Replace WoSIS_Latest_With_R.R

R_scripts/WoSIS_Latest_With_R.R

-## ----setup, include=FALSE---------------------------------------------------------------------------------------------------------
+## ----setup, include=FALSE----------------------------------------------------------------------------------------------
 knitr::opts_chunk$set(echo = TRUE, warnings = FALSE, purl = FALSE)
 
 
-## ----load.package-----------------------------------------------------------------------------------------------------------------
+## ----load.package------------------------------------------------------------------------------------------------------
 library(rgdal)          # GDAL access from R
 library(gdalUtils)      # wrappers for GDAL utility programs that could be
                         #  called from the command line
@@ -13,7 +13,7 @@ library(ggplot2)        # gpplot graphics
 
 
 
-## ---------------------------------------------------------------------------------------------------------------------------------
+## ----------------------------------------------------------------------------------------------------------------------
 drivers <- ogrDrivers()
 # print(drivers)
 ix <- grep("GPKG", drivers$name,  fixed=TRUE)
@@ -22,18 +22,18 @@ ix <- grep("ESRI", drivers$name,  fixed=TRUE)
 drivers[ix,]
 
 
-## ----specify.wfs.address----------------------------------------------------------------------------------------------------------
-wfs <- "WFS:http://maps.isric.org/mapserv?map=/map/wosis_latest.map"
+## ----specify.wfs.address-----------------------------------------------------------------------------------------------
+wfs <- "WFS:https://maps.isric.org/mapserv?map=/map/wosis_latest.map"
 
 
-## ----ogrinfo.wfs------------------------------------------------------------------------------------------------------------------
+## ----ogrinfo.wfs-------------------------------------------------------------------------------------------------------
 system.time(
   layers.info <- ogrinfo(wfs, ro=TRUE, so=TRUE, q=TRUE)
 )
 cat(layers.info, sep = "\n")
 
 
-## ----ogrinfo.site-----------------------------------------------------------------------------------------------------------------
+## ----ogrinfo.site------------------------------------------------------------------------------------------------------
 system.time(
   profiles.info <-
     ogrinfo(wfs, layer="ms:wosis_latest_profiles",
@@ -42,7 +42,7 @@ system.time(
 cat(profiles.info, sep="\n")
 
 
-## ----ogrinfo.eu.profiles.1--------------------------------------------------------------------------------------------------------
+## ----ogrinfo.eu.profiles.1---------------------------------------------------------------------------------------------
 system.time(
   central.eu.profiles.info <-
     ogrinfo(wfs, ro=TRUE, so=TRUE, q=FALSE,
@@ -53,7 +53,7 @@ head(central.eu.profiles.info, 8)
 central.eu.profiles.info[41:60]
 
 
-## ----ogrinfo.eu.profiles.2--------------------------------------------------------------------------------------------------------
+## ----ogrinfo.eu.profiles.2---------------------------------------------------------------------------------------------
 ix.f <- grep("Feature Count", central.eu.profiles.info)
 central.eu.profiles.info[ix.f]
 ix.e <- grep("Extent", central.eu.profiles.info)
@@ -62,13 +62,13 @@ ix.g <- grep("GEOGCRS", central.eu.profiles.info)
 cat(paste(central.eu.profiles.info[ix.g:(ix.g+17)], collapse="\n"))
 
 
-## ----show.fields------------------------------------------------------------------------------------------------------------------
+## ----show.fields-------------------------------------------------------------------------------------------------------
 ix.p <- grep("Geometry Column", central.eu.profiles.info)
 n <- length(central.eu.profiles.info)
 central.eu.profiles.info[ix.p+1:n]
 
 
-## ----ogrinfo.india.profiles-------------------------------------------------------------------------------------------------------
+## ----ogrinfo.india.profiles--------------------------------------------------------------------------------------------
 system.time(
   india.profiles.info <-
     ogrinfo(wfs, ro=TRUE, so=TRUE, q=FALSE,
@@ -77,14 +77,14 @@ system.time(
 )
 
 
-## ----ogrinfo.india.profiles.2-----------------------------------------------------------------------------------------------------
+## ----ogrinfo.india.profiles.2------------------------------------------------------------------------------------------
 ix.f <- grep("Feature Count", india.profiles.info)
 india.profiles.info[ix.f]
 ix.e <- grep("Extent", india.profiles.info)
 india.profiles.info[ix.e]
 
 
-## ----ogrinfo.properties, warnings-------------------------------------------------------------------------------------------------
+## ----ogrinfo.properties, warnings--------------------------------------------------------------------------------------
 system.time(
   property.info <- ogrinfo(wfs, layer="ms:wosis_latest_bdfi33",
                            ro=TRUE, so=TRUE, q=FALSE)
@@ -94,7 +94,7 @@ ix.f <- grep("Feature Count", property.info)
 property.info[ix.f]
 
 
-## ----ogrinfo.bd.india-------------------------------------------------------------------------------------------------------------
+## ----ogrinfo.bd.india--------------------------------------------------------------------------------------------------
 system.time(
   bd.india.info <- ogrinfo(wfs, layer="ms:wosis_latest_bdfi33",
                            where="country_name='India' AND upper_depth > 100",
@@ -106,12 +106,12 @@ bd.india.info[ix.f]
                                  split=": ", fixed=TRUE)[[1]][2]))
 
 
-## ----setup.local.dir--------------------------------------------------------------------------------------------------------------
+## ----setup.local.dir---------------------------------------------------------------------------------------------------
 wosis.dir.name <- "./wosis_latest"
 if (!file.exists(wosis.dir.name)) dir.create(wosis.dir.name)
 
 
-## ----download.profiles------------------------------------------------------------------------------------------------------------
+## ----download.profiles-------------------------------------------------------------------------------------------------
 layer.name <- "wosis_latest_profiles"
 system.time(
   ogr2ogr(src=wfs,
@@ -123,7 +123,7 @@ system.time(
 )
 
 
-## ----download.profiles.india------------------------------------------------------------------------------------------------------
+## ----download.profiles.india-------------------------------------------------------------------------------------------
 wosis.dir.name.india <- "./wosis_latest/india"
 if (!file.exists(wosis.dir.name.india)) dir.create(wosis.dir.name.india)
 layer.name <- "wosis_latest_profiles"
@@ -138,7 +138,7 @@ system.time(
 )
 
 
-## ----import.profiles--------------------------------------------------------------------------------------------------------------
+## ----import.profiles---------------------------------------------------------------------------------------------------
 layer.name <- "ms_wosis_latest_profiles"
 profiles <- readOGR(dsn=wosis.dir.name, layer=layer.name,
                 stringsAsFactors = FALSE)
@@ -148,13 +148,13 @@ names(profiles@data)
 head(profiles@data, 1)
 
 
-## ----import.profiles.india--------------------------------------------------------------------------------------------------------
+## ----import.profiles.india---------------------------------------------------------------------------------------------
 profiles.india <- readOGR(dsn=wosis.dir.name.india, layer=layer.name,
                 stringsAsFactors = FALSE)
 dim(profiles.india)
 
 
-## ----download.bd------------------------------------------------------------------------------------------------------------------
+## ----download.bd-------------------------------------------------------------------------------------------------------
 layer.name <- "wosis_latest_bdfi33"
 system.time(
   ogr2ogr(src=wfs,
@@ -166,7 +166,7 @@ system.time(
 )
 
 
-## ----download.bd.india------------------------------------------------------------------------------------------------------------
+## ----download.bd.india-------------------------------------------------------------------------------------------------
 system.time(
   ogr2ogr(src=wfs,
           dst=wosis.dir.name.india,
@@ -178,7 +178,7 @@ system.time(
 )
 
 
-## ----import.bd--------------------------------------------------------------------------------------------------------------------
+## ----import.bd---------------------------------------------------------------------------------------------------------
 # here strings are just that, not to be interpreted as R factors
 layer.name <- "ms_wosis_latest_bdfi33"
 bd33 <- readOGR(dsn=wosis.dir.name, layer=layer.name,
@@ -188,15 +188,15 @@ names(bd33@data)
 head(bd33@data, 1)
 
 
-## ----head.bd----------------------------------------------------------------------------------------------------------------------
+## ----head.bd-----------------------------------------------------------------------------------------------------------
 head(bd33@data$bdfi33_val)
 
 
-## ----example.bd-------------------------------------------------------------------------------------------------------------------
+## ----example.bd--------------------------------------------------------------------------------------------------------
 bd33@data[75:80, c("profile_id","upper_dept","lower_dept","bdfi33_val","bdfi33_v_1")]
 
 
-## ----import.bd.india--------------------------------------------------------------------------------------------------------------
+## ----import.bd.india---------------------------------------------------------------------------------------------------
 layer.name <- "ms_wosis_latest_bdfi33"
 bd33.india <- readOGR(dsn=wosis.dir.name.india, layer=layer.name,
                 stringsAsFactors = FALSE)
@@ -208,11 +208,7 @@ hist(bd33.india@data$bdfi33_v_1, main="Bulk density, Layers in India",
      xlab="g cm-3")
 
 
-## ---------------------------------------------------------------------------------------------------------------------------------
-
-
-
-## ----download.profiles.csv--------------------------------------------------------------------------------------------------------
+## ----download.profiles.csv---------------------------------------------------------------------------------------------
 wosis.dir.name.ceu <- "./wosis_latest/central_europe"
 if (!file.exists(wosis.dir.name.ceu)) dir.create(wosis.dir.name.ceu)
 src.layer.name <- "ms:wosis_latest_profiles"
@@ -228,7 +224,7 @@ ogr2ogr(src=wfs,
 round(file.info(dst.target.name)$size/1024,1)
 
 
-## ----import.profiles.csv----------------------------------------------------------------------------------------------------------
+## ----import.profiles.csv-----------------------------------------------------------------------------------------------
 layer.name <- "wosis_latest_profiles_ceu"
 system.time(
   profiles.ceu <- read.csv(paste0(wosis.dir.name.ceu, "/",layer.name,".csv"),
@@ -237,7 +233,7 @@ system.time(
 names(profiles.ceu)
 
 
-## ----download.bd.csv--------------------------------------------------------------------------------------------------------------
+## ----download.bd.csv---------------------------------------------------------------------------------------------------
 src.layer.name <- "wosis_latest_bdfi33"
 dst.layer.name <- "wosis_latest_bdfi33"
 (dst.target.name <- paste0(wosis.dir.name,"/",dst.layer.name,".csv"))
@@ -247,10 +243,10 @@ ogr2ogr(src=wfs,
         layer=src.layer.name,
         f="CSV",
         overwrite=TRUE)
-file.info(dst.target.name)$size
+file.info(dst.target.name)$size/1024/1024
 
 
-## ----import.bd.csv----------------------------------------------------------------------------------------------------------------
+## ----import.bd.csv-----------------------------------------------------------------------------------------------------
 layer.name <- "wosis_latest_bdfi33"
 system.time(
   bd33.pts <- read.csv(file=paste0(wosis.dir.name,"/",layer.name,".csv"),
@@ -260,7 +256,7 @@ dim(bd33.pts)
 names(bd33.pts)
 
 
-## ----download.profile.gpkg--------------------------------------------------------------------------------------------------------
+## ----download.profile.gpkg---------------------------------------------------------------------------------------------
 layer.name <- "wosis_latest_profiles"
 (dst.target.name <- paste0(wosis.dir.name,"/", layer.name, ".gpkg"))
 if (file.exists(dst.target.name)) { file.remove(dst.target.name) }
@@ -272,52 +268,53 @@ system.time(
           overwrite=TRUE,
           skipfailures=TRUE)
 )
+file.info(dst.target.name)$size/1024/1024
 
 
-## ----read.profile.gpkg------------------------------------------------------------------------------------------------------------
+## ----read.profile.gpkg-------------------------------------------------------------------------------------------------
 profiles.gpkg <- st_read(dst.target.name)
 class(profiles.gpkg)
 dim(profiles.gpkg)
 names(profiles.gpkg)
 
 
-## ---------------------------------------------------------------------------------------------------------------------------------
+## ----------------------------------------------------------------------------------------------------------------------
 head(sort(table(profiles.gpkg$country_name), decreasing=TRUE))
 
 
-## ----map.profiles.gpkg, fig.width=12, fig.height=12-------------------------------------------------------------------------------
+## ----map.profiles.gpkg, fig.width=12, fig.height=12--------------------------------------------------------------------
 ggplot(data=profiles.gpkg[(profiles.gpkg$country_name=="Brazil"), ]) +
   aes(col=dataset_id) +
   geom_sf(shape=21, size=0.8, fill="black")
 
 
-## ----coordinates.profiles---------------------------------------------------------------------------------------------------------
+## ----coordinates.profiles----------------------------------------------------------------------------------------------
 coordinates(profiles.ceu) <- c("longitude", "latitude")
 proj4string(profiles.ceu) <- CRS("+init=epsg:4326")
 class(profiles.ceu)
 
 
-## ----coordinates.profiles.sf------------------------------------------------------------------------------------------------------
+## ----coordinates.profiles.sf-------------------------------------------------------------------------------------------
 profiles.ceu.sf <- st_as_sf(profiles.ceu)
 class(profiles.ceu.sf)
 
 
-## ----profiles.wrb-----------------------------------------------------------------------------------------------------------------
+## ----profiles.wrb------------------------------------------------------------------------------------------------------
 table(profiles.ceu@data$cwrb_reference_soil_group)
 table(profiles.ceu.sf$cwrb_reference_soil_group)
 
 
-## ----map.profiles.wrb-------------------------------------------------------------------------------------------------------------
+## ----map.profiles.wrb--------------------------------------------------------------------------------------------------
 ggplot(data=profiles.ceu.sf) +
   aes(col=cwrb_reference_soil_group) +
   geom_sf()
 
 
-## ----load.aqp---------------------------------------------------------------------------------------------------------------------
+## ----load.aqp----------------------------------------------------------------------------------------------------------
 library(aqp)            # Algorithms for Quantitative Pedology
 
 
-## ----bd.aqp-----------------------------------------------------------------------------------------------------------------------
+## ----bd.aqp------------------------------------------------------------------------------------------------------------
 ds.aqp <- bd33@data
 depths(ds.aqp) <- profile_id ~ upper_dept + lower_dept
 is(ds.aqp)
@@ -328,6 +325,6 @@ head(ds.aqp@site)
 head(ds.aqp@horizons[c(2,5,6,7,9)],12)
 
 
-## ----plot.bd.spc,fig.width=12, fig.height=8---------------------------------------------------------------------------------------
+## ----plot.bd.spc,fig.width=12, fig.height=8----------------------------------------------------------------------------
 plotSPC(ds.aqp[1:24,], name="layer_name", color='bdfi33_v_1')