README.md

In XiaodanLyu/viscover: Visualize SSURGO and CDL and their Overlay

Installation

Run the following from an R console:

if(!require("devtools"))  install.packages("devtools")
devtools::install_github("XiaodanLyu/viscover")

Introduction

This tiny package is developed to web-scrape USDA-NASS cropland data layer (CDL) and USDA-NRCS soil data layer (SDL) at point-level and small domain. This package also embeds a Shiny(Chang et al. 2018) application I developed to visualize the two data layers. You can run this tool from R console using runTool() or interact with this tool lively at https://lyux.shinyapps.io/viscover/.

This Shiny tool is now featured in the RStudio Shiny Gallery. If you are interested in learning more about my experience or seeking for general advice about R Shiny development, please refer to this blog post I wrote on my personal website. :bowtie:

The following screenshot of the tool shows our lovely Iowa State University campus (center grey area) is surrounded by large fields of soybeans (green pixels) and corns (yellow pixels).

Web Scraping

Point level

library(viscover)
GetCDLValue(year = 2018, lon = -93.65, lat = 42.03)
#> $value
#> [1] "124"
#> 
#> $category
#> [1] "Developed/High Intensity"
#> 
#> $color
#> [1] "#9C9C9C"
GetSDLValue(lon = -93.65, lat = 42.03)
#> Loading required namespace: rgeos
#> single result set, returning a data.frame
#>   areasymbol musym   mukey                               muname muacres
#> 1      IA169   L55 2800480 Nicollet loam, 1 to 3 percent slopes   45662

Small domain

poly is an example soil spatial polygon data frame embedded in this package.

setwd("C:/Users/lyux/")
sp::bbox(poly)
#>         min       max
#> x -93.67166 -93.65910
#> y  42.05230  42.07128
GetCDLFile(year = 2018, b = poly)
#> class       : RasterLayer 
#> dimensions  : 72, 37, 2664  (nrow, ncol, ncell)
#> resolution  : 30, 30  (x, y)
#> extent      : 191325, 192435, 2119095, 2121255  (xmin, xmax, ymin, ymax)
#> coord. ref. : +proj=aea +lat_1=29.5 +lat_2=45.5 +lat_0=23 +lon_0=-96 +x_0=0 +y_0=0 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs 
#> data source : C:\Users\lyux\Temp\tmp.tif 
#> names       : tmp 
#> values      : 0, 255  (min, max)

R package soilDB(Skovlin and Roecker 2019) provides a convenient function for fetching soil data by bounding box.

soilDB::mapunit_geom_by_ll_bbox(sp::bbox(poly))
#> OGR data source with driver: GML 
#> Source: "C:\Users\lyux\AppData\Local\Temp\RtmpCQXrw9\file1f046be166a9.gml", layer: "mapunitpoly"
#> with 89 features
#> It has 8 fields
#> class       : SpatialPolygonsDataFrame 
#> features    : 89 
#> extent      : -93.69867, -93.505, 41.86315, 42.20929  (xmin, xmax, ymin, ymax)
#> coord. ref. : NA 
#> variables   : 7
#> names       : areasymbol, spatialversion, musym, nationalmusym,   mukey, muareaacres, mupolygonkey 
#> min values  :      IA169,              9,   108,         2s088, 2765537,  0.66275951,    210801004 
#> max values  :      IA169,              9,     W,          ft19,  411348,  9.50876739,    210839804

Overlay

TileinPoly gives a tabular result of the tile points overlaid with the spatial polygon.

library(tidyverse)
cdl_tmp <- raster::raster(system.file("tif/cdl_tmp.tif", package = "viscover"))
scover <- TileinPoly(tile = cdl_tmp, poly = poly)
glimpse(scover)
#> Observations: 9
#> Variables: 2
#> $ .    <fct> 1, 5, 27, 36, 121, 141, 176, 190, 195
#> $ Freq <int> 255, 5, 1, 7, 18, 161, 69, 27, 18

One can refer cdl.dbf to interpret the CDL code. cdl.dbf also contains the RGB color code used by CDL legend (https://www.nass.usda.gov/Research_and_Science/Cropland/docs/US_2018_CDL_legend.jpg).

cdl.dbf %>% glimpse()
#> Observations: 255
#> Variables: 6
#> $ VALUE      <int> 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 1...
#> $ CLASS_NAME <fct> Background, Corn, Cotton, Rice, Sorghum, Soybeans, ...
#> $ RED        <dbl> 0.0000000, 1.0000000, 1.0000000, 0.0000000, 1.00000...
#> $ GREEN      <dbl> 0.0000000, 0.8274510, 0.1490196, 0.6588235, 0.61960...
#> $ BLUE       <dbl> 0.00000000, 0.00000000, 0.14901961, 0.89803922, 0.0...
#> $ OPACITY    <dbl> 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, ...
scover %>% 
  mutate_if(is.factor, funs(as.integer(as.character(.)))) %>% 
  left_join(cdl.dbf %>% select(VALUE, CLASS_NAME), by = c("." = "VALUE")) %>% 
  glimpse()
#> Observations: 9
#> Variables: 3
#> $ .          <int> 1, 5, 27, 36, 121, 141, 176, 190, 195
#> $ Freq       <int> 255, 5, 1, 7, 18, 161, 69, 27, 18
#> $ CLASS_NAME <fct> Corn, Soybeans, Rye, Alfalfa, Developed/Open Space,...

One can also produce a plot of the overlaid result using ggplot2(Wickham 2016). cdlpal returns a Hex color code when a CDL category code is provided.

library(sp)
library(raster)
cdl_pt <- cdl_tmp %>% rasterToPoints(spatial = TRUE) 
sdl_poly <- poly %>% spTransform(cdl_pt@proj4string)
cdl_pt[geometry(sdl_poly),] %>% data.frame() %>% 
  ggplot() +
  geom_tile(aes(x = x, y = y, fill = cdlpal(cdl_tmp))) + 
  scale_fill_identity() + coord_equal() +
  geom_path(aes(x = long, y = lat, group = group), data = fortify(sdl_poly))

References

Chang, Winston, Joe Cheng, JJ Allaire, Yihui Xie, and Jonathan McPherson. 2018. *Shiny: Web Application Framework for R*. .

Skovlin, Jay, and Stephen Roecker. 2019. *SoilDB: Soil Database Interface*. .

Wickham, Hadley. 2016. *Ggplot2: Elegant Graphics for Data Analysis*. Springer-Verlag New York. .

XiaodanLyu/viscover documentation built on July 27, 2020, 9:53 p.m.