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Warning message: attribute variables are assumed to be spatially constant throughout all geometries | This not making graphs #4

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Adil19K opened this issue Mar 28, 2024 · 0 comments
Open

Warning message: attribute variables are assumed to be spatially constant throughout all geometries | This not making graphs #4

Adil19K opened this issue Mar 28, 2024 · 0 comments

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@Adil19K
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Adil19K commented Mar 28, 2024 •
edited
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Hi Milos, I am very new to geomapping in R so, I have taken your code and used it in R studio, here is the code and the warnings

###################################################

Mapping river basins with R

Milos Popovic

2023/07/07

###################################################
libs <- c(

  • "tidyverse", "sf",

  • "giscoR", "magick"
  • )

installed_libraries <- libs %in% rownames(

  • installed.packages()
  • )

if (any(installed_libraries == F)) {

  • install.packages(

  •     libs[!installed_libraries]

  • )
  • }
    WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Installing packages into ‘C:/Users/Adil/AppData/Local/R/win-library/4.3’
(as ‘lib’ is unspecified)
also installing the dependencies ‘fastmap’, ‘colorspace’, ‘sys’, ‘bit’, ‘ps’, ‘base64enc’, ‘sass’, ‘digest’, ‘cachem’, ‘farver’, ‘labeling’, ‘munsell’, ‘RColorBrewer’, ‘viridisLite’, ‘rematch’, ‘askpass’, ‘bit64’, ‘prettyunits’, ‘processx’, ‘evaluate’, ‘highr’, ‘xfun’, ‘yaml’, ‘bslib’, ‘fontawesome’, ‘htmltools’, ‘jquerylib’, ‘tinytex’, ‘proxy’, ‘backports’, ‘ellipsis’, ‘generics’, ‘glue’, ‘lifecycle’, ‘memoise’, ‘blob’, ‘R6’, ‘tidyselect’, ‘vctrs’, ‘withr’, ‘data.table’, ‘gtable’, ‘isoband’, ‘scales’, ‘gargle’, ‘uuid’, ‘cellranger’, ‘ids’, ‘rematch2’, ‘cpp11’, ‘pkgconfig’, ‘mime’, ‘openssl’, ‘timechange’, ‘fansi’, ‘utf8’, ‘systemfonts’, ‘textshaping’, ‘clipr’, ‘crayon’, ‘vroom’, ‘tzdb’, ‘progress’, ‘callr’, ‘fs’, ‘knitr’, ‘rmarkdown’, ‘selectr’, ‘stringi’, ‘e1071’, ‘wk’, ‘geometries’, ‘jsonify’, ‘rapidjsonr’, ‘sfheaders’, ‘broom’, ‘conflicted’, ‘cli’, ‘dbplyr’, ‘dplyr’, ‘dtplyr’, ‘forcats’, ‘ggplot2’, ‘googledrive’, ‘googlesheets4’, ‘haven’, ‘hms’, ‘httr’, ‘lubridate’, ‘magrittr’, ‘modelr’, ‘pillar’, ‘purrr’, ‘ragg’, ‘readr’, ‘readxl’, ‘reprex’, ‘rlang’, ‘rstudioapi’, ‘rvest’, ‘stringr’, ‘tibble’, ‘tidyr’, ‘xml2’, ‘classInt’, ‘DBI’, ‘s2’, ‘units’, ‘countrycode’, ‘geojsonsf’, ‘rappdirs’, ‘curl’

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/fastmap_1.1.1.zip'
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trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/sys_3.4.2.zip'
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trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/giscoR_0.4.2.zip'
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The downloaded binary packages are in
C:\Users\Adil\AppData\Local\Temp\RtmpMBQ68t\downloaded_packages

invisible(

  • lapply(

  •     libs, library,

  •     character.only = T

  • )
  • )
    ── Attaching core tidyverse packages ────────────────────────────────────────────────── tidyverse 2.0.0 ──
    ✔ dplyr 1.1.4 ✔ readr 2.1.5
    ✔ forcats 1.0.0 ✔ stringr 1.5.1
    ✔ ggplot2 3.5.0 ✔ tibble 3.2.1
    ✔ lubridate 1.9.3 ✔ tidyr 1.3.1
    ✔ purrr 1.0.2
    ── Conflicts ──────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
    ✖ dplyr::filter() masks stats::filter()
    ✖ dplyr::lag() masks stats::lag()
    ℹ Use the conflicted package to force all conflicts to become errors
    Linking to GEOS 3.11.2, GDAL 3.8.2, PROJ 9.3.1; sf_use_s2() is TRUE
    Linking to ImageMagick 6.9.12.98
    Enabled features: cairo, freetype, fftw, ghostscript, heic, lcms, pango, raw, rsvg, webp
    Disabled features: fontconfig, x11
    There were 13 warnings (use warnings() to see them)

1. GET COUNTRY BORDERS

#-----------------------
print("GET COUNTRY BORDERS")
[1] "GET COUNTRY BORDERS"
get_country_borders <- function() {

  • country_borders <- giscoR::gisco_get_countries(

  •     resolution = "3",

  •     country = "US"

  • )

  • return(country_borders)
  • }

country_borders <- get_country_borders()

2. GET BASINS

#---------------
print("GET BASINS")
[1] "GET BASINS"

https://data.hydrosheds.org/file/HydroBASINS/standard/hybas_sa_lev03_v1c.zip

get_basins <- function() {

  • url <- "https://data.hydrosheds.org/file/HydroBASINS/standard/hybas_na_lev03_v1c.zip"

  • file_name <- "hybas_na_lev03_v1c.zip"

  • download.file(

  •     url = url,

  •     destfile = file_name,

  •     mode = "wb"

  • )

  • unzip(file_name)
  • }

get_basins()
trying URL 'https://data.hydrosheds.org/file/HydroBASINS/standard/hybas_na_lev03_v1c.zip'
Content type 'application/zip' length 3728058 bytes (3.6 MB)
downloaded 3.6 MB

print("basin downloaded")
[1] "basin downloaded"

list.files()
[1] "hybas_na_lev03_v1c.dbf" "hybas_na_lev03_v1c.prj" "hybas_na_lev03_v1c.sbn"
[4] "hybas_na_lev03_v1c.sbx" "hybas_na_lev03_v1c.shp" "hybas_na_lev03_v1c.shp.xml"
[7] "hybas_na_lev03_v1c.shx" "hybas_na_lev03_v1c.zip" "HydroBASINS_TechDoc_v1c.pdf"
[10] "Test_RiverBasin.Rproj"

print("load basin")
[1] "load basin"
load_basins <- function() {

  • print("loading filenames")

  • filenames <- list.files(

  •     pattern = ".shp$",

  •     full.names = TRUE

  • )

  • print(filenames)

  • namerica_basin <- sf::st_read(

  •     filenames

  • )

  • return(namerica_basin)
  • }

namerica_basin <- load_basins()
[1] "loading filenames"
[1] "./hybas_na_lev03_v1c.shp"
Reading layer hybas_na_lev03_v1c' from data source C:\Users\Adil\Documents\Test_RiverBasin\hybas_na_lev03_v1c.shp' using driver `ESRI Shapefile'
Simple feature collection with 29 features and 13 fields
Geometry type: MULTIPOLYGON
Dimension: XY
Bounding box: xmin: -137.9625 ymin: 5.495833 xmax: -52.61605 ymax: 62.74232
Geodetic CRS: WGS 84
print("basin loaded")
[1] "basin loaded"

print("Intersect Basin with only the wanted Country Boundary.")
[1] "Intersect Basin with only the wanted Country Boundary."
sf::sf_use_s2(F)
Spherical geometry (s2) switched off

brazil_basin <- namerica_basin |>

  • sf::st_intersection(

  •     country_borders

  • ) |>

  • dplyr::select(

  •     HYBAS_ID

  • )

although coordinates are longitude/latitude, st_intersection assumes that they are planar
Warning message:
attribute variables are assumed to be spatially constant throughout all geometries

3. GET RIVERS DATA

#-------------------
print("Get Rivers")
[1] "Get Rivers"

https://data.hydrosheds.org/file/HydroRIVERS/HydroRIVERS_v10_sa_shp.zip

get_rivers <- function() {

  • url <- "https://data.hydrosheds.org/file/HydroRIVERS/HydroRIVERS_v10_na_shp.zip"

  • file_name <- "na-rivers.zip"

  • download.file(

  •     url = url,

  •     destfile = file_name,

  •     mode = "wb"

  • )

  • unzip(file_name)
  • }

get_rivers()
trying URL 'https://data.hydrosheds.org/file/HydroRIVERS/HydroRIVERS_v10_na_shp.zip'
Content type 'application/zip' length 66335898 bytes (63.3 MB)
downloaded 63.3 MB

print("Getting Rivers")
[1] "Getting Rivers"
list.files()
[1] "hybas_na_lev03_v1c.dbf" "hybas_na_lev03_v1c.prj" "hybas_na_lev03_v1c.sbn"
[4] "hybas_na_lev03_v1c.sbx" "hybas_na_lev03_v1c.shp" "hybas_na_lev03_v1c.shp.xml"
[7] "hybas_na_lev03_v1c.shx" "hybas_na_lev03_v1c.zip" "HydroBASINS_TechDoc_v1c.pdf"
[10] "HydroRIVERS_TechDoc_v10.pdf" "HydroRIVERS_v10_na_shp" "na-rivers.zip"
[13] "Test_RiverBasin.Rproj"

load_rivers <- function() {

  • filenames <- list.files(

  •     path = "HydroRIVERS_v10_na_shp",

  •     pattern = ".shp$",

  •     full.names = T

  • )

  • print(filenames)

  • namerica_rivers <- sf::st_read(

  •     filenames

  • )

  • return(namerica_rivers)
  • }

namerica_rivers <- load_rivers()
[1] "HydroRIVERS_v10_na_shp/HydroRIVERS_v10_na.shp"
Reading layer HydroRIVERS_v10_na' from data source C:\Users\Adil\Documents\Test_RiverBasin\HydroRIVERS_v10_na_shp\HydroRIVERS_v10_na.shp'
using driver `ESRI Shapefile'
Simple feature collection with 986463 features and 14 fields
Geometry type: LINESTRING
Dimension: XY
Bounding box: xmin: -137.9354 ymin: 5.510417 xmax: -52.66458 ymax: 62.67292
Geodetic CRS: WGS 84

brazil_rivers <- namerica_rivers |>

  • dplyr::select(

  •     ORD_FLOW

  • ) |>

  • sf::st_intersection(

  •     country_borders

  • )

although coordinates are longitude/latitude, st_intersection assumes that they are planar
Warning message:
attribute variables are assumed to be spatially constant throughout all geometries

4. DETERMINE BASIN FOR EVERY RIVER

#-----------------------------------

brazil_river_basin <- sf::st_intersection(

  • brazil_rivers,

  • brazil_basin
  • )
    although coordinates are longitude/latitude, st_intersection assumes that they are planar
    Warning message:
    attribute variables are assumed to be spatially constant throughout all geometries

5. RIVER WIDTH

#---------------

unique(brazil_river_basin$ORD_FLOW)
[1] 8 9 7 10 6 5 4 3 2

brazil_river_basin_width <- brazil_river_basin |>

  • dplyr::mutate(

  •     width = as.numeric(

  •         ORD_FLOW

  •     ),

  •     width = dplyr::case_when(

  •         width == 1 ~ .8,

  •         width == 2 ~ .7,

  •         width == 3 ~ .6,

  •         width == 4 ~ .45,

  •         width == 5 ~ .35,

  •         width == 6 ~ .25,

  •         width == 7 ~ .2,

  •         width == 8 ~ .15,

  •         width == 9 ~ .1,

  •         TRUE ~ 0

  •     )

  • ) |>

  • sf::st_as_sf()

6. PLOT

#--------

unique(

  • brazil_river_basin_width$HYBAS_ID
  • )
    [1] 7030000010 7030008710 7030008720 7030014250 7030014930 7030014940 7030022240 7030034520 7030034530
    [10] 7030038340 7030042040 7030046750 7030047060 7030047070 7030047840 7030049270 7030073620

hcl.pals("qualitative")
[1] "Pastel 1" "Dark 2" "Dark 3" "Set 2" "Set 3" "Warm" "Cold" "Harmonic" "Dynamic"

p <- ggplot() +

  • geom_sf(

  •     data = brazil_river_basin_width,

  •     aes(

  •         color = factor(

  •             HYBAS_ID

  •         ),

  •         size = width,

  •         alpha = width

  •     )

  • ) +

  • scale_color_manual(

  •     name = "",

  •     values = hcl.colors(

  •         17, "Dark 3",

  •         alpha = 1

  •     )

  • ) +

  • scale_size(

  •     range = c(.1, .7)

  • ) +

  • scale_alpha(

  •     range = c(.01, .7)

  • ) +

  • theme_void() +

  • theme(

  •     legend.position = "none",

  •     plot.caption = element_text(

  •         size = 9, color = "grey60",

  •         hjust = .1, vjust = 10

  •     ),

  •     plot.margin = unit(

  •         c(

  •             t = 0, r = 0,

  •             b = 0, l = 0

  •         ),

  •         "lines"

  •     ),

  •     plot.background = element_rect(

  •         fill = "black",

  •         color = NA

  •     ),

  •     panel.background = element_rect(

  •         fill = "black",

  •         color = NA

  •     )

  • ) +

  • labs(

  •     title = "",

  •     x = "",

  •     y = "",

  •     # caption = "Source: ©World Wildlife Fund, Inc. (2006-2013) HydroSHEDS database http://www.hydrosheds.org"

  • )

ggsave(

  • filename = "us-river-basins.png",

  • width = 7, height = 7.75, dpi = 600,

  • bg = "white", device = "png", p
  • )

st_write(brazil_river_basin_width, "us-river-basins.geojson", layer = NULL, driver = "GeoJson")
Writing layer us-river-basins' to data source us-river-basins.geojson' using driver `GeoJson'
Writing 464880 features with 8 fields and geometry type Unknown (any).
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