version 2024.03.05

DESCRIPTION

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+Package: movegroup
+Title: Visualizing and Quantifying Space Use Data for Groups of Animals
+Version: 2024.03.05
+Authors@R: c(
+    person("Simon", "Dedman", email = "simondedman@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9108-972X")),
+    person("Maurits", "van Zinnicq Bergmann", email = "mauritsvzb@gmail.com", role = c("aut"), comment = c(ORCID = "0000-0002-8414-5025")))
+Description: Offers an easy and automated way to scale up individual-level space use analysis to 
+    that of groups. Contains a function from the 'move' package to calculate a dynamic Brownian 
+    bridge movement model from movement data for individual animals, as well as functions to 
+    visualize and quantify space use for individuals aggregated in groups. Originally written with 
+    passive acoustic telemetry in mind, this package also provides functionality to account for
+    unbalanced acoustic receiver array designs, and satellite tag data.
+Depends: R (>= 4.1.0)
+License: MIT + file LICENSE
+Encoding: UTF-8
+Language: en-GB
+LazyData: true
+Imports: ggplot2 (>= 3.3.5), utils, beepr (>= 1.3), dplyr (>= 1.0.8),
+        ggmap (>= 3.0.0), knitr (>= 1.45), lubridate (>= 1.8.0), magick
+        (>= 2.8.2), methods, move (>= 4.1.6), purrr (>= 1.0.2), raster
+        (>= 3.5-15), rlang (>= 1.0.2), sf (>= 1.0-7), sp (>= 1.4-6),
+        stars (>= 0.5-5), starsExtra (>= 0.2.7), stringr (>= 1.4.0),
+        terra (>= 1.7-39), tidyr (>= 1.2.0), tidyselect (>= 1.2.0),
+        viridis (>= 0.6.4)
+RoxygenNote: 7.3.1
+Suggests: rmarkdown
+VignetteBuilder: knitr
+NeedsCompilation: no
+Packaged: 2024-03-05 17:31:10 UTC; simon
+Author: Simon Dedman [aut, cre] (<https://orcid.org/0000-0002-9108-972X>),
+  Maurits van Zinnicq Bergmann [aut]
+    (<https://orcid.org/0000-0002-8414-5025>)
+Maintainer: Simon Dedman <simondedman@gmail.com>
+Repository: CRAN
+Date/Publication: 2024-03-07 10:10:02 UTC

LICENSE

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+YEAR: 2024
+COPYRIGHT HOLDER: movegroup authors

MD5

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+58536556a1fb30f850babda03d67f3b6 *DESCRIPTION
+76b68b4e55c084c0fea9e66c50a1cb0b *LICENSE
+73455c1826e0a2e3f810f6e0ec2f2f68 *NAMESPACE
+4295b5bee2bed31cf46f573937622504 *NEWS.md
+4fddaef28ddec57953dcb7d22fdb9f47 *R/alignraster.R
+57d78896bdaaf12719bd30196d52c664 *R/data.R
+90fb4e2013a27881b2535b2aa245617c *R/moveLocErrorCalc.R
+21d025d45528718e3df50f21c0fc16ec *R/movegroup-package.R
+28739d173ac55d5941fd868c93f292bc *R/movegroup.R
+1ee51f89755916cd678d4a2d323c82d5 *R/plotRasterIsometric.R
+f43ca44f3397f77c30e017e722759472 *R/plotraster.R
+8afebd4def29d420a5e604ba69d26c17 *R/scaleraster.R
+56e9d1a6abb10288917ca1401019a0dc *R/utils.R
+3006aa268d9bfa7c6df48025a2bab7ac *README.md
+78d3e5cedcea9f876d7071001d54bc93 *build/vignette.rds
+32d74e8c5806498def4a22aab1e7dc68 *data/TracksCleaned.RData
+87fe4e6e57ca71e54998b54a7cfc316e *data/argosFiltered.RData
+c6fdf1ca23610e8672a65906e142add6 *inst/CITATION
+2bbd1c54a7b58ba2f26d6d39453490df *inst/Misc/RunScriptExample.R
+31d6ae223cf149aebfc66d2eb927b436 *inst/doc/Using-the-movegroup-package.R
+0ffc94f7d6f608e75c7485c7bd7218d8 *inst/doc/Using-the-movegroup-package.Rmd
+29c3dec51dfaaa374eac7e4486cd9d1f *inst/doc/Using-the-movegroup-package.html
+a9c7027f32ea4789efc3adb6450c0f5c *man/TracksCleaned.Rd
+8d9ce83accda1848da3e562517ad75c2 *man/alignraster.Rd
+a7d9d06697d2a3f5dd241354775a6d8e *man/argosFiltered.Rd
+a1cbaf3f328e8d74e747faacf640c7fc *man/figures/lifecycle-archived.svg
+6f521fb1819410630e279d1abf88685a *man/figures/lifecycle-defunct.svg
+391f696f961e28914508628a7af31b74 *man/figures/lifecycle-deprecated.svg
+691b1eb2aec9e1bec96b79d11ba5e631 *man/figures/lifecycle-experimental.svg
+405e252e54a79b33522e9699e4e9051c *man/figures/lifecycle-maturing.svg
+f41ed996be135fb35afe00641621da61 *man/figures/lifecycle-questioning.svg
+306bef67d1c636f209024cf2403846fd *man/figures/lifecycle-soft-deprecated.svg
+ed42e3fbd7cc30bc6ca8fa9b658e24a8 *man/figures/lifecycle-stable.svg
+bf2f1ad432ecccee3400afe533404113 *man/figures/lifecycle-superseded.svg
+a4cf8f6456b0eb071feee24301af1ca2 *man/figures/logo.png
+092e4f2209e5820868aa88a0989db74c *man/moveLocErrorCalc.Rd
+e9c404fdeb8e6467aa1a01eab59e04d4 *man/movegroup-package.Rd
+b11337355f0b87fddb702e5a069143b1 *man/movegroup.Rd
+36ea0c526ae32ed313f12bd4cab3bc10 *man/plotraster.Rd
+d4f5f6885c7804a3f43aa7633e6cf235 *man/scaleraster.Rd
+0ffc94f7d6f608e75c7485c7bd7218d8 *vignettes/Using-the-movegroup-package.Rmd
+6a066e0c74cf1a730457128963107ea0 *vignettes/figures/BBtrajectoryvignette.png
+ddb3bdc1f92e71a36b0f71f2f8ebde1d *vignettes/figures/BBvariancesvignette.png
+0ff9d396a91a90a8c0713289bc8a4e14 *vignettes/figures/plotrasterVignette.png
+0a2f6bf5428c63c6eea7fc131bd421c4 *vignettes/figures/relocationsUDvignette.png

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(alignraster)
+export(moveLocErrorCalc)
+export(movegroup)
+export(plotraster)
+export(scaleraster)
+import(ggmap)
+import(ggplot2)
+import(utils)
+importFrom(beepr,beep)
+importFrom(dplyr,across)
+importFrom(dplyr,arrange)
+importFrom(dplyr,bind_cols)
+importFrom(dplyr,distinct)
+importFrom(dplyr,filter)
+importFrom(dplyr,group_by)
+importFrom(dplyr,mutate)
+importFrom(dplyr,pull)
+importFrom(dplyr,rename)
+importFrom(dplyr,select)
+importFrom(dplyr,semi_join)
+importFrom(dplyr,summarise)
+importFrom(dplyr,ungroup)
+importFrom(grDevices,graphics.off)
+importFrom(graphics,par)
+importFrom(knitr,plot_crop)
+importFrom(lubridate,is.POSIXt)
+importFrom(lubridate,today)
+importFrom(magick,image_trim)
+importFrom(methods,as)
+importFrom(methods,new)
+importFrom(move,brownian.bridge.dyn)
+importFrom(move,brownian.motion.variance.dyn)
+importFrom(move,burst)
+importFrom(move,getVolumeUD)
+importFrom(move,move)
+importFrom(move,timeLag)
+importFrom(purrr,map2)
+importFrom(purrr,map_df)
+importFrom(raster,calc)
+importFrom(raster,crs)
+importFrom(raster,extend)
+importFrom(raster,maxValue)
+importFrom(raster,ncell)
+importFrom(raster,nlayers)
+importFrom(raster,projectExtent)
+importFrom(raster,projectRaster)
+importFrom(raster,raster)
+importFrom(raster,res)
+importFrom(raster,setMinMax)
+importFrom(raster,setValues)
+importFrom(raster,stack)
+importFrom(raster,stackApply)
+importFrom(raster,values)
+importFrom(raster,writeRaster)
+importFrom(rlang,.data)
+importFrom(rlang,set_names)
+importFrom(sf,st_as_sf)
+importFrom(sf,st_as_sfc)
+importFrom(sf,st_bbox)
+importFrom(sf,st_distance)
+importFrom(sf,st_set_crs)
+importFrom(sf,st_transform)
+importFrom(sp,CRS)
+importFrom(sp,SpatialPoints)
+importFrom(sp,bbox)
+importFrom(sp,proj4string)
+importFrom(sp,spTransform)
+importFrom(stars,read_stars)
+importFrom(stars,st_contour)
+importFrom(stars,st_raster_type)
+importFrom(starsExtra,trim2)
+importFrom(stats,sd)
+importFrom(stats,setNames)
+importFrom(stringr,str_remove)
+importFrom(terra,project)
+importFrom(tidyr,drop_na)
+importFrom(tidyselect,everything)
+importFrom(viridis,scale_fill_viridis)

NEWS.md

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+---
+title: "NEWS.md"
+author: "Simon Dedman"
+date: "2024-03-05"
+output: html_document
+---
+# v2024.03.05
+* first CRAN release
+
+
+<!-- If an item is related to an issue in GitHub, include the issue number in parentheses, e.g. (#​10).
+If an item is related to a pull request, include the pull request number and the author, e.g. (#​101, @hadley).
+Doing this makes it easy to navigate to the relevant issues on GitHub.-->

R/alignraster.R

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+#' Combines region-specific group-level UD rasters into a single raster.
+#'
+#' Extends the spatial extent of each area-specific group-level raster to the spatial extent shared by all rasters.
+#' This will only be required if you have multiple individuals (e.g. different sharks) divided amongst a few discrete areas
+#'  (e.g. around different islands) and the effort (e.g. receiver coverage) is different among islands.
+#'  Not required for multiple individuals all within the same region or sampling regime.
+#'
+#' @param folderroots Character vector of locations of folder roots output by movegroup. Function
+#'  expects CRS.Rds file and a subfolder with the scaled raster.
+#' @param foldernames Character vector names of folders corresponding to files in folderroots, i.e.
+#'  the names of the objects, arrays, regions, etc.
+#' @param pattern For input rasters from scaleraster. Default ".asc".
+#' @param scalefolder For input rasters from scaleraster. Default "Scaled".
+#' @param scaledweightedname For input rasters from scaleraster. Default "All_Rasters_Scaled".
+#' @param savefolder E.g. "/myfolder/Aligned". Single character entry of folder to save outputs, no trailing slash.
+#' @param format Character. Output file type for raster::writeRaster param format. Default ascii,
+#'  other options have generally not worked well in SD's experience.
+#' @param datatype Character. Data type for writing values to disk for raster::writeRaster param
+#'  datatype. Default FLT4S.
+#' @param bylayer For raster::writeRaster param bylayer. Default TRUE.
+#' @param overwrite For raster::writeRaster param overwrite. Default TRUE.
+#' @param returnObj Logical. Return the scaled object to the parent environment to be assigned as an
+#'  object? Default FALSE.
+#' 
+#' @return Region-specific group-level UD rasters that share the same spatial extent.
+#'
+#' @details When used in a movegroup pipeline, the order would be: movegroup.R, scaleraster.R,
+#'  alignraster.R if required, plotraster.R.
+#' 
+#' @examples
+#' \donttest{
+#' # load data
+#' data("TracksCleaned")
+#' # loop movegroup and scaleraster through tide subsets
+#' tide <- c("H", "M", "L")
+#' for (i in tide) {
+#' dir.create(file.path(tempdir(), i))
+#'   movegroup(
+#'     data = TracksCleaned[TracksCleaned$T.Ph == i, ],
+#'     ID = "Shark",
+#'     Datetime = "Datetime",
+#'     Lat = "Lat",
+#'     Lon = "Lon",
+#'     savedir = file.path(tempdir(), i, "/"))
+#'   
+#'   scaleraster(path = file.path(tempdir(), i),
+#'               crsloc = file.path(tempdir(), i))
+#' }
+#' 
+#' alignraster(folderroots = file.path(tempdir(), tide),
+#'             foldernames = tide,
+#'             savefolder = file.path(tempdir(), "Aligned"))
+#' }
+#'
+#' @author Simon Dedman, \email{simondedman@@gmail.com}
+#' @author Maurits van Zinnicq Bergmann, \email{mauritsvzb@@gmail.com}
+
+#' @export alignraster
+
+#' @importFrom methods as
+#' @importFrom purrr map2
+#' @importFrom raster crs setMinMax raster extend writeRaster
+#' @importFrom sp bbox
+#' @importFrom terra project
+
+
+
+# read in rasters & add to list####
+alignraster <- function(folderroots = c("/myfolder/H", # character vector of locations of folder roots output by movegroup. Function expects CRS.Rds file and a subfolder with the scaled raster.
+                                        "/myfolder/L", # these were /home/simon/Dropbox/PostDoc Work/Rob Bullock accelerometer Lemons 2020.09/dBBMM ASCII/H L M
+                                        "/myfolder/M"),
+                        foldernames = c("H", "L", "M"), # character vector names of folders corresponding to files in folderroots, i.e. the names of the objects, arrays, regions, etc.
+                        pattern = ".asc", # for input rasters from scaleraster
+                        scalefolder = "Scaled", # for input rasters from scaleraster
+                        scaledweightedname = "All_Rasters_Scaled_Weighted", # for input rasters from scaleraster.
+                        savefolder = tempdir(), # e.g. "/myfolder/Aligned". Single character entry, no trailing slash.
+                        format = "ascii", # save format
+                        datatype = "FLT4S", # save format
+                        bylayer = TRUE, # save format
+                        overwrite = TRUE, # save format
+                        returnObj = FALSE # return rasterlist object?
+) {
+  if (length(folderroots) != length(foldernames)) stop("length of folderroots and foldernames must be equal")
+  # If folderroots or savefolder have a terminal slash, remove it, it's added later
+  for (folders in folderroots) {
+    if (substr(x = folders, start = nchar(folders), stop = nchar(folders)) == "/") folderroots[which(folderroots %in% folders)] = substr(x = folders, start = 1, stop = nchar(folders) - 1)
+  }
+
+  if (substr(x = savefolder, start = nchar(savefolder), stop = nchar(savefolder)) == "/") savefolder = substr(x = savefolder, start = 1, stop = nchar(savefolder) - 1)
+
+  foldernames <- as.list(foldernames)
+
+  # Read in CRS files as list
+  crslist <- as.list(file.path(folderroots, "CRS.Rds"))  |> 
+    lapply(function(x) readRDS(x))
+  names(crslist) <- foldernames # unnecessary?
+
+  rasterlist <- 
+    as.list(file.path(folderroots, scalefolder, paste0(scaledweightedname, pattern)))  |> # Pull all raster names from folderroots into a list
+    lapply(function(x) raster::raster(x))  |>  # read in rasters
+    lapply(function(x) raster::setMinMax(x))  |>  # set minmax values
+    # https://stackoverflow.com/questions/72063819/use-an-arrow-assignment-function-as-r-purrr-map2
+    purrr::map2(crslist, ~ {raster::crs(.x) <- .y;.x})  |> 
+    purrr::map2(foldernames, ~ {names(.x) <- .y;.x})
+
+  # calculate full shared extent
+  sharedextent <- lapply(rasterlist, function(x) as.vector(sp::bbox(x))) # xmin #ymin #xmax #ymax
+  sharedextent <- data.frame(t(sapply(sharedextent, c)))
+  sharedextent <- c(min(sharedextent[1]), # xmin
+                    max(sharedextent[3]), # xmax
+                    min(sharedextent[2]), # ymin
+                    max(sharedextent[4])) # ymax
+
+  # align to same spatial extent
+  rasterlist <- lapply(rasterlist, function(x) raster::extend(x, sharedextent))
+
+  # Convert to SpatRaster format to be used by {terra}
+  rasterlist <- lapply(rasterlist, function(x) as(x, "SpatRaster")) # methods::as
+
+  # Reproject all rasters simultaneously
+  rasterlist <- lapply(rasterlist, function(x) project(x, y = rasterlist[[length(rasterlist)]]))
+
+  # Convert back to RasterLayer to save CRS
+  rasterlist <- lapply(rasterlist, function(x) raster::raster(x))
+
+  # Save CRS
+  rasterlistCRS <- sp::CRS(sp::proj4string(rasterlist[[1]]))
+  class(rasterlistCRS) # CRS
+
+  # if savefolder doesn't exist, create it
+  if (!file.exists(savefolder)) dir.create(savefolder)
+  write.csv(sp::proj4string(rasterlistCRS), file.path(savefolder, "CRS.csv"), row.names = FALSE)
+  saveRDS(rasterlistCRS, file = file.path(savefolder, "CRS.Rds"))
+
+  rasterlist <- lapply(rasterlist, function(x) raster::writeRaster(x = x, # resave individual rasters
+                                                         filename = file.path(savefolder, names(x)), # , pattern: removed ability to resave as different format
+                                                         # error: adds X to start of numerical named objects####
+                                                         format = format,
+                                                         datatype = datatype,
+                                                         if (format != "CDF") bylayer = bylayer,
+                                                         overwrite = overwrite))
+
+  if (returnObj) return(rasterlist)
+} # close function

R/data.R

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+#' Data: Tracks of lemon sharks off Bimini, Bahamas
+#'
+#' Tracks of 17 lemon sharks (Negaprion brevirostris) tagged off Bimini, Bahamas, 2012:2014, by
+#'  Bimini Biological Field Station employees and volunteers, with accompanying tidal phase.
+#'
+#' @format A data frame with 1308 rows and 5 variables:
+#' \describe{
+#'   \item{Datetime}{POSIXct datetime, format YYYY-MM-DD HH:MM:SS.}
+#'   \item{Shark}{Individual shark ID code.}
+#'   \item{T.Ph}{Tidal phase, H M L High Medium Low.}
+#'   \item{Lat}{Decimal latitudes.}
+#'   \item{Lon}{Decimal longitudes.}
+#' }
+#'
+#' @docType data
+#' @keywords datasets
+#' @name TracksCleaned
+#' @usage data(TracksCleaned)
+#' @author Simon Dedman, \email{simondedman@@gmail.com}
+#' @author Maurits van Zinnicq Bergmann, \email{mauritsvzb@@gmail.com}
+#' @source \url{https://www.biminisharklab.com}
+"TracksCleaned"
+
+#' Data: Tracks of two great hammerhead sharks with position confidence intervals
+#'
+#' Tracks of 2 great hammerhead sharks tagged in Jupiter, and The Keys, Florida, USA, in 2022 and 
+#' 2023 respectively, by Saving The Blue (savingtheblue.org), filtered by argosfilter::sdafilter and
+#'  with state space model applied using aniMotum package, using scripts by Vital Heim, see 
+#'  https://github.com/SimonDedman/SavingTheBlue/blob/main/R/06A_Filter_SPOT_data.R and 
+#'  https://github.com/SimonDedman/SavingTheBlue/blob/main/R/06B_CTCRW_SPOT_data_usin_animotum.R .
+#'
+#' @format A data frame with 1492 rows and 8 variables:
+#' \describe{
+#'   \item{id}{Character, shark ID.}
+#'   \item{date}{POSIXct datetime, format YYYY-MM-DD HH:MM:SS.}
+#'   \item{lon}{Decimal longitudes.}
+#'   \item{lon025}{Decimal longitudes, lower 95% confidence interval bound.}
+#'   \item{lon975}{Decimal longitudes, upper 95% confidence interval bound.}
+#'   \item{lat}{Decimal latitudes.}
+#'   \item{lat025}{Decimal latitudes, lower 95% confidence interval bound.}
+#'   \item{lat975}{Decimal latitudes, upper 95% confidence interval bound.}
+#' }
+#'
+#' @docType data
+#' @keywords datasets
+#' @name argosFiltered
+#' @usage data(argosFiltered)
+#' @author Simon Dedman, \email{simondedman@@gmail.com}
+#' @author Vital Heim, \email{vital.heim@@gmail.com}
+#' @source \url{https://www.savingtheblue.org}
+"argosFiltered"