diff --git a/country_outputs/forest_biomass_summary_DRC_output.ipynb b/country_outputs/forest_biomass_summary_DRC_output.ipynb
index 0022339f0354c6c63832273c5fdfc268c0051854..7bdc970e57784fb76f6b40b9fc6355a51a4e0228 100644
--- a/country_outputs/forest_biomass_summary_DRC_output.ipynb
+++ b/country_outputs/forest_biomass_summary_DRC_output.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "markdown",
- "id": "multiple-shift",
+ "id": "domestic-poverty",
"metadata": {},
"source": [
"# ESA Biomass Climate Change Initiative global forest aboveground biomass dataset v2.0 2010, 2017, 2018\n",
@@ -18,7 +18,7 @@
},
{
"cell_type": "markdown",
- "id": "amended-providence",
+ "id": "unlimited-minnesota",
"metadata": {},
"source": [
"#### Install these R packages first, and load them into the R session. Source R script with support functions."
@@ -26,10 +26,175 @@
},
{
"cell_type": "code",
- "execution_count": 14,
- "id": "packed-integral",
- "metadata": {},
- "outputs": [],
+ "execution_count": 1,
+ "id": "exterior-nightmare",
+ "metadata": {
+ "collapsed": true,
+ "jupyter": {
+ "outputs_hidden": true
+ }
+ },
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "Loading required package: raster\n",
+ "\n",
+ "Loading required package: sp\n",
+ "\n",
+ "Loading required package: rgdal\n",
+ "\n",
+ "rgdal: version: 1.5-23, (SVN revision 1121)\n",
+ "Geospatial Data Abstraction Library extensions to R successfully loaded\n",
+ "Loaded GDAL runtime: GDAL 3.3.2, released 2021/09/01\n",
+ "Path to GDAL shared files: /opt/conda/envs/r-with-gdal/share/gdal\n",
+ "GDAL binary built with GEOS: TRUE \n",
+ "Loaded PROJ runtime: Rel. 8.0.1, March 5th, 2021, [PJ_VERSION: 801]\n",
+ "Path to PROJ shared files: /opt/conda/envs/r-with-gdal/share/proj\n",
+ "PROJ CDN enabled: TRUE\n",
+ "Linking to sp version:1.4-5\n",
+ "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n",
+ "use options(\"rgdal_show_exportToProj4_warnings\"=\"none\") before loading rgdal.\n",
+ "\n",
+ "Loading required package: rgeos\n",
+ "\n",
+ "Warning message in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :\n",
+ "“there is no package called ‘rgeos’â€\n",
+ "also installing the dependencies ‘foreign’, ‘maptools’, ‘maps’\n",
+ "\n",
+ "\n",
+ "Updating HTML index of packages in '.Library'\n",
+ "\n",
+ "Making 'packages.html' ...\n",
+ " done\n",
+ "\n",
+ "rgeos version: 0.5-8, (SVN revision 679)\n",
+ " GEOS runtime version: 3.9.1-CAPI-1.14.2 \n",
+ " Please note that rgeos will be retired by the end of 2023,\n",
+ "plan transition to sf functions using GEOS at your earliest convenience.\n",
+ " GEOS using OverlayNG\n",
+ " Linking to sp version: 1.4-5 \n",
+ " Polygon checking: TRUE \n",
+ "\n",
+ "\n",
+ "Loading required package: geosphere\n",
+ "\n",
+ "Warning message in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :\n",
+ "“there is no package called ‘geosphere’â€\n",
+ "Updating HTML index of packages in '.Library'\n",
+ "\n",
+ "Making 'packages.html' ...\n",
+ " done\n",
+ "\n",
+ "Loading required package: RColorBrewer\n",
+ "\n",
+ "Loading required package: gdalUtils\n",
+ "\n",
+ "Loading required package: ff\n",
+ "\n",
+ "Warning message in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :\n",
+ "“there is no package called ‘ff’â€\n",
+ "also installing the dependency ‘biglm’\n",
+ "\n",
+ "\n",
+ "Updating HTML index of packages in '.Library'\n",
+ "\n",
+ "Making 'packages.html' ...\n",
+ " done\n",
+ "\n",
+ "\n",
+ "Attaching package: ‘bit’\n",
+ "\n",
+ "\n",
+ "The following object is masked from ‘package:rgeos’:\n",
+ "\n",
+ " symdiff\n",
+ "\n",
+ "\n",
+ "The following object is masked from ‘package:base’:\n",
+ "\n",
+ " xor\n",
+ "\n",
+ "\n",
+ "Attaching package ff\n",
+ "\n",
+ "- getOption(\"fftempdir\")==\"/tmp/RtmpPRaI0t/ff\"\n",
+ "\n",
+ "\n",
+ "- getOption(\"ffextension\")==\"ff\"\n",
+ "\n",
+ "\n",
+ "- getOption(\"ffdrop\")==TRUE\n",
+ "\n",
+ "\n",
+ "- getOption(\"fffinonexit\")==TRUE\n",
+ "\n",
+ "\n",
+ "- getOption(\"ffpagesize\")==65536\n",
+ "\n",
+ "\n",
+ "- getOption(\"ffcaching\")==\"mmnoflush\" -- consider \"ffeachflush\" if your system stalls on large writes\n",
+ "\n",
+ "\n",
+ "- getOption(\"ffbatchbytes\")==16777216 -- consider a different value for tuning your system\n",
+ "\n",
+ "\n",
+ "- getOption(\"ffmaxbytes\")==536870912 -- consider a different value for tuning your system\n",
+ "\n",
+ "\n",
+ "\n",
+ "Attaching package: ‘ff’\n",
+ "\n",
+ "\n",
+ "The following objects are masked from ‘package:raster’:\n",
+ "\n",
+ " filename, is.factor, ncol<-, nrow<-\n",
+ "\n",
+ "\n",
+ "The following objects are masked from ‘package:utils’:\n",
+ "\n",
+ " write.csv, write.csv2\n",
+ "\n",
+ "\n",
+ "The following objects are masked from ‘package:base’:\n",
+ "\n",
+ " is.factor, is.ordered\n",
+ "\n",
+ "\n",
+ "Loading required package: parallel\n",
+ "\n",
+ "Loading required package: snow\n",
+ "\n",
+ "Warning message in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :\n",
+ "“there is no package called ‘snow’â€\n",
+ "Warning message:\n",
+ "“dependency ‘nws’ is not availableâ€\n",
+ "also installing the dependencies ‘Rmpi’, ‘rlecuyer’\n",
+ "\n",
+ "\n",
+ "Warning message in install.packages(x, dependencies = TRUE):\n",
+ "“installation of package ‘Rmpi’ had non-zero exit statusâ€\n",
+ "Updating HTML index of packages in '.Library'\n",
+ "\n",
+ "Making 'packages.html' ...\n",
+ " done\n",
+ "\n",
+ "\n",
+ "Attaching package: ‘snow’\n",
+ "\n",
+ "\n",
+ "The following objects are masked from ‘package:parallel’:\n",
+ "\n",
+ " clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n",
+ " clusterExport, clusterMap, clusterSplit, makeCluster, parApply,\n",
+ " parCapply, parLapply, parRapply, parSapply, splitIndices,\n",
+ " stopCluster\n",
+ "\n",
+ "\n"
+ ]
+ }
+ ],
"source": [
"packages <- c(\"raster\", \"rgdal\", \"rgeos\", \"geosphere\",\"RColorBrewer\",\"gdalUtils\",\"ff\",\"parallel\", \"snow\")\n",
"package.check <- lapply(packages, FUN = function(x) {\n",
@@ -44,7 +209,7 @@
},
{
"cell_type": "markdown",
- "id": "floral-miracle",
+ "id": "united-district",
"metadata": {},
"source": [
"#### Set the path to the CCI Biomass data folder & read in world countries shapefile"
@@ -52,14 +217,9 @@
},
{
"cell_type": "code",
- "execution_count": 16,
- "id": "sunset-celebrity",
- "metadata": {
- "collapsed": true,
- "jupyter": {
- "outputs_hidden": true
- }
- },
+ "execution_count": 2,
+ "id": "searching-deployment",
+ "metadata": {},
"outputs": [
{
"name": "stdout",
@@ -101,7 +261,7 @@
},
{
"cell_type": "markdown",
- "id": "smaller-accent",
+ "id": "fifteen-wedding",
"metadata": {},
"source": [
"#### Generate 10x10 degree WGS84 grid that the CCI Biomass and Hansen Forest Cover products are tiled on"
@@ -109,8 +269,8 @@
},
{
"cell_type": "code",
- "execution_count": 17,
- "id": "written-chancellor",
+ "execution_count": 3,
+ "id": "sacred-rings",
"metadata": {},
"outputs": [
{
@@ -132,7 +292,7 @@
},
{
"cell_type": "markdown",
- "id": "minimal-think",
+ "id": "german-device",
"metadata": {},
"source": [
"#### Print out country names in Africa to select from"
@@ -140,8 +300,8 @@
},
{
"cell_type": "code",
- "execution_count": 22,
- "id": "compressed-population",
+ "execution_count": 6,
+ "id": "developmental-aruba",
"metadata": {},
"outputs": [
{
@@ -449,7 +609,7 @@
},
{
"cell_type": "markdown",
- "id": "filled-german",
+ "id": "bigger-racing",
"metadata": {},
"source": [
"#### Select a country in Africa to plot with corresponding data tiles"
@@ -457,8 +617,8 @@
},
{
"cell_type": "code",
- "execution_count": 27,
- "id": "offshore-allergy",
+ "execution_count": 7,
+ "id": "chronic-packing",
"metadata": {},
"outputs": [
{
@@ -509,7 +669,7 @@
" tiles <- cci_tiles[intersecting,]\n",
" }\n",
"\n",
- "plot(Africa, col=\"gray\", main=iso3)\n",
+ "plot(Cont, col=\"gray\", main=iso3)\n",
"plot(cci_tiles, lty=2, add=T)\n",
"plot(tiles, lwd=2, border=\"red\", add=T)\n",
"plot(aoi, col=\"red\", add=T)"
@@ -517,8 +677,8 @@
},
{
"cell_type": "code",
- "execution_count": 29,
- "id": "expected-thumbnail",
+ "execution_count": 8,
+ "id": "likely-reflection",
"metadata": {},
"outputs": [],
"source": [
@@ -528,7 +688,7 @@
},
{
"cell_type": "markdown",
- "id": "latin-hardware",
+ "id": "emotional-consistency",
"metadata": {},
"source": [
"#### Read in the CCI Biomass data for this AOI from the downloaded CCI Biomass tiles, mosaicing multiple tiles as necessary"
@@ -536,8 +696,8 @@
},
{
"cell_type": "code",
- "execution_count": 30,
- "id": "classical-remainder",
+ "execution_count": 9,
+ "id": "honey-stewart",
"metadata": {},
"outputs": [
{
@@ -548,7 +708,7 @@
"resolution : 0.0008888889, 0.0008888889 (x, y)\n",
"extent : 12.21067, 31.28089, -13.45867, 5.375111 (xmin, xmax, ymin, ymax)\n",
"crs : +proj=longlat +datum=WGS84 +no_defs \n",
- "source : r_tmp_2021-10-18_180804_880_66008.tif \n",
+ "source : r_tmp_2021-10-25_142438_1337_91161.tif \n",
"names : agbd_2020, agbd_sd_2020 \n",
"min values : 0, 0 \n",
"max values : 552, 1068 \n"
@@ -565,7 +725,7 @@
},
{
"cell_type": "markdown",
- "id": "interpreted-package",
+ "id": "careful-delivery",
"metadata": {},
"source": [
"#### Read in the NCEO Biomass data for this AOI from the downloaded data. NCEO data is stored as a single file for the continent of Africa, rather than multiple tiles."
@@ -573,10 +733,36 @@
},
{
"cell_type": "code",
- "execution_count": null,
- "id": "polished-offset",
+ "execution_count": 13,
+ "id": "fatty-activation",
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "[1] \"/projects/shared-buckets/minord/data/nceo_africa_biomass/AGB_map_2017v0.tif\" \n",
+ "[2] \"/projects/shared-buckets/minord/data/nceo_africa_biomass/SD_AGB_map_2017v0.tif\"\n"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "class : RasterBrick \n",
+ "dimensions : 20966, 21228, 445066248, 2 (nrow, ncol, ncell, nlayers)\n",
+ "resolution : 0.0008983153, 0.0008983153 (x, y)\n",
+ "extent : 12.2108, 31.28024, -13.45856, 5.375519 (xmin, xmax, ymin, ymax)\n",
+ "crs : +proj=longlat +datum=WGS84 +no_defs \n",
+ "source : r_tmp_2021-10-25_145108_1337_50743.grd \n",
+ "names : agbd_2017, agbd_sd_2017 \n",
+ "min values : 0, 0 \n",
+ "max values : 730, 310 \n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"file_name <- paste0('AGB_map_2017v0.tif')\n",
"file_name_sd <- paste0('SD_AGB_map_2017v0.tif')\n",
@@ -609,11 +795,47 @@
},
{
"cell_type": "code",
- "execution_count": null,
- "id": "injured-ability",
+ "execution_count": 14,
+ "id": "hawaiian-bargain",
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "ename": "ERROR",
+ "evalue": "Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': invalid layer names\n",
+ "output_type": "error",
+ "traceback": [
+ "Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': invalid layer names\nTraceback:\n",
+ "1. plot(cci$agbd_2017, main = \"CCI AGBD 2017\", zlim = c(0, 700))",
+ "2. cci$agbd_2017",
+ "3. cci$agbd_2017",
+ "4. x[[name]]",
+ "5. x[[name]]",
+ "6. .local(x, i, j, ...)",
+ "7. subset(x, i, drop = drop)",
+ "8. subset(x, i, drop = drop)",
+ "9. .local(x, ...)",
+ "10. stop(\"invalid layer names\")",
+ "11. .handleSimpleError(function (cond) \n . .Internal(C_tryCatchHelper(addr, 1L, cond)), \"invalid layer names\", \n . base::quote(.local(x, ...)))",
+ "12. h(simpleError(msg, call))"
+ ]
+ },
+ {
+ "ename": "ERROR",
+ "evalue": "Error in polypath(x = mcrds[, 1], y = mcrds[, 2], border = border, col = col, : plot.new has not been called yet\n",
+ "output_type": "error",
+ "traceback": [
+ "Error in polypath(x = mcrds[, 1], y = mcrds[, 2], border = border, col = col, : plot.new has not been called yet\nTraceback:\n",
+ "1. plot(aoi, add = T)",
+ "2. plot(aoi, add = T)",
+ "3. plot.SpatialPolygons(x, ...)",
+ "4. .polygonRingHoles(polys[[j]], col = col[j], border = border[j], \n . xpd = xpd, pbg = pbg, lty = lty, ..., usePolypath = usePolypath, \n . rule = rule)",
+ "5. polypath(x = mcrds[, 1], y = mcrds[, 2], border = border, col = col, \n . lty = lty, rule = rule, xpd = xpd, ...)"
+ ]
+ }
+ ],
"source": [
+ "# Fix this cell\n",
+ "\n",
"par(mfrow=c(2,2), mai=c(0.5,0.5,0.5,0.5))\n",
"options(repr.plot.width=10, repr.plot.height=10)\n",
"plot(cci$agbd_2017, main=\"CCI AGBD 2017\", zlim = c(0,700)); plot(aoi, add=T)\n",
@@ -624,7 +846,7 @@
},
{
"cell_type": "markdown",
- "id": "compound-louisville",
+ "id": "caroline-infrared",
"metadata": {},
"source": [
"#### Calculate total aboveground biomass and average aboveground biomass density for 2017 CCI and NCEO biomass for the selected country"
@@ -633,7 +855,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "inner-majority",
+ "id": "sophisticated-photographer",
"metadata": {},
"outputs": [],
"source": [
@@ -777,7 +999,7 @@
},
{
"cell_type": "markdown",
- "id": "impossible-banks",
+ "id": "continuing-crest",
"metadata": {},
"source": [
"#### Print out basic forest aboveground biomass statistics for the selected country\n",
@@ -787,7 +1009,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "endless-platinum",
+ "id": "professional-vertical",
"metadata": {},
"outputs": [],
"source": [
@@ -798,7 +1020,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "young-repeat",
+ "id": "premier-wallace",
"metadata": {},
"outputs": [],
"source": [
@@ -832,7 +1054,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "architectural-halloween",
+ "id": "statutory-chess",
"metadata": {},
"outputs": [],
"source": [
@@ -843,7 +1065,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "constitutional-output",
+ "id": "dedicated-grass",
"metadata": {},
"outputs": [],
"source": [
@@ -853,7 +1075,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "typical-falls",
+ "id": "signal-tractor",
"metadata": {},
"outputs": [],
"source": [
@@ -863,7 +1085,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "distant-scenario",
+ "id": "focal-trunk",
"metadata": {},
"outputs": [],
"source": []
@@ -871,7 +1093,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "nervous-expert",
+ "id": "several-spokesman",
"metadata": {},
"outputs": [],
"source": []