finally got a set of models to run, very preliminary.

CU-ESIIL · Nov 19, 2024 · 377687d · 377687d
1 parent a5fe037
commit 377687d
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Showing 8 changed files with 1,509 additions and 375 deletions.
diff --git a/.gitignore b/.gitignore
@@ -46,3 +46,9 @@ po/*~
 
 # RStudio Connect folder
 rsconnect/
+
+# Some GIS files I dont want on github
+processing/gis/*/
+processing/gis/gssurgo_1km.nc
+processing/gis/gssurgo_1km.nc.aux.xml
+processing/gis/gis_data_1km.nc
diff --git a/analysis/requirements.yml → analysis/biotic_analysis.yml b/analysis/requirements.yml → analysis/biotic_analysis.yml
@@ -1,8 +1,11 @@
-name: base
+name: biotic_analysis
 channels:
   - conda-forge
+  - r
 dependencies:
+  - jupyter
   - r-base
+  - r-irkernel
   - r-cairo
   - r-dplyr
   - r-tidyr
@@ -11,5 +14,11 @@ dependencies:
   - r-ggplot2
   - r-rnaturalearth
   - r-rnaturalearthdata
+  - r-devtools
   - r-sf
   - r-terra
+  - r-rastervis
+  - r-tidyterra
+  - r-gdalcubes
+  - r-car
+  - r-corrplot
diff --git a/analysis/globalamfungi_analysis.ipynb b/analysis/globalamfungi_analysis.ipynb
diff --git a/processing/amfungi_lsu.duckdb.wal b/processing/amfungi_lsu.duckdb.wal
diff --git a/processing/daymet/daymet.ipynb b/processing/daymet/daymet.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {
     "vscode": {
      "languageId": "r"
@@ -44,19 +44,136 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "metadata": {
     "vscode": {
      "languageId": "r"
     }
    },
    "outputs": [],
    "source": [
-    "if(!dir.exists(\"/data-store/iplant/home/rjramos/daymet\")) dir.create(\"/data-store/iplant/home/rjramos/daymet\")\n",
+    "download_dir <- \"../gis/daymet/\"\n",
+    "# download_dir <- \"/data-store/iplant/home/rjramos/daymet/\"\n",
+    "if(!dir.exists(download_dir)) dir.create(download_dir)\n",
     "url <- \"https://thredds.daac.ornl.gov/thredds/fileServer/ornldaac/2130/\" # base url for thredds data server\n",
     "options(timeout = 1200) # Set the maximum download time to 20min"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Warning message in download.file(url = x, destfile = paste0(download_dir, last(unlist(strsplit(x, :\n",
+      "“downloaded length 310066927 != reported length 442579946”\n",
+      "Warning message in download.file(url = x, destfile = paste0(download_dir, last(unlist(strsplit(x, :\n",
+      "“URL 'https://thredds.daac.ornl.gov/thredds/fileServer/ornldaac/2130/daymet_v4_prcp_annttl_na_2015.nc': Timeout of 1200 seconds was reached”\n"
+     ]
+    },
+    {
+     "ename": "ERROR",
+     "evalue": "\u001b[1m\u001b[33mError\u001b[39m in `map()`:\u001b[22m\n\u001b[1m\u001b[22m\u001b[36mℹ\u001b[39m In index: 36.\n\u001b[1mCaused by error in `download.file()`:\u001b[22m\n\u001b[33m!\u001b[39m download from 'https://thredds.daac.ornl.gov/thredds/fileServer/ornldaac/2130/daymet_v4_prcp_annttl_na_2015.nc' failed\n",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1m\u001b[33mError\u001b[39m in `map()`:\u001b[22m\n\u001b[1m\u001b[22m\u001b[36mℹ\u001b[39m In index: 36.\n\u001b[1mCaused by error in `download.file()`:\u001b[22m\n\u001b[33m!\u001b[39m download from 'https://thredds.daac.ornl.gov/thredds/fileServer/ornldaac/2130/daymet_v4_prcp_annttl_na_2015.nc' failed\nTraceback:\n",
+      "1. map_(\"list\", .x, .f, ..., .progress = .progress)",
+      "2. with_indexed_errors(i = i, names = names, error_call = .purrr_error_call, \n .     call_with_cleanup(map_impl, environment(), .type, .progress, \n .         n, names, i))",
+      "3. withCallingHandlers(expr, error = function(cnd) {\n .     if (i == 0L) {\n .     }\n .     else {\n .         message <- c(i = \"In index: {i}.\")\n .         if (!is.null(names) && !is.na(names[[i]]) && names[[i]] != \n .             \"\") {\n .             name <- names[[i]]\n .             message <- c(message, i = \"With name: {name}.\")\n .         }\n .         else {\n .             name <- NULL\n .         }\n .         cli::cli_abort(message, location = i, name = name, parent = cnd, \n .             call = error_call, class = \"purrr_error_indexed\")\n .     }\n . })",
+      "4. call_with_cleanup(map_impl, environment(), .type, .progress, \n .     n, names, i)",
+      "5. .f(.x[[i]], ...)",
+      "6. download.file(url = x, destfile = paste0(download_dir, last(unlist(strsplit(x, \n .     \"/\")))))",
+      "7. .handleSimpleError(function (cnd) \n . {\n .     if (i == 0L) {\n .     }\n .     else {\n .         message <- c(i = \"In index: {i}.\")\n .         if (!is.null(names) && !is.na(names[[i]]) && names[[i]] != \n .             \"\") {\n .             name <- names[[i]]\n .             message <- c(message, i = \"With name: {name}.\")\n .         }\n .         else {\n .             name <- NULL\n .         }\n .         cli::cli_abort(message, location = i, name = name, parent = cnd, \n .             call = error_call, class = \"purrr_error_indexed\")\n .     }\n . }, \"download from 'https://thredds.daac.ornl.gov/thredds/fileServer/ornldaac/2130/daymet_v4_prcp_annttl_na_2015.nc' failed\", \n .     base::quote(download.file(url = x, destfile = paste0(download_dir, \n .         last(unlist(strsplit(x, \"/\")))))))",
+      "8. h(simpleError(msg, call))",
+      "9. cli::cli_abort(message, location = i, name = name, parent = cnd, \n .     call = error_call, class = \"purrr_error_indexed\")",
+      "10. rlang::abort(message, ..., call = call, use_cli_format = TRUE, \n  .     .frame = .frame)",
+      "11. signal_abort(cnd, .file)",
+      "12. signalCondition(cnd)"
+     ]
+    }
+   ],
+   "source": [
+    "prcp_files <- map(\n",
+    "  seq(1980, 2022, 1),\n",
+    "  \\(x) paste0(url, \"daymet_v4_prcp_annttl_na_\", x, \".nc\")\n",
+    ")\n",
+    "map(\n",
+    "  prcp_files,\n",
+    "  function(x) {\n",
+    "    download.file(\n",
+    "      url = x,\n",
+    "      destfile = paste0(\n",
+    "        download_dir,\n",
+    "        last(unlist(strsplit(x, \"/\")))\n",
+    "      )\n",
+    "    )\n",
+    "  }\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "prcp_files <- map(\n",
+    "  seq(1980, 2022, 1),\n",
+    "  \\(x) paste0(url, \"daymet_v4_swe_annavg_na_\", x, \".nc\")\n",
+    ")\n",
+    "map(\n",
+    "  prcp_files,\n",
+    "  function(x) {\n",
+    "    download.file(\n",
+    "      url = x,\n",
+    "      destfile = paste0(\n",
+    "        download_dir,\n",
+    "        last(unlist(strsplit(x, \"/\")))\n",
+    "      )\n",
+    "    )\n",
+    "  }\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "vscode": {
+     "languageId": "r"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "prcp_files <- map(\n",
+    "  seq(1980, 2022, 1),\n",
+    "  \\(x) paste0(url, \"daymet_v4_tmax_annavg_na_\", x, \".nc\")\n",
+    ")\n",
+    "map(\n",
+    "  prcp_files,\n",
+    "  function(x) {\n",
+    "    download.file(\n",
+    "      url = x,\n",
+    "      destfile = paste0(\n",
+    "        download_dir,\n",
+    "        last(unlist(strsplit(x, \"/\")))\n",
+    "      )\n",
+    "    )\n",
+    "  }\n",
+    ")"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 3,
@@ -344,90 +461,6 @@
      "output_type": "display_data"
     }
    ],
-   "source": [
-    "prcp_files <- map(\n",
-    "  seq(1980, 2022, 1),\n",
-    "  \\(x) paste0(url, \"daymet_v4_prcp_annttl_na_\", x, \".nc\")\n",
-    ")\n",
-    "map(\n",
-    "  prcp_files,\n",
-    "  function(x) {\n",
-    "    download.file(\n",
-    "      url = x,\n",
-    "      destfile = paste0(\n",
-    "        \"/data-store/iplant/home/rjramos/daymet/\",\n",
-    "        last(unlist(strsplit(x, \"/\")))\n",
-    "      )\n",
-    "    )\n",
-    "  }\n",
-    ")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "prcp_files <- map(\n",
-    "  seq(1980, 2022, 1),\n",
-    "  \\(x) paste0(url, \"daymet_v4_swe_annavg_na_\", x, \".nc\")\n",
-    ")\n",
-    "map(\n",
-    "  prcp_files,\n",
-    "  function(x) {\n",
-    "    download.file(\n",
-    "      url = x,\n",
-    "      destfile = paste0(\n",
-    "        \"/data-store/iplant/home/rjramos/daymet/\",\n",
-    "        last(unlist(strsplit(x, \"/\")))\n",
-    "      )\n",
-    "    )\n",
-    "  }\n",
-    ")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "prcp_files <- map(\n",
-    "  seq(1980, 2022, 1),\n",
-    "  \\(x) paste0(url, \"daymet_v4_tmax_annavg_na_\", x, \".nc\")\n",
-    ")\n",
-    "map(\n",
-    "  prcp_files,\n",
-    "  function(x) {\n",
-    "    download.file(\n",
-    "      url = x,\n",
-    "      destfile = paste0(\n",
-    "        \"/data-store/iplant/home/rjramos/daymet/\",\n",
-    "        last(unlist(strsplit(x, \"/\")))\n",
-    "      )\n",
-    "    )\n",
-    "  }\n",
-    ")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "vscode": {
-     "languageId": "r"
-    }
-   },
-   "outputs": [],
    "source": [
     "prcp_files <- map(\n",
     "  seq(1980, 2022, 1),\n",
@@ -439,7 +472,7 @@
     "    download.file(\n",
     "      url = x,\n",
     "      destfile = paste0(\n",
-    "        \"/data-store/iplant/home/rjramos/daymet/\",\n",
+    "        download_dir,\n",
     "        last(unlist(strsplit(x, \"/\")))\n",
     "      )\n",
     "    )\n",
@@ -449,7 +482,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 6,
    "metadata": {
     "vscode": {
      "languageId": "r"
@@ -745,7 +778,7 @@
     "    download.file(\n",
     "      url = x,\n",
     "      destfile = paste0(\n",
-    "        \"/data-store/iplant/home/rjramos/daymet/\",\n",
+    "        download_dir,\n",
     "        last(unlist(strsplit(x, \"/\")))\n",
     "      )\n",
     "    )\n",
@@ -766,7 +799,7 @@
    "mimetype": "text/x-r-source",
    "name": "R",
    "pygments_lexer": "r",
-   "version": "4.3.3"
+   "version": "4.4.1"
   }
  },
  "nbformat": 4,

diff --git a/processing/daymet/daymet.yml b/processing/daymet/daymet.yml
@@ -0,0 +1,13 @@
+name: daymet
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - jupyter
+  - r-base
+  - r-irkernel
+  - r-languageserver
+  - r-Cairo
+  - r-dplyr
+  - r-tidyr
+  - r-purrr
diff --git a/processing/gis/gis.ipynb b/processing/gis/gis.ipynb
diff --git a/processing/requirements.yml b/processing/requirements.yml