shapefiles package refs removed post RGDAL purge, wasn't being used a…

…nyway

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: gbm.auto
 Title: Automated Boosted Regression Tree Modelling and Mapping Suite
-Version: 2023.12.14
+Version: 2024.02.06
 Authors@R: person("Simon", "Dedman", , "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9108-972X"))
 Description: Automates delta log-normal boosted regression tree abundance
     prediction. Loops through parameters provided (LR (learning rate), TC
@@ -41,5 +41,5 @@ Imports:
 Encoding: UTF-8
 Language: en-GB
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)

Gbm.auto_extras/gbm.loop_functionrun.R

@@ -33,9 +33,8 @@ mygrids <- gbm.auto::grids # load grids
 mysamples <- gbm.auto::samples # load samples
 setwd("/home/simon/Dropbox/Galway/Project Sections/5. Intro & Conclusion/Extra graphics/CofV/")
 
-# library("shapefiles")
-# Crop_Map <- read.shapefile("/home/simon/Desktop/gbm temp/CroppedMap/Crop_Map")
-library(mapplots)
+# Crop_Map <- st_read(dsn = paste0("Crop_Map", ".shp"), layer = savename, quiet = TRUE)
+# library(mapplots)
 data(coast)
 shape <- coast
 

Gbm.auto_extras/gbmauto.sepbingaus.runscript.R

@@ -1,10 +1,9 @@
 library("gbm.auto")
 mygrids <- gbm.auto::grids # load grids
 mysamples <- gbm.auto::samples # load samples
-setwd("/home/simon/Desktop/gbm temp/sepParamTestbench/")
-source('~/Dropbox/Galway/Analysis/R/gbm.auto/R/gbm.utils.R')
-library("shapefiles")
-Crop_Map <- read.shapefile("/home/simon/Desktop/gbm temp/CroppedMap/Crop_Map")
+# setwd("/home/simon/Desktop/gbm temp/sepParamTestbench/")
+# source('~/Dropbox/Galway/Analysis/R/gbm.auto/R/gbm.utils.R')
+Crop_Map <- st_read(dsn = paste0("Crop_Map", ".shp"), layer = savename, quiet = TRUE)
 #source('~/Dropbox/Galway/Analysis/R/gbm.auto/Gbm.auto_extras/gbm.auto.binGausSepParams.R')
 
 # test1 basic clean run
@@ -175,24 +174,23 @@ gbm.auto(samples = mysamples, grids = mygrids, expvar = c(4:9), resvar = 11,
 # (bf is a list with a vector AND lr OR tc are lists)
 # if fails. Purple lines not printed in fail runs.
 # [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX  Variable interactions done XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
-[1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX  Binomial predictions done  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
-[1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX  Gaussian predictions done  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
-[1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Final abundance calculated  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
+# [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX  Binomial predictions done  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
+# [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX  Gaussian predictions done  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
+# [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Final abundance calculated  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
 # [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX     Output CSVs written     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
 # [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX     Report CSV written      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
-[1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX       RSB CSV written       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
-[1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX    Reticulating splines     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
-[1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX    Colour map generated     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
-[1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Black & white map generated XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
-[1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX  Colour RSB bin map done    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
-[1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Colour RSB Gaus map done    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
-[1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Colour RSB combo map done   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
-[1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX     B&W RSB bin map done    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
-[1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX    B&W RSB Gaus map done    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
-[1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX    B&W RSB combo map done   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
+# [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX       RSB CSV written       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
+# [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX    Reticulating splines     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
+# [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX    Colour map generated     XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
+# [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Black & white map generated XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
+# [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX  Colour RSB bin map done    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
+# [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Colour RSB Gaus map done    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
+# [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Colour RSB combo map done   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
+# [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX     B&W RSB bin map done    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
+# [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX    B&W RSB Gaus map done    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
+# [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX    B&W RSB combo map done   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
 # [1] "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Grids/maps/everything done  XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
 # > gbm.auto(samples = mysamples, grids = mygrids, expvar = c(4:9), resvar = 11,
-# THE FAIL ONES DIDN'T HAVE GRIDS YOU FUCKING FUCK!! JESUS BOY!
 gbm.auto(samples = mysamples, grids = mygrids, expvar = c(4:9), resvar = 11,
          tc = list(2,c(2,3)),
          lr = list(c(0.01, 0.02), 0.005),
@@ -230,4 +228,4 @@ gbm.auto(samples = mysamples, grids = mygrids, expvar = c(4:9), resvar = 11,
          tc = list(2,c(2,3)),
          lr = list(c(0.01, 0.02), 0.005),
          bf = 0.5,
-         mapshape = Crop_Map, simp = F)
+         mapshape = Crop_Map, simp = F)

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2021
-COPYRIGHT HOLDER: Simon Dedman
+YEAR: 2024
+COPYRIGHT HOLDER: gbm.auto authors

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2021 Simon Dedman
+Copyright (c) 2024 gbm.auto authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

R/gbm.basemap.R

@@ -34,7 +34,6 @@
 #' @importFrom graphics lines par
 #' @importFrom utils download.file unzip
 #' @importFrom sf st_crop st_read st_write sf_use_s2
-# #' @importFrom shapefiles read.shapefile
 #' @author Simon Dedman, \email{simondedman@@gmail.com}
 #' @examples
 #' \donttest{
@@ -56,21 +55,14 @@
 #' 2. If rgdal install fails in Linux try:
 #' sudo apt-get install libgdal-dev && sudo apt-get install libproj-dev"
 #'
-#' 3. Error in as.environment(pos):no item called "package:shapefiles" on the
-#' search list: strange error occurring despite shapefiles being coded like all
-#' other packages. Correct output produced regardless.
-#'
-#' 4. subscript out of bounds: can't crop world map to your bounds.
+#' 3. subscript out of bounds: can't crop world map to your bounds.
 #' Check lat/lon are the right way around: check gridslat and gridslon point to the correct columns
 #' for lat and lon in grids, and those columns named (something like) lat and lon, ARE ACTUALLY the
 #' latitudes and longitudes, and not the wrong way around.
 #'
-#' 5. If your download is timing out use options(timeout = 240).
-#'
-#' 6. Error in attachNamespace("shapefiles"): namespace is already attached. Use:
-#' unloadNamespace("shapefiles") .
+#' 4. If your download is timing out use options(timeout = 240).
 #'
-#' 7. Error in if (scope >= 160) res <- "c" : missing value where TRUE/FALSE needed. Check gridslat
+#' 5. Error in if (scope >= 160) res <- "c" : missing value where TRUE/FALSE needed. Check gridslat
 #'  and gridslon are indexing the correct columns in grids.
 #'
 gbm.basemap <- function(
@@ -88,11 +80,6 @@ gbm.basemap <- function(
     # returnsf = FALSE # obviated by gbm.mapsf
 ) { # Return object as simple features object? Default FALSE, returns as list format for draw.shape in mapplots, used in gbm.map
 
-  attachNamespace("shapefiles") # else Error in as.environment(pos): no item called "package:shapefiles" on the search list
-  # or Error during wrapup: no item called "package:shapefiles" on the search list
-  # despite shapefiles being in imports here, in namespace, & in description. Doesn't do this for any other package.
-  # But if I include this the line can get run twice, giving the error: "namespace(shapefiles) was already taken."
-
   oldwd <- getwd() # record original directory
   on.exit(setwd(oldwd), add = TRUE) # defensive block, thanks to Gregor Sayer
   sf::sf_use_s2(FALSE) # 2021 addition of s2 code to sf often causes: Error in s2_geography_from_wkb(x, oriented = oriented, check = check):
@@ -159,19 +146,10 @@ gbm.basemap <- function(
 
   world <- st_read(dsn = paste0("GSHHS_", res, "_L1.shp"), layer = paste0("GSHHS_", res, "_L1"), quiet = TRUE) # read in worldmap
   cropshp <- st_crop(world, xmin = xmin, xmax = xmax, ymin = ymin, ymax = ymax) # crop to extents
-  # setwd(savedir) # setwd to savedir else saves CroppedMap folder in res folder
   setwd("../../") # setwd to savedir else saves CroppedMap folder in res folder
   dir.create("CroppedMap") # create conservation maps directory
   setwd("CroppedMap")
   st_write(cropshp, dsn = paste0(savename, ".shp"), append = FALSE) # append FALSE overwrites existing files
-
-  # if (returnsf) {
-  #   cropshp <- st_read(dsn = paste0(savename, ".shp"), layer = savename, quiet = TRUE) # read in worldmap
-  # } else {
-  #   cropshp <- shapefiles::read.shapefile(savename) # read it back in with read.shapefile which results in the expected format for draw.shape in mapplots, used in gbm.map # shapefiles::
-  # }
-
-  cropshp <- st_read(dsn = paste0(savename, ".shp"), layer = savename, quiet = TRUE) # read in worldmap
-
+  # cropshp <- st_read(dsn = paste0(savename, ".shp"), layer = savename, quiet = TRUE) # read in worldmap
   print(paste("World map cropped and saved successfully"))
   return(cropshp)}

R/gbm.lmplots.R

@@ -33,10 +33,11 @@
 #'
 ## Simon Dedman 2018.08.30 & 2023-03-07
 ## To Run:
-# lmplot(x = samples[,expvar],
-#        y = samples[,resvar],
-#        xname = expvar,
-#        yname = resvar)
+# gbm.lmplots(samples = samples[,c(resvar, expvar)],
+#        expvar = expvar,
+#        resvar = resvar,
+#        expvarnames = expvar,
+#        resvarname = resvar)
 
 
 gbm.lmplots <- function(samples = NULL, # dataframe

R/gbm.map.R

@@ -29,7 +29,7 @@
 #' @param colournumber Number of colours to spread heatcol over, default:8.
 #' @param shape Basemap shape to draw, from draw.shape in mapplots. Defaults to
 #' NULL which calls gbm.basemap to generate it for you. First read in a shp file e.g. myshape <-
-#' shapefiles::read.shapefile("Crop_Map") WITHOUT the .shp extension, then use shape = myshape.
+#' sf::st_read(dsn = paste0(savename, ".shp"), layer = savename, quiet = TRUE), then use shape = myshape.
 #' @param landcol Colour for 'null' area of map (for marine plots, this is
 #' land), from draw.shape in mapplots. Default "grey80" (light grey).
 #' @param mapback Basemap background colour, defaults to lightblue (ocean for