diff --git a/R/01_range_map_preparation.R b/R/01_01_range_map_preparation.R
similarity index 100%
rename from R/01_range_map_preparation.R
rename to R/01_01_range_map_preparation.R
diff --git a/R/01_02_raster_preparation.R b/R/01_02_raster_preparation.R
new file mode 100644
index 0000000000000000000000000000000000000000..fae113ffcaccd416c22167fc1d8c5e35d01d1331
--- /dev/null
+++ b/R/01_02_raster_preparation.R
@@ -0,0 +1,55 @@
+library(tidyverse)
+library(terra)
+library(rnaturalearth)
+library(furrr)
+
+# Define Study extent ####
+study_extent = rnaturalearth::ne_countries() %>%
+ dplyr::filter(continent == "South America") %>%
+ sf::st_union() %>%
+ sf::st_bbox() %>%
+ ext()
+
+# CHELSA bioclim target variables ####
+chelsa_urls = c("https://os.zhdk.cloud.switch.ch/chelsav2/GLOBAL/climatologies/1981-2010/bio/CHELSA_cmi_mean_1981-2010_V.2.1.tif",
+ "https://os.zhdk.cloud.switch.ch/chelsav2/GLOBAL/climatologies/1981-2010/bio/CHELSA_rsds_1981-2010_mean_V.2.1.tif",
+ "https://os.zhdk.cloud.switch.ch/chelsav2/GLOBAL/climatologies/1981-2010/bio/CHELSA_bio6_1981-2010_V.2.1.tif",
+ "https://os.zhdk.cloud.switch.ch/chelsav2/GLOBAL/climatologies/1981-2010/bio/CHELSA_bio17_1981-2010_V.2.1.tif")
+
+chelsa = terra::rast(chelsa_urls) %>%
+ crop(study_extent)
+set.names(chelsa, c("cmi", "rsds", "bio6", "bio17"))
+terra::writeRaster(chelsa, filename = file.path("data", "geospatial", "raster", basename(chelsa_urls)), overwrite = T)
+
+# Tree canopy cover ####
+igfc = list.files("I:/mas_data/00_data/processed/iGFC/", pattern = "canopyDensity_(199[0-9]|200[0-9]|2010)", full.names = TRUE) %>%
+ terra::rast() %>%
+ terra::resample(chelsa) %>%
+ app(mean, na.rm = TRUE)
+terra::set.names(igfc, "igfc")
+terra::writeRaster(igfc, filename = file.path("data", "geospatial", "raster", "mean_canopyDensity_1992-2010.tif"), overwrite = T)
+
+# Seasonal inundation ####
+igsw = list.files("I:/mas_data/00_data/processed/iGSW/", pattern = "seasonal_(199[0-9]|200[0-9]|2010)", full.names = TRUE) %>%
+ terra::rast() %>%
+ terra::resample(chelsa) %>%
+ app(mean, na.rm = TRUE)
+terra::set.names(igsw, "igsw")
+terra::writeRaster(igsw, filename = file.path("data", "geospatial", "raster", "mean_seasonalInundation_1992-2010.tif"), overwrite = T)
+
+# Distance to freshwater ####
+dtfw = list.files("I:/mas_data/00_data/processed/linearDistance/", pattern = "lake|reservoirs|river", full.names = TRUE) %>%
+ terra::rast() %>%
+ crop(study_extent) %>%
+ min(na.rm = T) %>%
+ terra::resample(chelsa)
+terra::set.names(dtfw, "dtfw")
+terra::writeRaster(dtfw, filename = file.path("data", "geospatial", "raster", "mean_distanceToWater.tif"), overwrite = T)
+
+# Terrain ####
+roughness = list.files("C:/Users/ye87zine/Downloads", pattern = "roughness", full.names = T) %>%
+ terra::rast() %>%
+ crop(study_extent) %>%
+ terra::resample(chelsa)
+terra::set.names(roughness, "roughness")
+terra::writeRaster(roughness, filename = file.path("data", "geospatial", "raster", "terrain_roughness.tif"), overwrite = T)
diff --git a/renv.lock b/renv.lock
index 1a9a7b40483c6aaa87c451e9ce64e07e50a9a25b..ff0fc5aa5dcee66526155c43af29c34119242c22 100644
--- a/renv.lock
+++ b/renv.lock
@@ -8,7 +8,29 @@
}
]
},
+ "Bioconductor": {
+ "Version": "3.18"
+ },
"Packages": {
+ "BiocManager": {
+ "Package": "BiocManager",
+ "Version": "1.30.25",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "utils"
+ ],
+ "Hash": "3aec5928ca10897d7a0a1205aae64627"
+ },
+ "BiocVersion": {
+ "Package": "BiocVersion",
+ "Version": "3.18.1",
+ "Source": "Bioconductor",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "2ecaed86684f5fae76ed5530f9d29c4a"
+ },
"CoordinateCleaner": {
"Package": "CoordinateCleaner",
"Version": "3.0.1",
@@ -42,6 +64,17 @@
],
"Hash": "065ae649b05f1ff66bb0c793107508f5"
},
+ "DEoptim": {
+ "Package": "DEoptim",
+ "Version": "2.2-8",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "methods",
+ "parallel"
+ ],
+ "Hash": "3d75dd10e7228c9d734237dda013ed90"
+ },
"DT": {
"Package": "DT",
"Version": "0.33",
@@ -211,6 +244,25 @@
],
"Hash": "2288423bb0f20a457800d7fc47f6aa54"
},
+ "ape": {
+ "Package": "ape",
+ "Version": "5.8",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "Rcpp",
+ "digest",
+ "graphics",
+ "lattice",
+ "methods",
+ "nlme",
+ "parallel",
+ "stats",
+ "utils"
+ ],
+ "Hash": "16b5ff4dff0ead9ea955f62f794b1535"
+ },
"arrow": {
"Package": "arrow",
"Version": "17.0.0.1",
@@ -411,7 +463,7 @@
},
"caret": {
"Package": "caret",
- "Version": "6.0-94",
+ "Version": "7.0-1",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
@@ -433,7 +485,7 @@
"utils",
"withr"
],
- "Hash": "528692344d5a174552e3bf7acdfbaebd"
+ "Hash": "304c0d28bda6454aae3b14ae953e7824"
},
"cellranger": {
"Package": "cellranger",
@@ -560,6 +612,28 @@
],
"Hash": "5edbbabab6ce0bf7900a74fd4358628e"
},
+ "clusterGeneration": {
+ "Package": "clusterGeneration",
+ "Version": "1.3.8",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "MASS",
+ "R"
+ ],
+ "Hash": "62df4b1fe7abefcf921dd7e52a801a6b"
+ },
+ "coda": {
+ "Package": "coda",
+ "Version": "0.19-4.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "lattice"
+ ],
+ "Hash": "af436915c590afc6fffc3ce3a5be1569"
+ },
"codetools": {
"Package": "codetools",
"Version": "0.2-19",
@@ -584,6 +658,20 @@
],
"Hash": "d954cb1c57e8d8b756165d7ba18aa55a"
},
+ "combinat": {
+ "Package": "combinat",
+ "Version": "0.0-8",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "f0acb9dcb71a9cd9d5ae233c5035b1c5"
+ },
+ "commonmark": {
+ "Package": "commonmark",
+ "Version": "1.9.2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Hash": "14eb0596f987c71535d07c3aff814742"
+ },
"conflicted": {
"Package": "conflicted",
"Version": "1.2.0",
@@ -744,6 +832,20 @@
],
"Hash": "33698c4b3127fc9f506654607fb73676"
},
+ "doParallel": {
+ "Package": "doParallel",
+ "Version": "1.0.17",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "foreach",
+ "iterators",
+ "parallel",
+ "utils"
+ ],
+ "Hash": "451e5edf411987991ab6a5410c45011f"
+ },
"dplyr": {
"Package": "dplyr",
"Version": "1.1.4",
@@ -850,6 +952,17 @@
],
"Hash": "3db813596387e90573ad092d5e3fde37"
},
+ "expm": {
+ "Package": "expm",
+ "Version": "1.0-0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "Matrix",
+ "methods"
+ ],
+ "Hash": "a44b2810f36c1cda5d52eee6ec96cafa"
+ },
"fansi": {
"Package": "fansi",
"Version": "1.0.6",
@@ -876,6 +989,16 @@
"Repository": "CRAN",
"Hash": "aa5e1cd11c2d15497494c5292d7ffcc8"
},
+ "fastmatch": {
+ "Package": "fastmatch",
+ "Version": "1.1-4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "8c406b7284bbaef08e01c6687367f195"
+ },
"filelock": {
"Package": "filelock",
"Version": "1.0.3",
@@ -1572,6 +1695,18 @@
],
"Hash": "7ce2733a9826b3aeb1775d56fd305472"
},
+ "maps": {
+ "Package": "maps",
+ "Version": "3.4.2.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "graphics",
+ "utils"
+ ],
+ "Hash": "354a8094c634031421eeb5103f2e1f80"
+ },
"memoise": {
"Package": "memoise",
"Version": "2.0.1",
@@ -1620,6 +1755,16 @@
],
"Hash": "785ef8e22389d4a7634c6c944f2dc07d"
},
+ "mnormt": {
+ "Package": "mnormt",
+ "Version": "2.1.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "c83992ef63553d1e4b97162a4a753470"
+ },
"modelr": {
"Package": "modelr",
"Version": "0.1.11",
@@ -1716,6 +1861,18 @@
],
"Hash": "d413e0fef796c9401a4419485f709ca1"
},
+ "optimParallel": {
+ "Package": "optimParallel",
+ "Version": "1.0-2",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "parallel",
+ "stats"
+ ],
+ "Hash": "5a15e068f0bd9bac4252f8f9e11dc79f"
+ },
"pROC": {
"Package": "pROC",
"Version": "1.18.5",
@@ -1767,6 +1924,62 @@
],
"Hash": "abf0ca85c1c752e0d04f46334e635046"
},
+ "phangorn": {
+ "Package": "phangorn",
+ "Version": "2.12.1",
+ "Source": "Bioconductor",
+ "Repository": "CRAN",
+ "Requirements": [
+ "Matrix",
+ "R",
+ "Rcpp",
+ "ape",
+ "digest",
+ "fastmatch",
+ "generics",
+ "grDevices",
+ "graphics",
+ "igraph",
+ "methods",
+ "parallel",
+ "quadprog",
+ "stats",
+ "utils"
+ ],
+ "Hash": "eea536597b96f3df44a2d6b963ac280e"
+ },
+ "phytools": {
+ "Package": "phytools",
+ "Version": "2.3-0",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "DEoptim",
+ "MASS",
+ "R",
+ "ape",
+ "clusterGeneration",
+ "coda",
+ "combinat",
+ "doParallel",
+ "expm",
+ "foreach",
+ "grDevices",
+ "graphics",
+ "maps",
+ "methods",
+ "mnormt",
+ "nlme",
+ "numDeriv",
+ "optimParallel",
+ "parallel",
+ "phangorn",
+ "scatterplot3d",
+ "stats",
+ "utils"
+ ],
+ "Hash": "592feaaac935ea62afa4399fd83201fd"
+ },
"pillar": {
"Package": "pillar",
"Version": "1.9.0",
@@ -1969,6 +2182,16 @@
],
"Hash": "1cba04a4e9414bdefc9dcaa99649a8dc"
},
+ "quadprog": {
+ "Package": "quadprog",
+ "Version": "1.5-8",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "5f919ae5e7f83a6f91dcf2288943370d"
+ },
"ragg": {
"Package": "ragg",
"Version": "1.3.3",
@@ -2305,6 +2528,19 @@
],
"Hash": "c19df082ba346b0ffa6f833e92de34d1"
},
+ "scatterplot3d": {
+ "Package": "scatterplot3d",
+ "Version": "0.3-44",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "grDevices",
+ "graphics",
+ "stats"
+ ],
+ "Hash": "10ee4b91ec812690bd55d9bf51edccee"
+ },
"secretbase": {
"Package": "secretbase",
"Version": "1.0.3",
@@ -2364,6 +2600,49 @@
],
"Hash": "5c47e84dc0a3ca761ae1d307889e796d"
},
+ "shiny": {
+ "Package": "shiny",
+ "Version": "1.9.1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "R6",
+ "bslib",
+ "cachem",
+ "commonmark",
+ "crayon",
+ "fastmap",
+ "fontawesome",
+ "glue",
+ "grDevices",
+ "htmltools",
+ "httpuv",
+ "jsonlite",
+ "later",
+ "lifecycle",
+ "methods",
+ "mime",
+ "promises",
+ "rlang",
+ "sourcetools",
+ "tools",
+ "utils",
+ "withr",
+ "xtable"
+ ],
+ "Hash": "6a293995a66e12c48d13aa1f957d09c7"
+ },
+ "sourcetools": {
+ "Package": "sourcetools",
+ "Version": "0.1.7-1",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R"
+ ],
+ "Hash": "5f5a7629f956619d519205ec475fe647"
+ },
"sp": {
"Package": "sp",
"Version": "2.1-4",
@@ -2889,6 +3168,18 @@
],
"Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61"
},
+ "xtable": {
+ "Package": "xtable",
+ "Version": "1.8-4",
+ "Source": "Repository",
+ "Repository": "CRAN",
+ "Requirements": [
+ "R",
+ "stats",
+ "utils"
+ ],
+ "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2"
+ },
"yaml": {
"Package": "yaml",
"Version": "2.3.10",