From 5e203fda4a65d90293dbdf0e13479dcceb92a806 Mon Sep 17 00:00:00 2001 From: mhesselbarth Date: Fri, 10 Jan 2025 13:48:26 +0100 Subject: [PATCH 1/2] Fix doc links --- DESCRIPTION | 2 +- R/calculate_energy.R | 4 ++-- R/classify_habitats.R | 2 +- R/get_dist_pairs.R | 2 +- R/list_to_randomized.R | 4 ++-- R/pack_randomized.R | 4 ++-- R/plot.rd_mar.R | 2 +- R/plot.rd_pat.R | 2 +- R/plot.rd_ras.R | 2 +- R/plot_energy.R | 2 +- R/print.rd_pat.R | 2 +- R/print.rd_ras.R | 2 +- R/reconstruct_pattern.R | 2 +- R/reconstruct_pattern_marks.R | 2 +- R/reconstruct_pattern_multi.R | 4 ++-- R/results_habitat_association.R | 2 +- R/unpack_randomized.R | 2 +- man/calculate_energy.Rd | 4 ++-- man/classify_habitats.Rd | 2 +- man/get_dist_pairs.Rd | 2 +- man/list_to_randomized.Rd | 4 ++-- man/pack_randomized.Rd | 4 ++-- man/plot.rd_mar.Rd | 2 +- man/plot.rd_pat.Rd | 2 +- man/plot.rd_ras.Rd | 2 +- man/plot_energy.Rd | 2 +- man/print.rd_pat.Rd | 2 +- man/print.rd_ras.Rd | 2 +- man/reconstruct_pattern.Rd | 2 +- man/reconstruct_pattern_marks.Rd | 2 +- man/reconstruct_pattern_multi.Rd | 4 ++-- man/results_habitat_association.Rd | 2 +- man/unpack_randomized.Rd | 2 +- 33 files changed, 41 insertions(+), 41 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 22b9e39c..3c586b85 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -45,7 +45,7 @@ Suggests: rmarkdown, spatstat (>= 2.0-0), testthat (>= 3.0.0) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 VignetteBuilder: knitr Encoding: UTF-8 LazyData: true diff --git a/R/calculate_energy.R b/R/calculate_energy.R index e8756221..285c2484 100644 --- a/R/calculate_energy.R +++ b/R/calculate_energy.R @@ -15,8 +15,8 @@ #' nearest neighbour distance function are used to describe the patterns. #' #' @seealso -#' \code{\link{plot_energy}} \cr -#' \code{\link{reconstruct_pattern}} \cr +#' \code{\link{plot_energy}}, +#' \code{\link{reconstruct_pattern}}, #' \code{\link{fit_point_process}} #' #' @return vector diff --git a/R/classify_habitats.R b/R/classify_habitats.R index 177699fc..9b8d5b42 100644 --- a/R/classify_habitats.R +++ b/R/classify_habitats.R @@ -17,7 +17,7 @@ #' of classes, fixed breaks, etc.). #' #' @seealso -#' \code{\link{classIntervals}} +#' \code{\link[classInt]{classIntervals}} #' #' @return SpatRaster #' diff --git a/R/get_dist_pairs.R b/R/get_dist_pairs.R index 5cd05c7e..b1077061 100644 --- a/R/get_dist_pairs.R +++ b/R/get_dist_pairs.R @@ -9,7 +9,7 @@ #' Returns matrix with point pairs and distances between them. #' #' @seealso -#' \code{\link{pcf.ppp}} +#' \code{\link[spatstat.explore]{pcf.ppp}} #' #' @return matrix #' diff --git a/R/list_to_randomized.R b/R/list_to_randomized.R index b4f0c5ae..25f40e9b 100644 --- a/R/list_to_randomized.R +++ b/R/list_to_randomized.R @@ -13,8 +13,8 @@ #' For more information, please see the "Parallelization" article. #' #' @seealso -#' \code{\link{randomize_raster}} \cr -#' \code{\link{translate_raster}} \cr +#' \code{\link{randomize_raster}}, +#' \code{\link{translate_raster}}, #' \code{\link{reconstruct_pattern}} #' #' @return rd_pat, rd_ras diff --git a/R/pack_randomized.R b/R/pack_randomized.R index e7a80b0f..16c06a9c 100644 --- a/R/pack_randomized.R +++ b/R/pack_randomized.R @@ -9,8 +9,8 @@ #' all raster objects and prepares them for saving first. For further details, see \code{wrap}. #' #' @seealso -#' \code{\link{unpack_randomized}} -#' \code{\link{wrap}} +#' \code{\link{unpack_randomized}}, +#' \code{\link[terra]{wrap}} #' #' @return rd_ras #' diff --git a/R/plot.rd_mar.R b/R/plot.rd_mar.R index a09de0d1..ded48c81 100644 --- a/R/plot.rd_mar.R +++ b/R/plot.rd_mar.R @@ -23,7 +23,7 @@ #' will be plotted. #' #' @seealso -#' \code{\link{reconstruct_pattern}} \cr +#' \code{\link{reconstruct_pattern}}, #' \code{\link{fit_point_process}} #' #' @return void diff --git a/R/plot.rd_pat.R b/R/plot.rd_pat.R index dd4c78fd..7e1b82fe 100644 --- a/R/plot.rd_pat.R +++ b/R/plot.rd_pat.R @@ -23,7 +23,7 @@ #' will be plotted. #' #' @seealso -#' \code{\link{reconstruct_pattern}} \cr +#' \code{\link{reconstruct_pattern}}, #' \code{\link{fit_point_process}} #' #' @return void diff --git a/R/plot.rd_ras.R b/R/plot.rd_ras.R index e5c10341..6a823cef 100644 --- a/R/plot.rd_ras.R +++ b/R/plot.rd_ras.R @@ -16,7 +16,7 @@ #' will be plotted. \code{col, nrow, ncol} are passed to \code{plot}. #' #' @seealso -#' \code{\link{randomize_raster}} \cr +#' \code{\link{randomize_raster}}, #' \code{\link{translate_raster}} #' #' @return void diff --git a/R/plot_energy.R b/R/plot_energy.R index 4906ec91..62f1cbb3 100644 --- a/R/plot_energy.R +++ b/R/plot_energy.R @@ -12,7 +12,7 @@ #' \code{reconstruct_pattern_*} . #' #' @seealso -#' \code{\link{reconstruct_pattern}} \cr +#' \code{\link{reconstruct_pattern}}, #' \code{\link{fit_point_process}} #' #' @return void diff --git a/R/print.rd_pat.R b/R/print.rd_pat.R index fc3f58ca..43767f46 100644 --- a/R/print.rd_pat.R +++ b/R/print.rd_pat.R @@ -10,7 +10,7 @@ #' Printing method for random patterns created with \code{reconstruct_pattern_*}. #' #' @seealso -#' \code{\link{reconstruct_pattern}} \cr +#' \code{\link{reconstruct_pattern}}, #' \code{\link{fit_point_process}} #' #' @return void diff --git a/R/print.rd_ras.R b/R/print.rd_ras.R index 42d0866d..0e62e3ce 100644 --- a/R/print.rd_ras.R +++ b/R/print.rd_ras.R @@ -10,7 +10,7 @@ #' \code{\link{translate_raster}}. #' #' @seealso -#' \code{\link{randomize_raster}} \cr +#' \code{\link{randomize_raster}}, #' \code{\link{translate_raster}} #' #' @return void diff --git a/R/reconstruct_pattern.R b/R/reconstruct_pattern.R index a0802e23..0a61b6a4 100644 --- a/R/reconstruct_pattern.R +++ b/R/reconstruct_pattern.R @@ -59,7 +59,7 @@ #' } #' #' @seealso -#' \code{\link{calculate_energy}} \cr +#' \code{\link{calculate_energy}}, #' \code{\link{reconstruct_pattern_marks}} #' #' @return rd_pat diff --git a/R/reconstruct_pattern_marks.R b/R/reconstruct_pattern_marks.R index bc7e1441..7d631b0f 100644 --- a/R/reconstruct_pattern_marks.R +++ b/R/reconstruct_pattern_marks.R @@ -35,7 +35,7 @@ #' the computational time while increasing the "bumpiness" of the summary function. #' #' @seealso -#' \code{\link{fit_point_process}} \cr +#' \code{\link{fit_point_process}}, #' \code{\link{reconstruct_pattern}} #' #' @return rd_mar diff --git a/R/reconstruct_pattern_multi.R b/R/reconstruct_pattern_multi.R index cad9cb08..f618df5c 100644 --- a/R/reconstruct_pattern_multi.R +++ b/R/reconstruct_pattern_multi.R @@ -66,8 +66,8 @@ #' A comprehensive description of the method can be found in Wudel et al. (2023). #' #' @seealso -#' \code{\link{fit_point_process}} \cr -#' \code{\link{reconstruct_pattern}} \cr +#' \code{\link{fit_point_process}}, +#' \code{\link{reconstruct_pattern}}, #' \code{\link{reconstruct_pattern_marks}} #' #' @return rd_multi diff --git a/R/results_habitat_association.R b/R/results_habitat_association.R index deb087b3..38a2ca69 100644 --- a/R/results_habitat_association.R +++ b/R/results_habitat_association.R @@ -26,7 +26,7 @@ #' the breaks will be included as well. #' #' @seealso -#' \code{\link{reconstruct_pattern}} \cr +#' \code{\link{reconstruct_pattern}}, #' \code{\link{fit_point_process}} #' #' @return data.frame diff --git a/R/unpack_randomized.R b/R/unpack_randomized.R index 43b677ac..0d88b829 100644 --- a/R/unpack_randomized.R +++ b/R/unpack_randomized.R @@ -11,7 +11,7 @@ #' #' @seealso #' \code{\link{pack_randomized}} -#' \code{\link{wrap}} +#' \code{\link[terra]{wrap}} #' #' @return rd_ras #' diff --git a/man/calculate_energy.Rd b/man/calculate_energy.Rd index b788f268..5de4deb3 100644 --- a/man/calculate_energy.Rd +++ b/man/calculate_energy.Rd @@ -58,7 +58,7 @@ Wiegand, T., Moloney, K.A., 2014. Handbook of spatial point-pattern analysis in ecology. Chapman and Hall/CRC Press, Boca Raton. ISBN 978-1-4200-8254-8 } \seealso{ -\code{\link{plot_energy}} \cr -\code{\link{reconstruct_pattern}} \cr +\code{\link{plot_energy}}, +\code{\link{reconstruct_pattern}}, \code{\link{fit_point_process}} } diff --git a/man/classify_habitats.Rd b/man/classify_habitats.Rd index 6eecff2b..781048e3 100644 --- a/man/classify_habitats.Rd +++ b/man/classify_habitats.Rd @@ -63,5 +63,5 @@ Wand, M. P., 1995. Data-based choice of histogram binwidth. The American Statistician 51, 59-64. } \seealso{ -\code{\link{classIntervals}} +\code{\link[classInt]{classIntervals}} } diff --git a/man/get_dist_pairs.Rd b/man/get_dist_pairs.Rd index 6c774fb9..e55b27cf 100644 --- a/man/get_dist_pairs.Rd +++ b/man/get_dist_pairs.Rd @@ -21,6 +21,6 @@ Distance between points Returns matrix with point pairs and distances between them. } \seealso{ -\code{\link{pcf.ppp}} +\code{\link[spatstat.explore]{pcf.ppp}} } \keyword{internal} diff --git a/man/list_to_randomized.Rd b/man/list_to_randomized.Rd index 70b4673d..66eeaf01 100644 --- a/man/list_to_randomized.Rd +++ b/man/list_to_randomized.Rd @@ -34,7 +34,7 @@ list_to_randomized(list = fit_list, observed = species_a) } \seealso{ -\code{\link{randomize_raster}} \cr -\code{\link{translate_raster}} \cr +\code{\link{randomize_raster}}, +\code{\link{translate_raster}}, \code{\link{reconstruct_pattern}} } diff --git a/man/pack_randomized.Rd b/man/pack_randomized.Rd index f15d66ad..3f7c9731 100644 --- a/man/pack_randomized.Rd +++ b/man/pack_randomized.Rd @@ -28,6 +28,6 @@ x <- pack_randomized(raster = landscape_random) } \seealso{ -\code{\link{unpack_randomized}} -\code{\link{wrap}} +\code{\link{unpack_randomized}}, +\code{\link[terra]{wrap}} } diff --git a/man/plot.rd_mar.Rd b/man/plot.rd_mar.Rd index 65644290..eba570c2 100644 --- a/man/plot.rd_mar.Rd +++ b/man/plot.rd_mar.Rd @@ -59,6 +59,6 @@ plot(marks_recon) } \seealso{ -\code{\link{reconstruct_pattern}} \cr +\code{\link{reconstruct_pattern}}, \code{\link{fit_point_process}} } diff --git a/man/plot.rd_pat.Rd b/man/plot.rd_pat.Rd index a6528638..7bc81eea 100644 --- a/man/plot.rd_pat.Rd +++ b/man/plot.rd_pat.Rd @@ -59,6 +59,6 @@ plot(pattern_recon) } \seealso{ -\code{\link{reconstruct_pattern}} \cr +\code{\link{reconstruct_pattern}}, \code{\link{fit_point_process}} } diff --git a/man/plot.rd_ras.Rd b/man/plot.rd_ras.Rd index 41c1fe7f..109109ad 100644 --- a/man/plot.rd_ras.Rd +++ b/man/plot.rd_ras.Rd @@ -40,6 +40,6 @@ plot(landscape_random) } \seealso{ -\code{\link{randomize_raster}} \cr +\code{\link{randomize_raster}}, \code{\link{translate_raster}} } diff --git a/man/plot_energy.Rd b/man/plot_energy.Rd index 9ec89773..5dd95ab1 100644 --- a/man/plot_energy.Rd +++ b/man/plot_energy.Rd @@ -36,6 +36,6 @@ plot_energy(marks_recon) } \seealso{ -\code{\link{reconstruct_pattern}} \cr +\code{\link{reconstruct_pattern}}, \code{\link{fit_point_process}} } diff --git a/man/print.rd_pat.Rd b/man/print.rd_pat.Rd index 614ec770..e8fd0d48 100644 --- a/man/print.rd_pat.Rd +++ b/man/print.rd_pat.Rd @@ -34,6 +34,6 @@ print(pattern_recon) } \seealso{ -\code{\link{reconstruct_pattern}} \cr +\code{\link{reconstruct_pattern}}, \code{\link{fit_point_process}} } diff --git a/man/print.rd_ras.Rd b/man/print.rd_ras.Rd index 2bbbef13..bc42f366 100644 --- a/man/print.rd_ras.Rd +++ b/man/print.rd_ras.Rd @@ -31,6 +31,6 @@ print(landscape_random) } \seealso{ -\code{\link{randomize_raster}} \cr +\code{\link{randomize_raster}}, \code{\link{translate_raster}} } diff --git a/man/reconstruct_pattern.Rd b/man/reconstruct_pattern.Rd index 0882402e..56183b7e 100644 --- a/man/reconstruct_pattern.Rd +++ b/man/reconstruct_pattern.Rd @@ -117,6 +117,6 @@ Wiegand, T., Moloney, K.A., 2014. Handbook of spatial point-pattern analysis in ecology. Chapman and Hall/CRC Press, Boca Raton. ISBN 978-1-4200-8254-8 } \seealso{ -\code{\link{calculate_energy}} \cr +\code{\link{calculate_energy}}, \code{\link{reconstruct_pattern_marks}} } diff --git a/man/reconstruct_pattern_marks.Rd b/man/reconstruct_pattern_marks.Rd index dbb23c6b..2feb4256 100644 --- a/man/reconstruct_pattern_marks.Rd +++ b/man/reconstruct_pattern_marks.Rd @@ -94,6 +94,6 @@ Wiegand, T., Moloney, K.A., 2014. Handbook of spatial point-pattern analysis in ecology. Chapman and Hall/CRC Press, Boca Raton. ISBN 978-1-4200-8254-8 } \seealso{ -\code{\link{fit_point_process}} \cr +\code{\link{fit_point_process}}, \code{\link{reconstruct_pattern}} } diff --git a/man/reconstruct_pattern_multi.Rd b/man/reconstruct_pattern_multi.Rd index 28941ac2..ee91be86 100644 --- a/man/reconstruct_pattern_multi.Rd +++ b/man/reconstruct_pattern_multi.Rd @@ -164,7 +164,7 @@ reconstruction of plant ecosystems. Methods in Ecology and Evolution, 14, 2668 https://doi.org/10.1111/2041-210X.14206 } \seealso{ -\code{\link{fit_point_process}} \cr -\code{\link{reconstruct_pattern}} \cr +\code{\link{fit_point_process}}, +\code{\link{reconstruct_pattern}}, \code{\link{reconstruct_pattern_marks}} } diff --git a/man/results_habitat_association.Rd b/man/results_habitat_association.Rd index fc34dac0..3e29c978 100644 --- a/man/results_habitat_association.Rd +++ b/man/results_habitat_association.Rd @@ -65,6 +65,6 @@ in tropical forests. Journal of Theoretical Biology 207, 81–99. } \seealso{ -\code{\link{reconstruct_pattern}} \cr +\code{\link{reconstruct_pattern}}, \code{\link{fit_point_process}} } diff --git a/man/unpack_randomized.Rd b/man/unpack_randomized.Rd index 26fb56a9..4d4a0f9c 100644 --- a/man/unpack_randomized.Rd +++ b/man/unpack_randomized.Rd @@ -31,5 +31,5 @@ y <- unpack_randomized(raster = y) } \seealso{ \code{\link{pack_randomized}} -\code{\link{wrap}} +\code{\link[terra]{wrap}} } From 9ee8a4da01025fedbd2ffd2819e5274028856ae5 Mon Sep 17 00:00:00 2001 From: mhesselbarth Date: Fri, 10 Jan 2025 12:49:40 +0000 Subject: [PATCH 2/2] Re-write codemeta.json --- codemeta.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/codemeta.json b/codemeta.json index ee0d900f..40160614 100644 --- a/codemeta.json +++ b/codemeta.json @@ -13,7 +13,7 @@ "name": "R", "url": "https://r-project.org" }, - "runtimePlatform": "R version 4.3.3 (2024-02-29)", + "runtimePlatform": "R version 4.4.2 (2024-10-31)", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -257,7 +257,7 @@ }, "SystemRequirements": null }, - "fileSize": "1074.197KB", + "fileSize": "1074.193KB", "citation": [ { "@type": "ScholarlyArticle",