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Update sf and terra [patch] #522

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Update sf and terra [patch] #522

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aa4098d
Update sf and terra [patch]
gmyenni Feb 12, 2024
7e47a42
Update sf and terra [patch]
gmyenni Feb 12, 2024
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17 changes: 8 additions & 9 deletions DataCleaningScripts/update_ndvi.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
# https://www.usgs.gov/landsat-missions/landsat-collection-2-level-2-science-products

`%>%` <- magrittr::`%>%`
library(raster)
library(terra)

#' @title create_portal_area
#'
Expand Down Expand Up @@ -50,24 +50,23 @@ extract_and_mask_raster <- function(records, targetpath = tempdir()) {

# read in raster files; crop to portal_box; apply scaling factor and offset; delete full-size raster files
# In Landsat 8-9, NDVI = (Band 5 – Band 4) / (Band 5 + Band 4).
B4 <- raster::raster(paste0(targetpath,"/", records["display_id"], "_SR_B4.TIF")) %>%
raster::crop(portal_area) * 0.0000275 + -0.2
B5 <- raster::raster(paste0(targetpath,"/", records["display_id"], "_SR_B5.TIF")) %>%
raster::crop(portal_area) * 0.0000275 + -0.2
B4 <- terra::rast(paste0(targetpath,"/", records["display_id"], "_SR_B4.TIF")) %>%
terra::crop(portal_area) * 0.0000275 + -0.2
B5 <- terra::rast(paste0(targetpath,"/", records["display_id"], "_SR_B5.TIF")) %>%
terra::crop(portal_area) * 0.0000275 + -0.2

sr_ndvi <- (B5 - B4)/(B5 + B4)

pixelqa <- raster::raster(paste0(targetpath,"/", records["display_id"], "_QA_PIXEL.TIF")) %>%
raster::crop(portal_area)
pixelqa <- terra::rast(paste0(targetpath,"/", records["display_id"], "_QA_PIXEL.TIF")) %>%
terra::crop(portal_area)

# mask ndvi data
# "clear" values of pixel_qa are derived from the CFMask algorithm version 3.3.1
# https://www.usgs.gov/media/files/landsat-8-9-collection-2-level-2-science-product-guide
clearvalues = c(21824, 21826, 22080, 23888, 30048, 54596, 54852)

pixelqa[!(pixelqa %in% clearvalues)] <- NA
ndvi_masked <- raster::mask(x=sr_ndvi, mask=pixelqa)
# raster::writeRaster(s,paste0(targetpath,"/", record_id,'_ndvi_masked.tif'), overwrite=TRUE)
ndvi_masked <- terra::mask(x=sr_ndvi, mask=pixelqa)

return(ndvi_masked)
}
Expand Down
39 changes: 28 additions & 11 deletions install-packages.R
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Original file line number Diff line number Diff line change
@@ -1,18 +1,35 @@
# Install pacman if it isn't already installed

if ("pacman" %in% rownames(installed.packages()) == FALSE) install.packages("pacman")

remove.packages("stringi")
remove.packages("stringr")
install.packages(c("Rcpp","stringi","stringr","RCurl","curl","Hmisc", "EML", "sf","rgdal","lwgeom", "git2r","remotes"), type="source", repos="https://cran.rstudio.com")
install.packages(c("curl",
"EML",
"git2r",
"Hmisc",
"lwgeom",
"Rcpp",
"RCurl",
"remotes",
"rgdal",
"stringi",
"stringr",
"sf"), type="source", repos="https://cran.rstudio.com")
install.packages('terra', repos='https://rspatial.r-universe.dev')
remotes::install_github("htmltab/htmltab")

# Install analysis packages using pacman
if ("pacman" %in% rownames(installed.packages()) == FALSE) install.packages("pacman")

# pacman::p_load(units, sf, rgdal, lwgeom, shiny, stringi, stringr, Hmisc, dplyr, git2r, openxlsx, lubridate, htmltab,
# lunar, jsonlite, devtools, sp, sqldf, raster, RCurl, EML, testthat, zoo, tidyr, semver, yaml)


pacman::p_load(units, shiny, dplyr, openxlsx, lubridate, htmltab,
lunar, jsonlite, devtools, sp, sqldf, raster, testthat, zoo, tidyr, semver, yaml)
pacman::p_load(devtools,
dplyr,
jsonlite,
lubridate,
lunar,
openxlsx,
semver,
shiny,
sp,
sqldf,
testthat,
tidyr,
units,
yaml,
zoo)
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