tree #> #> Phylogenetic tree with 68 tips and 67 internal nodes. #> #> Tip labels: #> Patagioenas_plumbea, Patagioenas_speciosa, Pyrrhura_cruentata, Pionopsitta_pileata, Amazona_rhodocorytha, Amazona_vinacea, ... #> #> Rooted; includes branch lengths. #>"},{"path":"https://flaviomoc.github.io/divraster/reference/range.list.html","id":null,"dir":"Reference","previous_headings":"","what":"Area calculation — range.list","title":"Area calculation — range.list","text":"Area calculation","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/range.list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Area calculation — range.list","text":"","code":"# S3 method for list range(x, unit = \"km\", r2 = NULL, r3 = NULL, filename = \"\")"},{"path":"https://flaviomoc.github.io/divraster/reference/range.list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Area calculation — range.list","text":"x list containing multiple SpatRaster presence-absence data (0 1) set species. unit Character. Default \"km\", \"m\" \"ha\" also available. r2 SpatRaster extent \"x\". r3 SpatRaster extent \"x\". filename Character. Save results name provided.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/range.list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Area calculation — range.list","text":"data.frame area values chosen unit.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/range.rast.html","id":null,"dir":"Reference","previous_headings":"","what":"Area calculation — range.rast","title":"Area calculation — range.rast","text":"Area calculation","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/range.rast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Area calculation — range.rast","text":"","code":"# S3 method for rast range(x, unit = \"km\", ...)"},{"path":"https://flaviomoc.github.io/divraster/reference/range.rast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Area calculation — range.rast","text":"x SpatRaster presence-absence data (0 1) given species. unit Character. Default \"km\", \"m\" \"ha\" also available. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/range.rast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Area calculation — range.rast","text":"vector area chosen unit.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.html","id":null,"dir":"Reference","previous_headings":"","what":"Alpha calculation for raster — spat.alpha","title":"Alpha calculation for raster — spat.alpha","text":"Calculates alpha diversity taxonomic (TD), functional (FD), phylogenetic (PD) dimensions. Adapted alpha","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Alpha calculation for raster — spat.alpha","text":"","code":"spat.alpha(bin, tree, cores = 1, filename = \"\", ...)"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Alpha calculation for raster — spat.alpha","text":"bin SpatRaster presence-absence data (0 1) set species. tree can 'data.frame' species traits 'phylo' rooted phylogenetic tree. Species names 'tree' 'bin' must match! cores positive integer. cores > 1, 'parallel' package cluster many cores created used. filename Character. Save results name provided. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Alpha calculation for raster — spat.alpha","text":"SpatRaster alpha result.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Alpha calculation for raster — spat.alpha","text":"Alpha calculations use tree-based approach TD, FD, PD (Cardoso et al. 2014). FD calculation, species traits matrix transformed distance matrix clustered create regional dendrogram (.e. dendrogram species raster stack), total branch length calculated. computing FD community (.e. raster cell), regional dendrogram subsetted create local dendrogram includes species present local community. branch lengths connecting species summed represent functional relationships locally present species (Petchey Gaston, 2002, 2006). Similarly, PD, cumulative branch lengths connecting species within community indicate shared phylogenetic relationships (Faith, 1992). Alpha TD can also visualized using tree diagram, species directly connected root edge unit length, reflecting number different taxa community (.e. species richness) since taxa level (Cardoso et al. 2014).","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Alpha calculation for raster — spat.alpha","text":"Cardoso, P. et al. 2014. Partitioning taxon, phylogenetic functional beta diversity replacement richness difference components. - Journal Biogeography 41: 749–761. Faith, D. P. 1992. Conservation evaluation phylogenetic diversity. - Biological Conservation 61: 1–10. Petchey, O. L. Gaston, K. J. 2002. Functional diversity (FD), species richness community composition. - Ecology Letters 5: 402–411. Rodrigues, . S. L. Gaston, K. J. 2002. Maximising phylogenetic diversity selection networks conservation areas. - Biological Conservation 105: 103–111.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Alpha calculation for raster — spat.alpha","text":"","code":"# \\donttest{ library(terra) bin1 <- terra::rast(system.file(\"extdata\", \"ref.tif\", package = \"divraster\")) traits <- read.csv(system.file(\"extdata\", \"traits.csv\", package = \"divraster\"), row.names = 1) tree <- ape::read.tree(system.file(\"extdata\", \"tree.tre\", package = \"divraster\")) spat.alpha(bin1) #> class : SpatRaster #> dimensions : 8, 8, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Alpha_TD #> min value : 2 #> max value : 8 spat.alpha(bin1, traits) #> class : SpatRaster #> dimensions : 8, 8, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Alpha_FD #> min value : 0.3492543 #> max value : 1.2493508 spat.alpha(bin1, tree) #> class : SpatRaster #> dimensions : 8, 8, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Alpha_PD #> min value : 3.101099 #> max value : 9.761420 # }"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.vec.html","id":null,"dir":"Reference","previous_headings":"","what":"Alpha calculation for vector — spat.alpha.vec","title":"Alpha calculation for vector — spat.alpha.vec","text":"Alpha calculation vector","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.vec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Alpha calculation for vector — spat.alpha.vec","text":"","code":"spat.alpha.vec(x, tree, resu, ...)"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.vec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Alpha calculation for vector — spat.alpha.vec","text":"x numeric vector presence-absence data (0 1) set species. tree can data frame species traits phylogenetic tree. resu Numeric. vector store results. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.vec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Alpha calculation for vector — spat.alpha.vec","text":"vector alpha result.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial beta diversity for raster — spat.beta","title":"Spatial beta diversity for raster — spat.beta","text":"Calculates spatial beta diversity taxonomic (TD), functional (FD), phylogenetic (PD) dimensions. Adapted beta.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial beta diversity for raster — spat.beta","text":"","code":"spat.beta( x, tree, filename = \"\", global = FALSE, fm = NULL, d = mean(terra::res(terra::rast(x))) * 2, type = \"circle\", na.policy = \"omit\", ... )"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial beta diversity for raster — spat.beta","text":"x SpatRaster presence-absence data (0 1) set species. tree can 'data.frame' species traits 'phylo' rooted phylogenetic tree. Species names 'tree' 'x' must match! filename Character. Save results name provided. global Logical. Mean pairwise comparisons focal cell neighbors (default) mean pairwise comparisons. fm Numeric. Focal matrix (\"moving window\"). d Window radius compute beta diversity. type Character. Window format. Default = \"circle\". na.policy Character. Default = \"omit\". See ?terra::focal3D details. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial beta diversity for raster — spat.beta","text":"SpatRaster beta results (total, replacement, richness difference, ratio).","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Spatial beta diversity for raster — spat.beta","text":"TD beta diversity partitioning framework used developed Podani Schmera (2011) Carvalho et al. (2012) expanded PD FD Cardoso et al. (2014).","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Spatial beta diversity for raster — spat.beta","text":"Cardoso, P. et al. 2014. Partitioning taxon, phylogenetic functional beta diversity replacement richness difference components. - Journal Biogeography 41: 749–761. Carvalho, J. C. et al. 2012. Determining relative roles species replacement species richness differences generating beta-diversity patterns. - Global Ecology Biogeography 21: 760–771. Podani, J. Schmera, D. 2011. new conceptual methodological framework exploring explaining pattern presence - absence data. - Oikos 120: 1625–1638. Hidasi-Neto, J. et al. 2019. Climate change drive mammal species loss biotic homogenization Cerrado Biodiversity Hotspot. - Perspectives Ecology Conservation 17: 57–63.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatial beta diversity for raster — spat.beta","text":"","code":"# \\donttest{ library(terra) bin1 <- terra::rast(system.file(\"extdata\", \"ref.tif\", package = \"divraster\")) traits <- read.csv(system.file(\"extdata\", \"traits.csv\", package = \"divraster\"), row.names = 1) rownames(traits) <- names(bin1) tree <- ape::read.tree(system.file(\"extdata\", \"tree.tre\", package = \"divraster\")) spat.beta(bin1) #> class : SpatRaster #> dimensions : 8, 8, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_TD, Brepl_TD, Brich_TD, Bratio_TD #> min values : 0.5515512, 0.1898990, 0.0952381, 0.3174335 #> max values : 0.8694805, 0.7207341, 0.5067460, 0.8529412 spat.beta(bin1, traits) #> class : SpatRaster #> dimensions : 8, 8, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_FD, Brepl_FD, Brich_FD, Bratio_FD #> min values : 0.3310466, 0.06122664, 0.1271726, 0.1285775 #> max values : 0.6641360, 0.41959062, 0.5680299, 0.7351086 spat.beta(bin1, tree) #> class : SpatRaster #> dimensions : 8, 8, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_PD, Brepl_PD, Brich_PD, Bratio_PD #> min values : 0.3250871, 0.04931651, 0.06867094, 0.1265763 #> max values : 0.7072649, 0.52737261, 0.46375695, 0.8271077 # }"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.vec.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial beta diversity for vector — spat.beta.vec","title":"Spatial beta diversity for vector — spat.beta.vec","text":"Spatial beta diversity vector","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.vec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial beta diversity for vector — spat.beta.vec","text":"","code":"spat.beta.vec(x, tree, global = FALSE, spp, nspp, ...)"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.vec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial beta diversity for vector — spat.beta.vec","text":"x numeric vector presence-absence data (0 1) set species. tree can data frame species traits phylogenetic tree. global Logical. Mean pairwise comparisons focal cell neighbors (default) mean pairwise comparisons. spp Character. Species names. nspp Numeric. Number species. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.vec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial beta diversity for vector — spat.beta.vec","text":"vector beta results (total, replacement, richness difference, ratio).","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.rand.html","id":null,"dir":"Reference","previous_headings":"","what":"Standardized Effect Size (SES) for raster — spat.rand","title":"Standardized Effect Size (SES) for raster — spat.rand","text":"Calculates standardized effect size functional phylogenetic alpha diversity. See bootspat_str bootspat_naive","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.rand.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Standardized Effect Size (SES) for raster — spat.rand","text":"","code":"spat.rand( x, tree, aleats, random = c(\"site\", \"species\", \"both\", \"spat\"), cores = 1, filename = \"\", ... )"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.rand.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standardized Effect Size (SES) for raster — spat.rand","text":"x SpatRaster. SpatRaster containing presence-absence data (0 1) set species. tree can 'data.frame' species traits 'phylo' rooted phylogenetic tree. Species names 'tree' 'x' must match! aleats positive integer. positive integer indicating many times calculation repeated. random character. character indicating type randomization. currently available randomization methods \"spat\", \"site\", \"species\" \"\" (site species). cores positive integer. cores > 1, 'parallel' package cluster many cores created used. filename character. Output filename. ... additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.rand.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standardized Effect Size (SES) for raster — spat.rand","text":"SpatRaster Mean, SD, Observed, SES.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.rand.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Standardized Effect Size (SES) for raster — spat.rand","text":"","code":"# \\donttest{ x <- terra::rast(system.file(\"extdata\", \"ref.tif\", package = \"divraster\")) traits <- read.csv(system.file(\"extdata\", \"traits.csv\", package = \"divraster\"), row.names = 1) tree <- ape::read.tree(system.file(\"extdata\", \"tree.tre\", package = \"divraster\")) spat.rand(x, tree, 3, \"site\") #> class : SpatRaster #> dimensions : 8, 8, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Mean_PD, SD_PD, Observed_PD, SES_PD #> min values : 4.217869, 0.05263325, 3.359948, -9.313514 #> max values : 9.524013, 1.26248756, 10.571964, 10.454383 spat.rand(x, traits, 3, \"site\") #> class : SpatRaster #> dimensions : 8, 8, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Mean_FD, SD_FD, Observed_FD, SES_FD #> min values : 0.3846142, 0.02100142, 0.3492543, -3.832472 #> max values : 1.2542336, 0.25886931, 1.2493508, 8.094669 # }"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.html","id":null,"dir":"Reference","previous_headings":"","what":"Average trait calculation for raster — spat.trait","title":"Average trait calculation for raster — spat.trait","text":"Compute average trait.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Average trait calculation for raster — spat.trait","text":"","code":"spat.trait(x, trait, cores = 1, filename = \"\", ...)"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Average trait calculation for raster — spat.trait","text":"x SpatRaster presence-absence data (0 1) set species. trait 'data.frame' species traits. Rownames must species names match 'x'! cores positive integer. cores > 1, 'parallel' package cluster many cores created used. filename Character. Save results name provided. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Average trait calculation for raster — spat.trait","text":"SpatRaster average traits.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Average trait calculation for raster — spat.trait","text":"","code":"# \\donttest{ library(terra) bin1 <- terra::rast(system.file(\"extdata\", \"ref.tif\", package = \"divraster\")) traits <- read.csv(system.file(\"extdata\", \"traits.csv\", package = \"divraster\"), row.names = 1) spat.trait(bin1, traits) #> class : SpatRaster #> dimensions : 8, 8, 2 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : beak.size, wing.length #> min values : 1.312311, 30.54550 #> max values : 3.310816, 45.84854 # }"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.vec.html","id":null,"dir":"Reference","previous_headings":"","what":"Average trait calculation for vector — spat.trait.vec","title":"Average trait calculation for vector — spat.trait.vec","text":"Average trait calculation vector","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.vec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Average trait calculation for vector — spat.trait.vec","text":"","code":"spat.trait.vec(x, col_trait, ...)"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.vec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Average trait calculation for vector — spat.trait.vec","text":"x numeric vector presence-absence data (0 1) set species. col_trait numeric vector trait numbers. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.vec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Average trait calculation for vector — spat.trait.vec","text":"Vector average trait.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/suit.change.html","id":null,"dir":"Reference","previous_headings":"","what":"Species suitability change between climate scenarios — suit.change","title":"Species suitability change between climate scenarios — suit.change","text":"Species suitability change climate scenarios","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/suit.change.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Species suitability change between climate scenarios — suit.change","text":"","code":"suit.change(r1, r2, filename = \"\")"},{"path":"https://flaviomoc.github.io/divraster/reference/suit.change.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Species suitability change between climate scenarios — suit.change","text":"r1 SpatRaster presence-absence data (0 1) set species. r2 SpatRaster presence-absence data (0 1) set species. filename Character. Save results name provided.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/suit.change.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Species suitability change between climate scenarios — suit.change","text":"SpatRaster suitability change (gain, loss, unchanged, unsuitable).","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/suit.change.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Species suitability change between climate scenarios — suit.change","text":"","code":"# \\donttest{ library(terra) r1 <- terra::rast(system.file(\"extdata\", \"ref.tif\", package = \"divraster\")) r2 <- terra::rast(system.file(\"extdata\", \"fut.tif\", package = \"divraster\")) suit.change(r1, r2) #> class : SpatRaster #> dimensions : 8, 8, 10 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> varname : fut #> names : A, B, C, D, E, F, ... #> min values : 1, 1, 1, 1, 1, 1, ... #> max values : 4, 4, 4, 4, 4, 4, ... # }"},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.html","id":null,"dir":"Reference","previous_headings":"","what":"Temporal beta diversity calculation for raster — temp.beta","title":"Temporal beta diversity calculation for raster — temp.beta","text":"Calculates temporal beta diversity taxonomic (TD), functional (FD), phylogenetic (PD) dimensions. Adapted beta","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Temporal beta diversity calculation for raster — temp.beta","text":"","code":"temp.beta(bin1, bin2, tree, filename = \"\", cores = 1, ...)"},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Temporal beta diversity calculation for raster — temp.beta","text":"bin1 SpatRaster presence-absence data (0 1) set species. bin2 SpatRaster presence-absence data (0 1) set species. Species names 'bin2' 'bin1' must match! tree can 'data.frame' species traits 'phylo' rooted phylogenetic tree. Species names 'tree', 'bin1', 'bin2' must match! filename Character. Save results name provided. cores positive integer. cores > 1, 'parallel' package cluster many cores created used. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Temporal beta diversity calculation for raster — temp.beta","text":"SpatRaster beta results (total, replacement, richness difference, ratio).","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Temporal beta diversity calculation for raster — temp.beta","text":"TD beta diversity partitioning framework used developed Podani Schmera (2011) Carvalho et al. (2012) expanded PD FD Cardoso et al. (2014).","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Temporal beta diversity calculation for raster — temp.beta","text":"Cardoso, P. et al. 2014. Partitioning taxon, phylogenetic functional beta diversity replacement richness difference components. - Journal Biogeography 41: 749–761. Carvalho, J. C. et al. 2012. Determining relative roles species replacement species richness differences generating beta-diversity patterns. - Global Ecology Biogeography 21: 760–771. Podani, J. Schmera, D. 2011. new conceptual methodological framework exploring explaining pattern presence - absence data. - Oikos 120: 1625–1638. Hidasi-Neto, J. et al. 2019. Climate change drive mammal species loss biotic homogenization Cerrado Biodiversity Hotspot. - Perspectives Ecology Conservation 17: 57–63.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Temporal beta diversity calculation for raster — temp.beta","text":"","code":"# \\donttest{ library(terra) bin1 <- terra::rast(system.file(\"extdata\", \"ref.tif\", package = \"divraster\")) bin2 <- terra::rast(system.file(\"extdata\", \"fut.tif\", package = \"divraster\")) traits <- read.csv(system.file(\"extdata\", \"traits.csv\", package = \"divraster\"), row.names = 1) tree <- ape::read.tree(system.file(\"extdata\", \"tree.tre\", package = \"divraster\")) temp.beta(bin1, bin2) #> class : SpatRaster #> dimensions : 8, 8, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_TD, Brepl_TD, Brich_TD, Bratio_TD #> min values : 0.2, 0.0000000, 0.0000000, 0 #> max values : 1.0, 0.8888889, 0.7142857, 1 temp.beta(bin1, bin2, traits) #> class : SpatRaster #> dimensions : 8, 8, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_FD, Brepl_FD, Brich_FD, Bratio_FD #> min values : 0.1522544, 0.0000000, 0.003222951, 0.0000000 #> max values : 0.8309776, 0.5852812, 0.830977572, 0.9905423 temp.beta(bin1, bin2, tree) #> class : SpatRaster #> dimensions : 8, 8, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_PD, Brepl_PD, Brich_PD, Bratio_PD #> min values : 0.1525273, 0.0000000, 0.004401637, 0.0000000 #> max values : 0.8223597, 0.7143422, 0.496646645, 0.9937685 # }"},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.vec.html","id":null,"dir":"Reference","previous_headings":"","what":"Temporal beta diversity calculation for vector — temp.beta.vec","title":"Temporal beta diversity calculation for vector — temp.beta.vec","text":"Temporal beta diversity calculation vector","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.vec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Temporal beta diversity calculation for vector — temp.beta.vec","text":"","code":"temp.beta.vec(x, nspp, spp, tree, resu, ...)"},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.vec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Temporal beta diversity calculation for vector — temp.beta.vec","text":"x numeric vector presence-absence data (0 1) set species. nspp Numeric. Number species. spp Character. Species name. tree can data frame species traits phylogenetic tree. resu Numeric. vector store results. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.vec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Temporal beta diversity calculation for vector — temp.beta.vec","text":"vector beta results (total, replacement, richness difference, ratio).","code":""},{"path":"https://flaviomoc.github.io/divraster/news/index.html","id":"divraster-104","dir":"Changelog","previous_headings":"","what":"divraster 1.0.4","title":"divraster 1.0.4","text":"CRAN release: 2023-10-10 New function added initial testing #3. Minor changes function documentation. Minor changes function tests. Citation updated.","code":""},{"path":"https://flaviomoc.github.io/divraster/news/index.html","id":"divraster-103","dir":"Changelog","previous_headings":"","what":"divraster 1.0.3","title":"divraster 1.0.3","text":"CRAN release: 2023-08-21 Improvements function descriptions. Improvements vignette (examples description). Minor correction function tests #2. Citation file added.","code":""},{"path":"https://flaviomoc.github.io/divraster/news/index.html","id":"divraster-102","dir":"Changelog","previous_headings":"","what":"divraster 1.0.2","title":"divraster 1.0.2","text":"CRAN release: 2023-06-27 Released 2023-06-27 Initial CRAN submission.","code":""}] +[{"path":"https://flaviomoc.github.io/divraster/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://flaviomoc.github.io/divraster/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"intro","dir":"Articles","previous_headings":"","what":"1 Introduction","title":"divraster-vignette","text":"Macroecological studies increasingly utilized context climate change, necessitating use tools analyze large datasets. examine comprehend intricate mechanisms underlie species distributions structure biological communities, diverse array metrics developed. metrics encompass alpha beta diversity patterns across taxonomic (TD), functional (FD), phylogenetic (PD) dimensions. package divraster addresses current gap field offering functions calculate diversity metrics directly rasters, eliminating need matrix transformations. capability especially valuable dealing extensive datasets, matrices often impose memory constraints.","code":""},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"alpha","dir":"Articles","previous_headings":"","what":"2 Alpha calculations","title":"divraster-vignette","text":"Alpha diversity calculations use tree-based approach taxonomic (TD), functional (FD), phylogenetic (PD) diversity. FD calculation, species traits matrix converted distance matrix clustered produce regional dendrogram (.e. dendrogram species raster stack) total branch length calculated. calculating FD community (.e. raster cell), regional dendrogram subsetted local dendrogram containing species present local community, branch lengths connecting summed represent functional relationships species locally present. Similarly, PD, sum branch lengths connecting species within community represents shared phylogenetic relationships cumulative evolutionary history. Alpha TD can also visualized using tree diagram, species directly connected root edge unit length, reflecting number different taxa community (.e. species richness) since taxa level.","code":""},{"path":[]},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"alpha-td","dir":"Articles","previous_headings":"","what":"2.1.1 Alpha TD","title":"divraster-vignette","text":"alpha taxonomic diversity first scenario ranges 0 67, second scenario, ranges 0 65, higher values concentrated towards north cases. comparing two scenarios, subtracting second first reveals greater species losses (n = 18) towards south.","code":"# Loading data # Presence-absence SpatRaster bin1 <- terra::rast(system.file(\"extdata\", \"ref_frugivor.tif\", package = \"divraster\")) bin2 <- terra::rast(system.file(\"extdata\", \"fut_frugivor.tif\", package = \"divraster\")) # Change extension to process faster terra::ext(bin1) #> SpatExtent : -41.875, -38.75, -21.375, -13 (xmin, xmax, ymin, ymax) e <- c(-41, -39, -15, -13) bin1 <- terra::crop(bin1, e) bin2 <- terra::crop(bin2, e) # Species traits traits <- read.csv(system.file(\"extdata\", \"traits_frugivor.csv\", package = \"divraster\"), sep = \";\", row.names = 1) # Phylogenetic tree tree <- ape::read.tree(system.file(\"extdata\", \"tree_frugivor.tre\", package = \"divraster\")) # Alpha TD calculation for scenario 1 alpha.td <- divraster::spat.alpha(bin1) alpha.td #> class : SpatRaster #> dimensions : 16, 16, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Alpha_TD #> min value : 0 #> max value : 67 terra::plot(alpha.td, main = paste0(names(alpha.td), \"_sce1\")) # Alpha TD calculation for scenario 2 alpha.td2 <- divraster::spat.alpha(bin2) alpha.td2 #> class : SpatRaster #> dimensions : 16, 16, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Alpha_TD #> min value : 0 #> max value : 65 terra::plot(alpha.td2, main = paste0(names(alpha.td2), \"_sce2\")) # Difference in Alpha TD between scenarios alpha.td2-alpha.td #> class : SpatRaster #> dimensions : 16, 16, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Alpha_TD #> min value : -18 #> max value : 0 terra::plot(alpha.td2-alpha.td, main = \"Delta Alpha TD\")"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"alpha-fd","dir":"Articles","previous_headings":"","what":"2.1.2 Alpha FD","title":"divraster-vignette","text":"alpha functional diversity first scenario ranges 3.7 4.4, higher values concentrated towards north, indicating greater functional diversity.","code":"alpha.fd <- divraster::spat.alpha(bin1, traits) alpha.fd #> class : SpatRaster #> dimensions : 16, 16, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Alpha_FD #> min value : 3.723151 #> max value : 4.378846 terra::plot(alpha.fd, main = names(alpha.fd))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"alpha-pd","dir":"Articles","previous_headings":"","what":"2.1.3 Alpha PD","title":"divraster-vignette","text":"alpha phylogenetic diversity first scenario ranges 1524 1860, higher values concentrated towards north, indicating greater phylogenetic diversity.","code":"# Alpha PD calculation alpha.pd <- divraster::spat.alpha(bin1, tree) alpha.pd #> class : SpatRaster #> dimensions : 16, 16, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Alpha_PD #> min value : 1523.921 #> max value : 1859.668 terra::plot(alpha.pd, main = names(alpha.pd))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"ses","dir":"Articles","previous_headings":"","what":"3 Standardized effect size (SES)","title":"divraster-vignette","text":"SES often used ecological studies measure magnitude difference observed randomized patterns generated null models, expressed standard deviation units. calculate SES using SESraster package, currently offers six community randomization methods. basic randomization methods include: keeping richness constant randomizing position species within raster cell (site), keeping range size constant randomizing position species presences space (species), randomizing site species simultaneously (). positive SES indicates observed functional/phylogenetic diversity higher expected solely based species richness (taxonomic diversity), whereas negative SES indicates opposite.","code":""},{"path":[]},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"ses-fd","dir":"Articles","previous_headings":"","what":"3.1.1 SES FD","title":"divraster-vignette","text":"SES indicates majority areas values close 0, suggesting functional diversity significantly differ expected change. However, one community projected functionally dispersed (SES_FD = 31), another community projected functionally clustered (SES_FD = -39). indicates increase decrease functional diversity within communities scenarios 1 2, respectively.","code":"# SES FD calculation ses.fd <- divraster::spat.rand(x = bin1, tree = traits, aleats = 3, random = \"site\") ses.fd #> class : SpatRaster #> dimensions : 16, 16, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Mean_FD, SD_FD, Observed_FD, SES_FD #> min values : 3.711791, 0.002639008, 3.723151, -18.594535 #> max values : 4.424008, 0.166680920, 4.378846, 4.860787 terra::plot(ses.fd, main = names(ses.fd))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"ses-pd","dir":"Articles","previous_headings":"","what":"3.1.2 SES PD","title":"divraster-vignette","text":"Similarly, SES phylogenetic diversity differ expected chance, communities presenting values close 0. However, one community projected phylogenetically dispersed (SES_PD = 10), another community projected phylogenetically clustered (SES_FD = -15). indicates increase decrease phylogenetic diversity within communities scenarios 1 2, respectively.","code":"# SES PD calculation ses.pd <- divraster::spat.rand(x = bin1, tree = tree, aleats = 3, random = \"site\") ses.pd #> class : SpatRaster #> dimensions : 16, 16, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Mean_PD, SD_PD, Observed_PD, SES_PD #> min values : 1617.695, 1.585962, 1623.451, -4.664356 #> max values : 1875.081, 97.284872, 1880.676, 11.069075 terra::plot(ses.pd, main = names(ses.pd))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"beta","dir":"Articles","previous_headings":"","what":"4 Beta diversity","title":"divraster-vignette","text":"Beta diversity captures variations species composition different communities. examining community comparison neighboring ones, referred spatial beta diversity. hand, assessing changes within community different time periods, termed temporal beta diversity. Beta diversity can partitioned two components: “replacement” “richness differences”. former accounts substitution one species another, latter encompasses discrepancies total number species (e.g. species gain loss). addition, since Btotal represents sum Brepl Brich components, proportion Brepl/Btotal (Bratio) can calculated, values close 0 indicating predominance Brich values close 1 indicating predominance Brepl. Moreover, concept beta diversity extends functional (FD) phylogenetic diversity (PD), using framework taxonomic diversity (TD). context TD, higher beta diversity represents higher dissimilarities species composition communities. contrast, FD, indicates higher dissimilarities functional traits, PD, reflects higher dissimilarities phylogenetic relationships species communities.","code":""},{"path":[]},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"betaspat-td","dir":"Articles","previous_headings":"","what":"4.1.1 Beta spatial TD","title":"divraster-vignette","text":"Spatial beta diversity TD indicates slight change species composition towards south, evidenced small values Btotal (~0.1). predominant component contributing change richness difference (Brich), suggesting dissimilarities community (.e. pixel) neighbors primarily due loss gain species. Bratio also indicates predominance Birch component communities.","code":"# Beta spatial TD calculation beta.td <- divraster::spat.beta(bin1) beta.td #> class : SpatRaster #> dimensions : 16, 16, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_TD, Brepl_TD, Brich_TD, Bratio_TD #> min values : 0.006060606, 0.00000000, 0.004264392, 0.0000000 #> max values : 0.109409606, 0.03638009, 0.103181683, 0.7259259 terra::plot(beta.td, main = names(beta.td))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"betaspat-fd","dir":"Articles","previous_headings":"","what":"4.1.2 Beta spatial FD","title":"divraster-vignette","text":"Similarly, spatial beta diversity FD indicates slight change functional traits composition towards south, evidenced small values Btotal (~0.08). predominant component contributing little change richness difference (Brich), suggesting dissimilarities community (.e. pixel) neighbors primarily due loss gain functional traits. Bratio also indicates predominance Birch component communities.","code":"# Beta spatial FD calculation beta.fd <- divraster::spat.beta(bin1, traits) beta.fd #> class : SpatRaster #> dimensions : 16, 16, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_FD, Brepl_FD, Brich_FD, Bratio_FD #> min values : 0.0004245858, 0.00000000, 0.0004245858, 0.000000 #> max values : 0.0793045655, 0.01846139, 0.0793045655, 0.756675 terra::plot(beta.fd, main = names(beta.fd))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"betaspat-pd","dir":"Articles","previous_headings":"","what":"4.1.3 Beta spatial PD","title":"divraster-vignette","text":"spatial beta diversity PD indicates slight change evolutionary history communities towards south. However change even lower compared TD FD, evidenced smallest values Btotal (~0.06). predominant component contributing little change also richness difference (Brich), suggesting dissimilarities community (.e. pixel) neighbors due loss gain evolutionary history. Bratio also indicates predominance Birch component communities.","code":"# Beta spatial PD calculation beta.pd <- divraster::spat.beta(bin1, tree) beta.pd #> class : SpatRaster #> dimensions : 16, 16, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_PD, Brepl_PD, Brich_PD, Bratio_PD #> min values : 0.002851805, 0.000000000, 0.001618621, 0.0000000 #> max values : 0.059656685, 0.008026876, 0.059656685, 0.8250616 terra::plot(beta.pd, main = names(beta.pd))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"betatemp-td","dir":"Articles","previous_headings":"","what":"4.1.4 Beta temporal TD","title":"divraster-vignette","text":"temporal beta diversity TD indicates future communities expected experience changes species composition, predominantly towards south, Btotal reaching approximately 0.3. predominance Brich component suggests dissimilarities attributed gains losses species. Bratio also indicates predominance Birch component communities.","code":"# Beta temporal TD calculation betatemp.td <- divraster::temp.beta(bin1, bin2) betatemp.td #> class : SpatRaster #> dimensions : 16, 16, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_TD, Brepl_TD, Brich_TD, Bratio_TD #> min values : 0.02985075, 0.00000000, 0.02985075, 0.0000000 #> max values : 0.31578947, 0.09836066, 0.31578947, 0.6666667 terra::plot(betatemp.td, main = names(betatemp.td))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"betatemp-fd","dir":"Articles","previous_headings":"","what":"4.1.5 Beta temporal FD","title":"divraster-vignette","text":"temporal beta diversity FD indicates less pronounced pattern compared TD, smaller values Btotal, reaching maximum 0.17. Brich component also predominant, suggesting small dissimilarities can attributed gains losses functional traits. Bratio also indicates predominance Birch component communities.","code":"# Beta temporal FD calculation betatemp.fd <- divraster::temp.beta(bin1, bin2, traits) betatemp.fd #> class : SpatRaster #> dimensions : 16, 16, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_FD, Brepl_FD, Brich_FD, Bratio_FD #> min values : 0.01733908, 0.00000000, 0.01012696, 0.0000000 #> max values : 0.17193290, 0.03741327, 0.17193290, 0.6872465 terra::plot(betatemp.fd, main = names(betatemp.fd))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"betatemp-pd","dir":"Articles","previous_headings":"","what":"4.1.6 Beta temporal PD","title":"divraster-vignette","text":"Likewise, temporal beta diversity PD indicates less pronounced pattern compared TD, smaller values Btotal, reaching maximum 0.18. Brich component also predominant, suggesting small dissimilarities can attributed gains losses evolutionary history. Bratio also indicates predominance Birch component communities.","code":"# Beta temporal PD calculation betatemp.pd <- divraster::temp.beta(bin1, bin2, tree) betatemp.pd #> class : SpatRaster #> dimensions : 16, 16, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_PD, Brepl_PD, Brich_PD, Bratio_PD #> min values : 0.0120217, 0.0000000, 0.009533166, 0.0000000 #> max values : 0.1792291, 0.0394096, 0.179229119, 0.7759122 terra::plot(betatemp.pd, main = names(betatemp.pd))"},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"traits-avg","dir":"Articles","previous_headings":"","what":"5 Traits average","title":"divraster-vignette","text":"Calculating average traits species climate scenario enables evaluation species traits contribute loss suitable habitat. Unlike functional diversity, combines functional traits index, approach provides direct insight spatial variations average traits. information can complement data necessary delineating conservation priority areas, shifts average traits—whether increasing decreasing—indicate potential loss species specific features. particular significance given functional traits closely tied ecological services provided species.","code":""},{"path":"https://flaviomoc.github.io/divraster/articles/divraster-vignette.html","id":"traits-ex","dir":"Articles","previous_headings":"","what":"5.1 Traits average examples","title":"divraster-vignette","text":"average beak depth first scenario ranges 8.5 9.6, second scenario, ranges 8.8 9.9. Beak depth increased 13.5% southern region decreased 4.5% central region. earlier analysis indicated prevalence species loss, implying rise average beak depth second scenario can attributed decline species smaller beak depths. Conversely, reduction beak size can attributed decline species larger beak depths.","code":"# Average traits calculation # Scenario 1 avg.traits1 <- divraster::spat.trait(bin1, traits) avg.traits1[[4]] #> class : SpatRaster #> dimensions : 16, 16, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Beak.Depth #> min value : 8.526923 #> max value : 9.601515 terra::plot(avg.traits1[[4]], main = paste0(names(avg.traits1[[4]]), \"_sce1\")) # Scenario 2 avg.traits2 <- divraster::spat.trait(bin2, traits) avg.traits2[[4]] #> class : SpatRaster #> dimensions : 16, 16, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Beak.Depth #> min value : 8.786792 #> max value : 9.942308 terra::plot(avg.traits2[[4]], main = paste0(names(avg.traits2[[4]]), \"_sce2\")) # Percentage of change change.traits <- (avg.traits2 - avg.traits1) / avg.traits1 * 100 change.traits[[4]] #> class : SpatRaster #> dimensions : 16, 16, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41, -39, -15, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Beak.Depth #> min value : -4.495893 #> max value : 13.541296 terra::plot(change.traits[[4]], main = paste0(names(change.traits[[4]]), \"_%\"))"},{"path":"https://flaviomoc.github.io/divraster/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Flávio M. M. Mota. Author, maintainer, copyright holder. Neander Marcel Heming. Author. Gabriela Alves-Ferreira. Author.","code":""},{"path":"https://flaviomoc.github.io/divraster/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Mota FMM, Alves-Ferreira G, Talora DC, Heming NM (2023). “divraster: R package calculate taxonomic, functional phylogenetic diversity rasters.” Ecography, e06905. doi:10.1111/ecog.06905. Cardoso P, Rigal F, Carvalho J (2015). “BAT – Biodiversity Assessment Tools, R package measurement estimation alpha beta taxon, phylogenetic functional diversity.” Methods Ecology Evolution, 6, 232–236. doi:10.1111/2041-210X.12310.","code":"@Article{, title = {divraster: an R package to calculate taxonomic, functional and phylogenetic diversity from rasters}, author = {F. M. M. Mota and G. Alves-Ferreira and D. C. Talora and N. M. Heming}, journal = {Ecography}, year = {2023}, pages = {e06905}, doi = {10.1111/ecog.06905}, } @Article{, title = {BAT -- Biodiversity Assessment Tools, an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity}, author = {P. Cardoso and F. Rigal and J. Carvalho}, journal = {Methods in Ecology and Evolution}, year = {2015}, volume = {6}, pages = {232--236}, doi = {10.1111/2041-210X.12310}, }"},{"path":"https://flaviomoc.github.io/divraster/index.html","id":"divraster","dir":"","previous_headings":"","what":"Diversity Metrics Calculations for Rasterized Data","title":"Diversity Metrics Calculations for Rasterized Data","text":"Alpha beta calculations using rasters taxonomic (TD), functional (FD), phylogenetic (PD) dimensions. Spatial temporal beta diversity can partitioned replacement richness difference components. Functions calculate standardized effect size functional phylogenetic alpha diversity average traits available.","code":""},{"path":"https://flaviomoc.github.io/divraster/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Diversity Metrics Calculations for Rasterized Data","text":"CRAN version divraster can installed using: development version divraster can installed Github using:","code":"install.packages(\"divraster\") devtools::install_github(\"flaviomoc/divraster\")"},{"path":"https://flaviomoc.github.io/divraster/index.html","id":"divraster-basics","dir":"","previous_headings":"","what":"divraster basics","title":"Diversity Metrics Calculations for Rasterized Data","text":"Basic information divraster can found package’s webpage vignette:","code":"vignette(\"divraster-vignette\")"},{"path":"https://flaviomoc.github.io/divraster/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Diversity Metrics Calculations for Rasterized Data","text":"use R package, please cite publications: Mota FMM, Alves-Ferreira G, Talora DC, Heming NM (2023). divraster: R package calculate taxonomic, functional phylogenetic diversity rasters. – Ecography, e06905. information:","code":"citation(\"divraster\")"},{"path":"https://flaviomoc.github.io/divraster/index.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Diversity Metrics Calculations for Rasterized Data","text":"question find bug, let us know topic Issues.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/area.calc.html","id":null,"dir":"Reference","previous_headings":"","what":"Area calculation — area.calc","title":"Area calculation — area.calc","text":"Area calculation","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/area.calc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Area calculation — area.calc","text":"","code":"area.calc(r1, unit = \"km\", r2 = NULL, r3 = NULL, filename = \"\")"},{"path":"https://flaviomoc.github.io/divraster/reference/area.calc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Area calculation — area.calc","text":"r1 SpatRaster list multiple SpatRasters. unit Character. Default \"km\", \"m\" \"ha\" also available. r2 SpatRaster resolution extent \"r1\". r3 SpatRaster resolution extent \"r1\". filename Character. Save results name provided.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/area.calc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Area calculation — area.calc","text":"vector data.frame area values chosen unit.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/area.calc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Area calculation — area.calc","text":"","code":"# \\donttest{ library(terra) #> terra 1.7.71 bin1 <- terra::rast(system.file(\"extdata\", \"ref.tif\", package = \"divraster\")) my.list <- list(bin1 = bin1[[1:2]]) area.calc(my.list) #> sp scenario total.area #> 1 A bin1 6154.240 #> 2 B bin1 6346.524 # }"},{"path":"https://flaviomoc.github.io/divraster/reference/inputs_chk.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if objects are valid — inputs_chk","title":"Check if objects are valid — inputs_chk","text":"Check objects valid","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/inputs_chk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if objects are valid — inputs_chk","text":"","code":"inputs_chk(bin1, bin2, tree)"},{"path":"https://flaviomoc.github.io/divraster/reference/inputs_chk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if objects are valid — inputs_chk","text":"bin1 SpatRaster presence-absence data (0 1) set species. bin2 SpatRaster presence-absence data (0 1) set species. Species names 'bin2' 'bin1' must match! tree can 'data.frame' species traits 'phylo' rooted phylogenetic tree. Species names 'tree', 'bin1', 'bin2' must match!","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/inputs_chk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if objects are valid — inputs_chk","text":"Either success message error.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/load.data.html","id":null,"dir":"Reference","previous_headings":"","what":"Load data adapted from Mota et al. (2022), Tobias et al. (2022), and Jetz et al. (2014) — load.data","title":"Load data adapted from Mota et al. (2022), Tobias et al. (2022), and Jetz et al. (2014) — load.data","text":"Load data adapted Mota et al. (2022), Tobias et al. (2022), Jetz et al. (2014)","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/load.data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load data adapted from Mota et al. (2022), Tobias et al. (2022), and Jetz et al. (2014) — load.data","text":"","code":"load.data()"},{"path":"https://flaviomoc.github.io/divraster/reference/load.data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load data adapted from Mota et al. (2022), Tobias et al. (2022), and Jetz et al. (2014) — load.data","text":"list binary maps species reference future climate scenarios, species traits, rooted phylogenetic tree species. species names across objects must match!","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/load.data.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Load data adapted from Mota et al. (2022), Tobias et al. (2022), and Jetz et al. (2014) — load.data","text":"Mota, F. M. M. et al. 2022. Climate change expected restructure forest frugivorous bird communities biodiversity hot-point within Atlantic Forest. - Diversity Distributions 28: 2886–2897. Tobias, J. . et al. 2022. AVONET: morphological, ecological geographical data birds. - Ecology Letters 25: 581–597. Jetz, W. et al. 2014. Global Distribution Conservation Evolutionary Distinctness Birds. - Current Biology 24: 919–930.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/load.data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Load data adapted from Mota et al. (2022), Tobias et al. (2022), and Jetz et al. (2014) — load.data","text":"","code":"data <- load.data() data #> $ref #> class : SpatRaster #> dimensions : 67, 25, 68 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41.875, -38.75, -21.375, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source : ref_frugivor.tif #> names : Amazo~inosa, Amazo~rytha, Amazo~nacea, Arrem~uatus, Arrem~urnus, Ptero~lloni, ... #> min values : 0, 0, 0, 0, 1, 0, ... #> max values : 1, 1, 1, 1, 1, 1, ... #> #> $fut #> class : SpatRaster #> dimensions : 67, 25, 68 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : -41.875, -38.75, -21.375, -13 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source : fut_frugivor.tif #> names : Amazo~inosa, Amazo~rytha, Amazo~nacea, Arrem~uatus, Arrem~urnus, Ptero~lloni, ... #> min values : 0, 1, 0, 0, 0, 0, ... #> max values : 1, 1, 1, 1, 1, 1, ... #> #> $traits #> Beak.Length_Culmen Beak.Length_Nares Beak.Width #> Amazona_farinosa 42.3 35.6 20.5 #> Amazona_rhodocorytha 37.6 29.4 18.0 #> Amazona_vinacea 33.5 24.6 16.2 #> Arremon_semitorquatus 15.2 9.4 5.7 #> Arremon_taciturnus 14.6 10.0 5.5 #> Pteroglossus_bailloni 70.2 62.2 20.9 #> Cacicus_cela 33.7 24.0 7.9 #> Carpornis_cucullata 18.3 9.2 5.6 #> Caryothraustes_canadensis 17.4 11.8 8.5 #> Chiroxiphia_caudata 13.8 7.3 4.0 #> Chiroxiphia_pareola 11.4 6.5 4.4 #> Chlorophanes_spiza 15.9 11.4 4.5 #> Patagioenas_speciosa 24.5 12.3 4.8 #> Cotinga_maculata 17.4 9.8 5.9 #> Crax_blumenbachii 45.7 23.4 15.3 #> Crypturellus_soui 24.2 8.0 4.2 #> Crypturellus_variegatus 33.6 13.7 5.3 #> Cyanerpes_cyaneus 19.4 12.8 3.8 #> Elaenia_mesoleuca 12.5 7.1 4.1 #> Euphonia_cyanocephala 9.4 5.4 4.1 #> Euphonia_pectoralis 10.9 7.6 4.7 #> Euphonia_xanthogaster 10.7 6.0 4.8 #> Ilicura_militaris 9.4 5.2 2.8 #> Iodopleura_pipra 8.2 4.5 3.6 #> Laniisoma_elegans 20.3 13.2 5.4 #> Legatus_leucophaius 13.0 8.3 6.3 #> Lipaugus_lanioides 26.1 16.0 8.0 #> Lipaugus_vociferans 26.9 13.8 8.0 #> Machaeropterus_regulus 9.9 5.6 3.3 #> Manacus_manacus 11.5 6.8 4.4 #> Melanerpes_flavifrons 27.2 20.9 6.5 #> Mionectes_oleagineus 11.8 8.2 4.2 #> Mionectes_rufiventris 14.1 9.3 4.3 #> Neopelma_aurifrons 12.7 8.3 4.2 #> Odontophorus_capueira 21.3 11.7 7.6 #> Oxyruncus_cristatus 17.9 11.3 5.5 #> Pachyramphus_marginatus 14.7 10.1 6.9 #> Patagioenas_plumbea 23.1 12.9 4.3 #> Penelope_obscura 34.5 16.6 10.2 #> Penelope_superciliaris 34.8 16.3 9.9 #> Phibalura_flavirostris 13.8 9.5 6.5 #> Phyllomyias_burmeisteri 11.4 6.9 3.5 #> Pionopsitta_pileata 25.3 19.0 11.6 #> Pipra_pipra 12.0 6.6 4.4 #> Pipra_rubrocapilla 10.4 6.0 3.8 #> Pipraeidea_melanonota 12.6 7.4 4.8 #> Turdus_flavipes 21.7 11.0 5.0 #> Procnias_nudicollis 27.0 10.9 7.1 #> Psarocolius_decumanus 51.8 34.1 11.2 #> Pteroglossus_aracari 99.1 93.4 27.7 #> Pyroderus_scutatus 42.5 26.3 13.8 #> Pyrrhura_cruentata 22.8 19.1 12.1 #> Ramphastos_dicolorus 104.3 100.0 30.1 #> Schiffornis_turdina 17.0 9.7 4.9 #> Schiffornis_virescens 13.9 8.6 3.8 #> Selenidera_maculirostris 55.0 47.8 19.3 #> Stephanophorus_diadematus 14.1 8.7 6.4 #> Tachyphonus_cristatus 15.9 11.1 5.6 #> Tangara_cyanocephala 10.9 8.0 4.0 #> Tangara_cyanoventris 12.0 7.7 4.0 #> Tangara_desmaresti 12.6 7.9 4.3 #> Tangara_seledon 11.8 7.7 5.1 #> Thraupis_cyanoptera 17.9 10.0 6.4 #> Tinamus_solitarius 37.9 11.4 5.8 #> Touit_melanonotus 18.9 14.3 8.8 #> Trogon_viridis 25.2 15.0 10.1 #> Turdus_fumigatus 24.2 13.8 5.0 #> Xipholena_atropurpurea 18.3 10.2 5.2 #> Beak.Depth Tarsus.Length Wing.Length Kipps.Distance #> Amazona_farinosa 35.4 26.6 244.9 68.7 #> Amazona_rhodocorytha 31.0 22.3 210.0 62.6 #> Amazona_vinacea 26.7 21.5 214.2 67.3 #> Arremon_semitorquatus 7.7 25.2 70.0 4.2 #> Arremon_taciturnus 7.3 23.8 72.0 7.9 #> Pteroglossus_bailloni 26.0 33.0 129.0 18.9 #> Cacicus_cela 11.8 29.8 145.3 39.5 #> Carpornis_cucullata 6.8 23.3 113.6 22.4 #> Caryothraustes_canadensis 11.2 20.5 90.8 15.8 #> Chiroxiphia_caudata 4.6 19.8 75.9 13.4 #> Chiroxiphia_pareola 4.9 17.8 69.4 8.2 #> Chlorophanes_spiza 4.6 18.9 68.3 16.7 #> Patagioenas_speciosa 6.0 23.7 184.7 65.5 #> Cotinga_maculata 5.3 22.5 114.2 29.7 #> Crax_blumenbachii 23.3 110.0 384.0 33.9 #> Crypturellus_soui 3.9 36.4 127.5 32.9 #> Crypturellus_variegatus 5.0 41.1 155.4 50.1 #> Cyanerpes_cyaneus 3.6 13.7 60.9 15.7 #> Elaenia_mesoleuca 3.8 16.0 80.0 17.7 #> Euphonia_cyanocephala 4.1 14.5 64.2 18.6 #> Euphonia_pectoralis 5.3 15.9 61.1 13.6 #> Euphonia_xanthogaster 4.8 16.4 61.4 13.7 #> Ilicura_militaris 3.1 17.8 61.2 13.8 #> Iodopleura_pipra 3.5 13.9 56.6 13.7 #> Laniisoma_elegans 6.1 22.5 103.5 26.9 #> Legatus_leucophaius 4.6 15.1 78.5 20.1 #> Lipaugus_lanioides 8.3 24.6 133.8 22.8 #> Lipaugus_vociferans 7.3 21.4 123.1 20.9 #> Machaeropterus_regulus 3.1 13.9 52.9 12.5 #> Manacus_manacus 4.2 20.9 52.2 8.4 #> Melanerpes_flavifrons 6.7 18.8 117.0 31.2 #> Mionectes_oleagineus 3.4 16.0 60.5 10.5 #> Mionectes_rufiventris 3.8 16.2 68.4 9.2 #> Neopelma_aurifrons 4.3 15.7 71.0 15.1 #> Odontophorus_capueira 13.1 37.8 146.8 15.2 #> Oxyruncus_cristatus 5.6 20.7 92.2 24.0 #> Pachyramphus_marginatus 5.2 18.5 67.7 15.0 #> Patagioenas_plumbea 5.1 23.1 177.8 61.9 #> Penelope_obscura 12.0 70.6 309.4 14.6 #> Penelope_superciliaris 11.0 71.8 248.6 34.1 #> Phibalura_flavirostris 6.0 19.3 99.0 32.9 #> Phyllomyias_burmeisteri 3.4 15.3 63.9 14.9 #> Pionopsitta_pileata 17.5 14.5 140.0 49.8 #> Pipra_pipra 4.1 14.1 62.0 10.6 #> Pipra_rubrocapilla 4.1 12.6 61.2 11.5 #> Pipraeidea_melanonota 5.0 17.9 80.1 21.4 #> Turdus_flavipes 5.7 25.7 110.6 28.6 #> Procnias_nudicollis 5.9 29.4 148.4 35.1 #> Psarocolius_decumanus 17.8 46.5 198.6 49.1 #> Pteroglossus_aracari 32.6 34.5 143.1 22.4 #> Pyroderus_scutatus 15.5 38.0 231.0 41.0 #> Pyrrhura_cruentata 22.7 15.7 147.4 59.5 #> Ramphastos_dicolorus 33.4 46.1 191.8 26.9 #> Schiffornis_turdina 6.0 22.1 92.1 14.1 #> Schiffornis_virescens 4.5 21.4 80.2 12.5 #> Selenidera_maculirostris 22.4 31.8 130.7 19.4 #> Stephanophorus_diadematus 7.5 23.2 98.2 20.4 #> Tachyphonus_cristatus 6.9 18.2 76.2 14.2 #> Tangara_cyanocephala 4.9 16.4 61.5 13.6 #> Tangara_cyanoventris 4.7 18.1 67.0 12.7 #> Tangara_desmaresti 4.7 18.9 71.0 14.2 #> Tangara_seledon 5.2 15.9 64.2 14.4 #> Thraupis_cyanoptera 7.8 20.8 96.1 24.0 #> Tinamus_solitarius 6.0 73.1 261.5 35.1 #> Touit_melanonotus 13.3 10.2 107.5 45.1 #> Trogon_viridis 11.7 14.2 146.1 50.6 #> Turdus_fumigatus 6.7 31.0 113.5 23.9 #> Xipholena_atropurpurea 5.4 20.3 110.2 24.0 #> Secondary1 Hand.Wing.Index Tail.Length Mass #> Amazona_farinosa 177.2 27.9 135.0 625.99 #> Amazona_rhodocorytha 146.7 29.9 115.0 474.34 #> Amazona_vinacea 145.0 31.6 121.8 254.00 #> Arremon_semitorquatus 65.8 6.1 70.5 25.00 #> Arremon_taciturnus 64.5 10.9 61.3 24.80 #> Pteroglossus_bailloni 110.4 14.5 169.0 146.00 #> Cacicus_cela 104.1 27.2 97.8 85.45 #> Carpornis_cucullata 90.9 19.8 101.8 74.19 #> Caryothraustes_canadensis 72.5 17.8 71.2 34.50 #> Chiroxiphia_caudata 63.0 17.6 57.8 25.60 #> Chiroxiphia_pareola 59.1 12.2 34.4 16.84 #> Chlorophanes_spiza 50.9 24.7 48.2 19.00 #> Patagioenas_speciosa 114.0 36.5 98.3 258.47 #> Cotinga_maculata 84.5 26.0 71.5 65.00 #> Crax_blumenbachii 307.1 9.7 333.8 3500.00 #> Crypturellus_soui 96.4 25.4 47.9 216.16 #> Crypturellus_variegatus 105.5 32.2 44.6 378.00 #> Cyanerpes_cyaneus 44.5 26.0 34.8 14.00 #> Elaenia_mesoleuca 62.2 22.1 66.4 17.60 #> Euphonia_cyanocephala 45.6 28.9 37.8 14.00 #> Euphonia_pectoralis 48.8 21.8 33.9 14.40 #> Euphonia_xanthogaster 47.7 22.4 36.0 13.00 #> Ilicura_militaris 46.9 22.6 50.8 12.70 #> Iodopleura_pipra 43.0 24.1 32.0 10.03 #> Laniisoma_elegans 76.6 26.0 61.0 47.40 #> Legatus_leucophaius 59.2 25.5 55.2 22.20 #> Lipaugus_lanioides 111.0 17.0 116.0 94.80 #> Lipaugus_vociferans 102.1 16.9 110.2 75.42 #> Machaeropterus_regulus 40.2 23.7 22.6 9.34 #> Manacus_manacus 44.5 15.9 32.8 16.70 #> Melanerpes_flavifrons 85.8 26.6 69.5 57.78 #> Mionectes_oleagineus 50.8 17.1 48.2 11.17 #> Mionectes_rufiventris 60.0 13.3 55.0 13.30 #> Neopelma_aurifrons 55.9 21.3 50.0 14.00 #> Odontophorus_capueira 130.1 10.5 75.0 425.40 #> Oxyruncus_cristatus 67.2 26.3 64.3 42.00 #> Pachyramphus_marginatus 53.7 21.8 50.4 18.40 #> Patagioenas_plumbea 115.7 34.9 141.6 178.77 #> Penelope_obscura 286.3 4.9 313.5 1770.00 #> Penelope_superciliaris 217.8 13.5 286.8 894.99 #> Phibalura_flavirostris 66.2 33.2 104.8 46.50 #> Phyllomyias_burmeisteri 48.8 23.3 48.1 11.10 #> Pionopsitta_pileata 89.8 35.8 70.2 119.00 #> Pipra_pipra 51.0 17.3 26.6 11.11 #> Pipra_rubrocapilla 47.0 19.7 31.4 12.00 #> Pipraeidea_melanonota 59.3 26.5 57.8 21.00 #> Turdus_flavipes 81.9 25.9 84.1 65.14 #> Procnias_nudicollis 111.6 24.0 82.6 172.04 #> Psarocolius_decumanus 146.2 24.8 170.3 206.30 #> Pteroglossus_aracari 120.8 15.6 147.0 250.16 #> Pyroderus_scutatus 183.8 18.2 152.2 357.00 #> Pyrrhura_cruentata 88.5 40.2 130.6 75.90 #> Ramphastos_dicolorus 164.9 14.0 181.2 331.00 #> Schiffornis_turdina 74.5 15.9 67.7 31.70 #> Schiffornis_virescens 67.0 15.7 64.2 25.60 #> Selenidera_maculirostris 111.2 14.8 111.3 164.00 #> Stephanophorus_diadematus 77.4 20.8 81.2 35.40 #> Tachyphonus_cristatus 60.0 19.2 70.4 18.80 #> Tangara_cyanocephala 50.4 21.3 44.7 18.00 #> Tangara_cyanoventris 54.0 19.1 48.4 16.50 #> Tangara_desmaresti 56.8 20.0 52.8 20.40 #> Tangara_seledon 49.9 22.4 47.5 18.70 #> Thraupis_cyanoptera 72.1 25.0 66.5 43.30 #> Tinamus_solitarius 223.7 13.7 156.2 1386.41 #> Touit_melanonotus 62.4 42.0 41.8 66.51 #> Trogon_viridis 95.6 34.6 158.4 89.69 #> Turdus_fumigatus 89.6 21.1 90.8 75.70 #> Xipholena_atropurpurea 86.0 21.8 65.1 61.32 #> Habitat Trophic.Niche Range.Size #> Amazona_farinosa Forest Omnivore 6793599.57 #> Amazona_rhodocorytha Forest Frugivore 2672.56 #> Amazona_vinacea Forest Omnivore 105992.85 #> Arremon_semitorquatus Forest Omnivore 215137.21 #> Arremon_taciturnus Forest Omnivore 6755484.62 #> Pteroglossus_bailloni Forest Frugivore 657171.58 #> Cacicus_cela Forest Omnivore 8569297.31 #> Carpornis_cucullata Forest Frugivore 251722.97 #> Caryothraustes_canadensis Shrubland Omnivore 2650244.99 #> Chiroxiphia_caudata Forest Omnivore 1459549.86 #> Chiroxiphia_pareola Forest Frugivore 5040298.89 #> Chlorophanes_spiza Forest Frugivore 7921066.07 #> Patagioenas_speciosa Forest Frugivore 7713359.51 #> Cotinga_maculata Forest Frugivore 30327.88 #> Crax_blumenbachii Forest Frugivore 1149.72 #> Crypturellus_soui Forest Omnivore 11151222.76 #> Crypturellus_variegatus Forest Omnivore 5436849.92 #> Cyanerpes_cyaneus Forest Omnivore 8340306.15 #> Elaenia_mesoleuca Forest Invertivore 2216525.02 #> Euphonia_cyanocephala Forest Frugivore 2711347.81 #> Euphonia_pectoralis Forest Frugivore 1361244.46 #> Euphonia_xanthogaster Forest Frugivore 3715684.50 #> Ilicura_militaris Forest Frugivore 840759.23 #> Iodopleura_pipra Forest Frugivore 130157.72 #> Laniisoma_elegans Forest Omnivore 172527.96 #> Legatus_leucophaius Forest Frugivore 11371457.31 #> Lipaugus_lanioides Forest Frugivore 201153.30 #> Lipaugus_vociferans Forest Frugivore 7063057.92 #> Machaeropterus_regulus Forest Frugivore 125343.35 #> Manacus_manacus Forest Frugivore 7524946.19 #> Melanerpes_flavifrons Forest Omnivore 1557771.44 #> Mionectes_oleagineus Forest Frugivore 8947569.12 #> Mionectes_rufiventris Forest Invertivore 1057487.40 #> Neopelma_aurifrons Forest Frugivore 5071.66 #> Odontophorus_capueira Forest Omnivore 1724256.70 #> Oxyruncus_cristatus Forest Frugivore 1872045.95 #> Pachyramphus_marginatus Forest Omnivore 6344951.42 #> Patagioenas_plumbea Forest Frugivore 6564806.47 #> Penelope_obscura Forest Frugivore 1012773.03 #> Penelope_superciliaris Forest Frugivore 5614395.75 #> Phibalura_flavirostris Forest Frugivore 1084489.75 #> Phyllomyias_burmeisteri Forest Invertivore 971005.03 #> Pionopsitta_pileata Forest Omnivore 728878.23 #> Pipra_pipra Forest Frugivore 4953783.66 #> Pipra_rubrocapilla Forest Frugivore 3391760.24 #> Pipraeidea_melanonota Forest Omnivore 2111740.74 #> Turdus_flavipes Forest Frugivore 940921.44 #> Procnias_nudicollis Forest Frugivore 1467436.56 #> Psarocolius_decumanus Forest Omnivore 10475235.80 #> Pteroglossus_aracari Forest Frugivore 3319977.82 #> Pyroderus_scutatus Forest Frugivore 2116677.80 #> Pyrrhura_cruentata Forest Omnivore 10274.69 #> Ramphastos_dicolorus Forest Frugivore 1394133.06 #> Schiffornis_turdina Forest Omnivore 5587673.67 #> Schiffornis_virescens Forest Omnivore 1662556.58 #> Selenidera_maculirostris Forest Frugivore 930797.49 #> Stephanophorus_diadematus Forest Frugivore 1088996.67 #> Tachyphonus_cristatus Forest Omnivore 6338485.76 #> Tangara_cyanocephala Forest Frugivore 444844.92 #> Tangara_cyanoventris Forest Frugivore 475625.93 #> Tangara_desmaresti Forest Frugivore 260465.02 #> Tangara_seledon Forest Frugivore 672563.84 #> Thraupis_cyanoptera Forest Frugivore 224069.57 #> Tinamus_solitarius Forest Omnivore 1069608.94 #> Touit_melanonotus Forest Frugivore 14296.54 #> Trogon_viridis Forest Frugivore 7907953.76 #> Turdus_fumigatus Forest Invertivore 4070825.39 #> Xipholena_atropurpurea Forest Frugivore 1836.59 #> #> $tree #> #> Phylogenetic tree with 68 tips and 67 internal nodes. #> #> Tip labels: #> Patagioenas_plumbea, Patagioenas_speciosa, Pyrrhura_cruentata, Pionopsitta_pileata, Amazona_rhodocorytha, Amazona_vinacea, ... #> #> Rooted; includes branch lengths. #>"},{"path":"https://flaviomoc.github.io/divraster/reference/range.list.html","id":null,"dir":"Reference","previous_headings":"","what":"Area calculation — range.list","title":"Area calculation — range.list","text":"Area calculation","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/range.list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Area calculation — range.list","text":"","code":"# S3 method for list range(x, unit = \"km\", r2 = NULL, r3 = NULL, filename = \"\")"},{"path":"https://flaviomoc.github.io/divraster/reference/range.list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Area calculation — range.list","text":"x list containing multiple SpatRaster presence-absence data (0 1) set species. unit Character. Default \"km\", \"m\" \"ha\" also available. r2 SpatRaster extent \"x\". r3 SpatRaster extent \"x\". filename Character. Save results name provided.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/range.list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Area calculation — range.list","text":"data.frame area values chosen unit.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/range.rast.html","id":null,"dir":"Reference","previous_headings":"","what":"Area calculation — range.rast","title":"Area calculation — range.rast","text":"Area calculation","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/range.rast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Area calculation — range.rast","text":"","code":"# S3 method for rast range(x, unit = \"km\", ...)"},{"path":"https://flaviomoc.github.io/divraster/reference/range.rast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Area calculation — range.rast","text":"x SpatRaster presence-absence data (0 1) given species. unit Character. Default \"km\", \"m\" \"ha\" also available. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/range.rast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Area calculation — range.rast","text":"vector area chosen unit.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.html","id":null,"dir":"Reference","previous_headings":"","what":"Alpha calculation for raster — spat.alpha","title":"Alpha calculation for raster — spat.alpha","text":"Calculates alpha diversity taxonomic (TD), functional (FD), phylogenetic (PD) dimensions. Adapted alpha","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Alpha calculation for raster — spat.alpha","text":"","code":"spat.alpha(bin, tree, cores = 1, filename = \"\", ...)"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Alpha calculation for raster — spat.alpha","text":"bin SpatRaster presence-absence data (0 1) set species. tree can 'data.frame' species traits 'phylo' rooted phylogenetic tree. Species names 'tree' 'bin' must match! cores positive integer. cores > 1, 'parallel' package cluster many cores created used. filename Character. Save results name provided. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Alpha calculation for raster — spat.alpha","text":"SpatRaster alpha result.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Alpha calculation for raster — spat.alpha","text":"Alpha calculations use tree-based approach TD, FD, PD (Cardoso et al. 2014). FD calculation, species traits matrix transformed distance matrix clustered create regional dendrogram (.e. dendrogram species raster stack), total branch length calculated. computing FD community (.e. raster cell), regional dendrogram subsetted create local dendrogram includes species present local community. branch lengths connecting species summed represent functional relationships locally present species (Petchey Gaston, 2002, 2006). Similarly, PD, cumulative branch lengths connecting species within community indicate shared phylogenetic relationships (Faith, 1992). Alpha TD can also visualized using tree diagram, species directly connected root edge unit length, reflecting number different taxa community (.e. species richness) since taxa level (Cardoso et al. 2014).","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Alpha calculation for raster — spat.alpha","text":"Cardoso, P. et al. 2014. Partitioning taxon, phylogenetic functional beta diversity replacement richness difference components. - Journal Biogeography 41: 749–761. Faith, D. P. 1992. Conservation evaluation phylogenetic diversity. - Biological Conservation 61: 1–10. Petchey, O. L. Gaston, K. J. 2002. Functional diversity (FD), species richness community composition. - Ecology Letters 5: 402–411. Rodrigues, . S. L. Gaston, K. J. 2002. Maximising phylogenetic diversity selection networks conservation areas. - Biological Conservation 105: 103–111.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Alpha calculation for raster — spat.alpha","text":"","code":"# \\donttest{ library(terra) bin1 <- terra::rast(system.file(\"extdata\", \"ref.tif\", package = \"divraster\")) traits <- read.csv(system.file(\"extdata\", \"traits.csv\", package = \"divraster\"), row.names = 1) tree <- ape::read.tree(system.file(\"extdata\", \"tree.tre\", package = \"divraster\")) spat.alpha(bin1) #> class : SpatRaster #> dimensions : 8, 8, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Alpha_TD #> min value : 2 #> max value : 8 spat.alpha(bin1, traits) #> class : SpatRaster #> dimensions : 8, 8, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Alpha_FD #> min value : 0.3492543 #> max value : 1.2493508 spat.alpha(bin1, tree) #> class : SpatRaster #> dimensions : 8, 8, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Alpha_PD #> min value : 3.101099 #> max value : 9.761420 # }"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.vec.html","id":null,"dir":"Reference","previous_headings":"","what":"Alpha calculation for vector — spat.alpha.vec","title":"Alpha calculation for vector — spat.alpha.vec","text":"Alpha calculation vector","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.vec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Alpha calculation for vector — spat.alpha.vec","text":"","code":"spat.alpha.vec(x, tree, resu, ...)"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.vec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Alpha calculation for vector — spat.alpha.vec","text":"x numeric vector presence-absence data (0 1) set species. tree can data frame species traits phylogenetic tree. resu Numeric. vector store results. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha.vec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Alpha calculation for vector — spat.alpha.vec","text":"vector alpha result.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha2.html","id":null,"dir":"Reference","previous_headings":"","what":"Alternative method to calculate alpha taxonomic diversity — spat.alpha2","title":"Alternative method to calculate alpha taxonomic diversity — spat.alpha2","text":"Alternative method calculate alpha taxonomic diversity","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Alternative method to calculate alpha taxonomic diversity — spat.alpha2","text":"","code":"spat.alpha2(bin, cores = 1, filename = \"\")"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Alternative method to calculate alpha taxonomic diversity — spat.alpha2","text":"bin SpatRaster presence-absence data (0 1) set species. cores positive integer. cores > 1, 'parallel' package cluster many cores created used. filename Character. Save results name provided.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Alternative method to calculate alpha taxonomic diversity — spat.alpha2","text":"SpatRaster object richness.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.alpha2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Alternative method to calculate alpha taxonomic diversity — spat.alpha2","text":"","code":"# \\donttest{ library(terra) bin1 <- terra::rast(system.file(\"extdata\", \"ref.tif\", package = \"divraster\")) spat.alpha2(bin1) #> class : SpatRaster #> dimensions : 8, 8, 1 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> name : Richness #> min value : 2 #> max value : 8 # }"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial beta diversity for raster — spat.beta","title":"Spatial beta diversity for raster — spat.beta","text":"Calculates spatial beta diversity taxonomic (TD), functional (FD), phylogenetic (PD) dimensions. Adapted beta.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial beta diversity for raster — spat.beta","text":"","code":"spat.beta( x, tree, filename = \"\", global = FALSE, fm = NULL, d = mean(terra::res(terra::rast(x))) * 2, type = \"circle\", na.policy = \"omit\", ... )"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial beta diversity for raster — spat.beta","text":"x SpatRaster presence-absence data (0 1) set species. tree can 'data.frame' species traits 'phylo' rooted phylogenetic tree. Species names 'tree' 'x' must match! filename Character. Save results name provided. global Logical. Mean pairwise comparisons focal cell neighbors (default) mean pairwise comparisons. fm Numeric. Focal matrix (\"moving window\"). d Window radius compute beta diversity. type Character. Window format. Default = \"circle\". na.policy Character. Default = \"omit\". See ?terra::focal3D details. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial beta diversity for raster — spat.beta","text":"SpatRaster beta results (total, replacement, richness difference, ratio).","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Spatial beta diversity for raster — spat.beta","text":"TD beta diversity partitioning framework used developed Podani Schmera (2011) Carvalho et al. (2012) expanded PD FD Cardoso et al. (2014).","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Spatial beta diversity for raster — spat.beta","text":"Cardoso, P. et al. 2014. Partitioning taxon, phylogenetic functional beta diversity replacement richness difference components. - Journal Biogeography 41: 749–761. Carvalho, J. C. et al. 2012. Determining relative roles species replacement species richness differences generating beta-diversity patterns. - Global Ecology Biogeography 21: 760–771. Podani, J. Schmera, D. 2011. new conceptual methodological framework exploring explaining pattern presence - absence data. - Oikos 120: 1625–1638. Hidasi-Neto, J. et al. 2019. Climate change drive mammal species loss biotic homogenization Cerrado Biodiversity Hotspot. - Perspectives Ecology Conservation 17: 57–63.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatial beta diversity for raster — spat.beta","text":"","code":"# \\donttest{ library(terra) bin1 <- terra::rast(system.file(\"extdata\", \"ref.tif\", package = \"divraster\")) traits <- read.csv(system.file(\"extdata\", \"traits.csv\", package = \"divraster\"), row.names = 1) rownames(traits) <- names(bin1) tree <- ape::read.tree(system.file(\"extdata\", \"tree.tre\", package = \"divraster\")) spat.beta(bin1) #> class : SpatRaster #> dimensions : 8, 8, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_TD, Brepl_TD, Brich_TD, Bratio_TD #> min values : 0.5515512, 0.1898990, 0.0952381, 0.3174335 #> max values : 0.8694805, 0.7207341, 0.5067460, 0.8529412 spat.beta(bin1, traits) #> class : SpatRaster #> dimensions : 8, 8, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_FD, Brepl_FD, Brich_FD, Bratio_FD #> min values : 0.3310466, 0.06122664, 0.1271726, 0.1285775 #> max values : 0.6641360, 0.41959062, 0.5680299, 0.7351086 spat.beta(bin1, tree) #> class : SpatRaster #> dimensions : 8, 8, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_PD, Brepl_PD, Brich_PD, Bratio_PD #> min values : 0.3250871, 0.04931651, 0.06867094, 0.1265763 #> max values : 0.7072649, 0.52737261, 0.46375695, 0.8271077 # }"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.vec.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial beta diversity for vector — spat.beta.vec","title":"Spatial beta diversity for vector — spat.beta.vec","text":"Spatial beta diversity vector","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.vec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial beta diversity for vector — spat.beta.vec","text":"","code":"spat.beta.vec(x, tree, global = FALSE, spp, nspp, ...)"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.vec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial beta diversity for vector — spat.beta.vec","text":"x numeric vector presence-absence data (0 1) set species. tree can data frame species traits phylogenetic tree. global Logical. Mean pairwise comparisons focal cell neighbors (default) mean pairwise comparisons. spp Character. Species names. nspp Numeric. Number species. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.beta.vec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial beta diversity for vector — spat.beta.vec","text":"vector beta results (total, replacement, richness difference, ratio).","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.rand.html","id":null,"dir":"Reference","previous_headings":"","what":"Standardized Effect Size (SES) for raster — spat.rand","title":"Standardized Effect Size (SES) for raster — spat.rand","text":"Calculates standardized effect size functional phylogenetic alpha diversity. See bootspat_str bootspat_naive","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.rand.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Standardized Effect Size (SES) for raster — spat.rand","text":"","code":"spat.rand( x, tree, aleats, random = c(\"site\", \"species\", \"both\", \"spat\"), cores = 1, filename = \"\", ... )"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.rand.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standardized Effect Size (SES) for raster — spat.rand","text":"x SpatRaster. SpatRaster containing presence-absence data (0 1) set species. tree can 'data.frame' species traits 'phylo' rooted phylogenetic tree. Species names 'tree' 'x' must match! aleats positive integer. positive integer indicating many times calculation repeated. random character. character indicating type randomization. currently available randomization methods \"spat\", \"site\", \"species\" \"\" (site species). cores positive integer. cores > 1, 'parallel' package cluster many cores created used. filename character. Output filename. ... additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.rand.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Standardized Effect Size (SES) for raster — spat.rand","text":"SpatRaster Mean, SD, Observed, SES.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.rand.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Standardized Effect Size (SES) for raster — spat.rand","text":"","code":"# \\donttest{ x <- terra::rast(system.file(\"extdata\", \"ref.tif\", package = \"divraster\")) traits <- read.csv(system.file(\"extdata\", \"traits.csv\", package = \"divraster\"), row.names = 1) tree <- ape::read.tree(system.file(\"extdata\", \"tree.tre\", package = \"divraster\")) spat.rand(x, tree, 3, \"site\") #> class : SpatRaster #> dimensions : 8, 8, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Mean_PD, SD_PD, Observed_PD, SES_PD #> min values : 4.217869, 0.05263325, 3.359948, -9.313514 #> max values : 9.524013, 1.26248756, 10.571964, 10.454383 spat.rand(x, traits, 3, \"site\") #> class : SpatRaster #> dimensions : 8, 8, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Mean_FD, SD_FD, Observed_FD, SES_FD #> min values : 0.3846142, 0.02100142, 0.3492543, -3.832472 #> max values : 1.2542336, 0.25886931, 1.2493508, 8.094669 # }"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.html","id":null,"dir":"Reference","previous_headings":"","what":"Average trait calculation for raster — spat.trait","title":"Average trait calculation for raster — spat.trait","text":"Compute average trait.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Average trait calculation for raster — spat.trait","text":"","code":"spat.trait(x, trait, cores = 1, filename = \"\", ...)"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Average trait calculation for raster — spat.trait","text":"x SpatRaster presence-absence data (0 1) set species. trait 'data.frame' species traits. Rownames must species names match 'x'! cores positive integer. cores > 1, 'parallel' package cluster many cores created used. filename Character. Save results name provided. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Average trait calculation for raster — spat.trait","text":"SpatRaster average traits.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Average trait calculation for raster — spat.trait","text":"","code":"# \\donttest{ library(terra) bin1 <- terra::rast(system.file(\"extdata\", \"ref.tif\", package = \"divraster\")) traits <- read.csv(system.file(\"extdata\", \"traits.csv\", package = \"divraster\"), row.names = 1) spat.trait(bin1, traits) #> class : SpatRaster #> dimensions : 8, 8, 2 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : beak.size, wing.length #> min values : 1.312311, 30.54550 #> max values : 3.310816, 45.84854 # }"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.vec.html","id":null,"dir":"Reference","previous_headings":"","what":"Average trait calculation for vector — spat.trait.vec","title":"Average trait calculation for vector — spat.trait.vec","text":"Average trait calculation vector","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.vec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Average trait calculation for vector — spat.trait.vec","text":"","code":"spat.trait.vec(x, col_trait, ...)"},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.vec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Average trait calculation for vector — spat.trait.vec","text":"x numeric vector presence-absence data (0 1) set species. col_trait numeric vector trait numbers. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/spat.trait.vec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Average trait calculation for vector — spat.trait.vec","text":"Vector average trait.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/suit.change.html","id":null,"dir":"Reference","previous_headings":"","what":"Species suitability change between climate scenarios — suit.change","title":"Species suitability change between climate scenarios — suit.change","text":"Species suitability change climate scenarios","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/suit.change.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Species suitability change between climate scenarios — suit.change","text":"","code":"suit.change(r1, r2, filename = \"\")"},{"path":"https://flaviomoc.github.io/divraster/reference/suit.change.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Species suitability change between climate scenarios — suit.change","text":"r1 SpatRaster presence-absence data (0 1) set species. r2 SpatRaster presence-absence data (0 1) set species. filename Character. Save results name provided.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/suit.change.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Species suitability change between climate scenarios — suit.change","text":"SpatRaster suitability change (gain, loss, unchanged, unsuitable).","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/suit.change.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Species suitability change between climate scenarios — suit.change","text":"","code":"# \\donttest{ library(terra) r1 <- terra::rast(system.file(\"extdata\", \"ref.tif\", package = \"divraster\")) r2 <- terra::rast(system.file(\"extdata\", \"fut.tif\", package = \"divraster\")) suit.change(r1, r2) #> class : SpatRaster #> dimensions : 8, 8, 10 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> varname : fut #> names : A, B, C, D, E, F, ... #> min values : 1, 1, 1, 1, 1, 1, ... #> max values : 4, 4, 4, 4, 4, 4, ... # }"},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.html","id":null,"dir":"Reference","previous_headings":"","what":"Temporal beta diversity calculation for raster — temp.beta","title":"Temporal beta diversity calculation for raster — temp.beta","text":"Calculates temporal beta diversity taxonomic (TD), functional (FD), phylogenetic (PD) dimensions. Adapted beta","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Temporal beta diversity calculation for raster — temp.beta","text":"","code":"temp.beta(bin1, bin2, tree, filename = \"\", cores = 1, ...)"},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Temporal beta diversity calculation for raster — temp.beta","text":"bin1 SpatRaster presence-absence data (0 1) set species. bin2 SpatRaster presence-absence data (0 1) set species. Species names 'bin2' 'bin1' must match! tree can 'data.frame' species traits 'phylo' rooted phylogenetic tree. Species names 'tree', 'bin1', 'bin2' must match! filename Character. Save results name provided. cores positive integer. cores > 1, 'parallel' package cluster many cores created used. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Temporal beta diversity calculation for raster — temp.beta","text":"SpatRaster beta results (total, replacement, richness difference, ratio).","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Temporal beta diversity calculation for raster — temp.beta","text":"TD beta diversity partitioning framework used developed Podani Schmera (2011) Carvalho et al. (2012) expanded PD FD Cardoso et al. (2014).","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Temporal beta diversity calculation for raster — temp.beta","text":"Cardoso, P. et al. 2014. Partitioning taxon, phylogenetic functional beta diversity replacement richness difference components. - Journal Biogeography 41: 749–761. Carvalho, J. C. et al. 2012. Determining relative roles species replacement species richness differences generating beta-diversity patterns. - Global Ecology Biogeography 21: 760–771. Podani, J. Schmera, D. 2011. new conceptual methodological framework exploring explaining pattern presence - absence data. - Oikos 120: 1625–1638. Hidasi-Neto, J. et al. 2019. Climate change drive mammal species loss biotic homogenization Cerrado Biodiversity Hotspot. - Perspectives Ecology Conservation 17: 57–63.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Temporal beta diversity calculation for raster — temp.beta","text":"","code":"# \\donttest{ library(terra) bin1 <- terra::rast(system.file(\"extdata\", \"ref.tif\", package = \"divraster\")) bin2 <- terra::rast(system.file(\"extdata\", \"fut.tif\", package = \"divraster\")) traits <- read.csv(system.file(\"extdata\", \"traits.csv\", package = \"divraster\"), row.names = 1) tree <- ape::read.tree(system.file(\"extdata\", \"tree.tre\", package = \"divraster\")) temp.beta(bin1, bin2) #> class : SpatRaster #> dimensions : 8, 8, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_TD, Brepl_TD, Brich_TD, Bratio_TD #> min values : 0.2, 0.0000000, 0.0000000, 0 #> max values : 1.0, 0.8888889, 0.7142857, 1 temp.beta(bin1, bin2, traits) #> class : SpatRaster #> dimensions : 8, 8, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_FD, Brepl_FD, Brich_FD, Bratio_FD #> min values : 0.1522544, 0.0000000, 0.003222951, 0.0000000 #> max values : 0.8309776, 0.5852812, 0.830977572, 0.9905423 temp.beta(bin1, bin2, tree) #> class : SpatRaster #> dimensions : 8, 8, 4 (nrow, ncol, nlyr) #> resolution : 0.125, 0.125 (x, y) #> extent : 0, 1, 0, 1 (xmin, xmax, ymin, ymax) #> coord. ref. : lon/lat WGS 84 (EPSG:4326) #> source(s) : memory #> names : Btotal_PD, Brepl_PD, Brich_PD, Bratio_PD #> min values : 0.1525273, 0.0000000, 0.004401637, 0.0000000 #> max values : 0.8223597, 0.7143422, 0.496646645, 0.9937685 # }"},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.vec.html","id":null,"dir":"Reference","previous_headings":"","what":"Temporal beta diversity calculation for vector — temp.beta.vec","title":"Temporal beta diversity calculation for vector — temp.beta.vec","text":"Temporal beta diversity calculation vector","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.vec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Temporal beta diversity calculation for vector — temp.beta.vec","text":"","code":"temp.beta.vec(x, nspp, spp, tree, resu, ...)"},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.vec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Temporal beta diversity calculation for vector — temp.beta.vec","text":"x numeric vector presence-absence data (0 1) set species. nspp Numeric. Number species. spp Character. Species name. tree can data frame species traits phylogenetic tree. resu Numeric. vector store results. ... Additional arguments passed passed calling function.","code":""},{"path":"https://flaviomoc.github.io/divraster/reference/temp.beta.vec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Temporal beta diversity calculation for vector — temp.beta.vec","text":"vector beta results (total, replacement, richness difference, ratio).","code":""},{"path":"https://flaviomoc.github.io/divraster/news/index.html","id":"divraster-104","dir":"Changelog","previous_headings":"","what":"divraster 1.0.4","title":"divraster 1.0.4","text":"CRAN release: 2023-10-10 New function added initial testing #3. Minor changes function documentation. Minor changes function tests. Citation updated.","code":""},{"path":"https://flaviomoc.github.io/divraster/news/index.html","id":"divraster-103","dir":"Changelog","previous_headings":"","what":"divraster 1.0.3","title":"divraster 1.0.3","text":"CRAN release: 2023-08-21 Improvements function descriptions. Improvements vignette (examples description). Minor correction function tests #2. Citation file added.","code":""},{"path":"https://flaviomoc.github.io/divraster/news/index.html","id":"divraster-102","dir":"Changelog","previous_headings":"","what":"divraster 1.0.2","title":"divraster 1.0.2","text":"CRAN release: 2023-06-27 Released 2023-06-27 Initial CRAN submission.","code":""}] diff --git a/sitemap.xml b/sitemap.xml index 62d60bd..0bc160b 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -45,6 +45,9 @@ https://flaviomoc.github.io/divraster/reference/spat.alpha.vec.html + + https://flaviomoc.github.io/divraster/reference/spat.alpha2.html + https://flaviomoc.github.io/divraster/reference/spat.beta.html