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Merge pull request #11 from weecology/years
Post-move cleanup
2 parents 56b4710 + c336000 commit 116494b

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‎DESCRIPTION‎

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Package: edenR
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Title: Access data from the Everglades Depth Estimation Network (EDEN)
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Version: 0.0.0.9000
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Version: 0.0.1
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Authors@R:
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c(person(given = c("Ethan", "P."),
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family = "White",
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Description: Access data from the Everglades Depth Estimation Network (EDEN)
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License: MIT + file LICENSE
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Imports:
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cubelyr,
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dplyr,
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glue,
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httr,
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units
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Encoding: UTF-8
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.3.2
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RoxygenNote: 7.3.3

‎NAMESPACE‎

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# Generated by roxygen2: do not edit by hand
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export("%>%")
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export(available_years)
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export(calc_dry_days)
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export(calc_recession)
@@ -17,3 +18,4 @@ export(load_boundaries)
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export(reshape_star)
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export(update_last_download)
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export(update_water)
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importFrom(magrittr,"%>%")

‎R/download_eden.R‎

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@@ -56,7 +56,7 @@ get_data_urls <- function(file_names) {
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#'
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#' @export
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#'
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get_last_download <- function(eden_path = file.path("Water"),
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get_last_download <- function(eden_path = file.path("~/water"),
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metadata = get_metadata(),
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force_update = FALSE) {
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if ("last_download.csv" %in% list.files(eden_path) & !force_update) {
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#'
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#' @export
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#'
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download_eden_depths <- function(eden_path = file.path("Water"),
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download_eden_depths <- function(eden_path = file.path("~/water"),
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force_update = FALSE) {
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if (!dir.exists(eden_path)) {
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dir.create(eden_path, recursive = TRUE)

‎R/eden_covariates.R‎

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@@ -9,10 +9,12 @@
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#'
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#' @export
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#'
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load_boundaries <- function(path = file.path("SiteandMethods/regions"),
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load_boundaries <- function(path = "https://raw.githubusercontent.com/weecology/EvergladesWadingBird/refs/heads/main/SiteandMethods/regions/",
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level = "subregions") {
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level <- tolower(level)
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boundaries <- sf::st_read(file.path(path,paste(level,".shp",sep = "")))
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boundaries <- sf::st_read(paste0(path,level,".geojson"))
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return(boundaries)
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}
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@@ -103,10 +105,10 @@ extract_region_means <- function(raster, regions) {
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dplyr::mutate(variable = var_name, value = NA)
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} else {
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region_means_spdf <- regions %>%
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dplyr::mutate(variable = var_name, value = as.numeric(region_means$value)) %>%
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dplyr::mutate_if(is.numeric, list(~dplyr::na_if(., Inf))) %>%
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dplyr::mutate_if(is.numeric, list(~dplyr::na_if(., -Inf))) %>%
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dplyr::mutate_if(is.numeric, list(~dplyr::na_if(., NaN)))
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dplyr::mutate(variable = var_name, value = as.double(region_means$value)) %>%
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dplyr::mutate_if(is.double, list(~dplyr::na_if(., Inf))) %>%
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dplyr::mutate_if(is.double, list(~dplyr::na_if(., -Inf))) %>%
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dplyr::mutate_if(is.double, list(~dplyr::na_if(., NaN)))
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}
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return(region_means_spdf)
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}
@@ -116,15 +118,22 @@ extract_region_means <- function(raster, regions) {
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#' @title Get list of years available for covariate calculation
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#'
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#' @param eden_path path where the EDEN data should be stored
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#' @param new logical, should `available_years` only list years which have changed
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#' since last download
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#'
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#' @return vector of years
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#'
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#' @export
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#'
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available_years <- function(eden_path = file.path("Water")) {
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available_years <- function(eden_path = file.path("~/water"), new = FALSE) {
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eden_data_files <- list.files(file.path(eden_path), pattern = '_depth.nc')
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years <- eden_data_files %>%
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stringr::str_split('_', simplify = TRUE) %>%
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.[, 1] %>%
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unique()
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if(new) {
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# Find which years need to be updated since last download
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metadata <- get_metadata()
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last_download <- get_last_download(eden_path, metadata)
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stringr::str_split('_', simplify = TRUE) %>%
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.[, 1] %>%
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unique() %>%
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.[. %in% c(new$year, new$year+1, new$year+2)]
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.[. %in% c(new$year, new$year+1, new$year+2)] }
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return(years)
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}
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@@ -156,9 +166,9 @@ available_years <- function(eden_path = file.path("Water")) {
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#' @export
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#'
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get_eden_covariates <- function(level = "subregions",
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eden_path = file.path("Water"),
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eden_path = file.path("~/water"),
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years = available_years(eden_path),
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boundaries_path = file.path("SiteandMethods/regions"))
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boundaries_path = "https://raw.githubusercontent.com/weecology/EvergladesWadingBird/refs/heads/main/SiteandMethods/regions/")
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{
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eden_data_files <- list.files(file.path(eden_path), pattern = '_depth.nc')
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get_eden_depths <- function(level="subregions",
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eden_path = file.path("Water"),
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years = available_years(eden_path),
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boundaries_path = file.path("SiteandMethods/regions"))
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boundaries_path = "https://raw.githubusercontent.com/weecology/EvergladesWadingBird/refs/heads/main/SiteandMethods/regions/")
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{
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eden_data_files <- list.files(eden_path, pattern = '_depth.nc', full.names = TRUE)

‎R/get_water_data.R‎

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#' @export
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#'
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get_eden_data <- function(eden_path = file.path("Water")) {
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get_eden_data <- function(eden_path = file.path("~/water")) {
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metadata <- get_metadata()
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last_download <- get_last_download(eden_path) %>% dplyr::select(-X)
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return(NULL)
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} else {
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download_eden_depths()
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download_eden_depths(eden_path, force_update = FALSE)
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years = available_years(eden_path, new = TRUE)
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covariate_data <- read.table("Water/eden_covariates.csv", header = TRUE, sep = ",")
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new_covariates <- get_eden_covariates(eden_path) %>%
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dplyr::bind_rows(get_eden_covariates(level="all")) %>%
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dplyr::bind_rows(get_eden_covariates(level="wcas")) %>%
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covariate_data <- read.table(file.path(eden_path,"eden_covariates.csv"), header = TRUE, sep = ",")
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new_covariates <- get_eden_covariates(eden_path = eden_path,
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years=years) %>%
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dplyr::bind_rows(get_eden_covariates(eden_path = eden_path,
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level="all",
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years=years)) %>%
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dplyr::bind_rows(get_eden_covariates(eden_path = eden_path,
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level="wcas",
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years=years)) %>%
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dplyr::select(year, region=Name, variable, value) %>%
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as.data.frame() %>%
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dplyr::select(-geometry) %>%
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rbind(new_covariates) %>%
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dplyr::arrange("year", "region")
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depth_data <- read.table("Water/eden_depth.csv", header = TRUE, sep = ",") %>%
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depth_data <- read.table(file.path(eden_path,"eden_depth.csv"), header = TRUE, sep = ",") %>%
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dplyr::mutate(date=as.Date(date))
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new_depths <- get_eden_depths(eden_path) %>%
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dplyr::bind_rows(get_eden_depths(level="all")) %>%
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dplyr::bind_rows(get_eden_depths(level="wcas")) %>%
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new_depths <- get_eden_depths(eden_path = eden_path,
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years=years) %>%
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dplyr::bind_rows(get_eden_depths(eden_path = eden_path,
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level="all",
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years=years)) %>%
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dplyr::bind_rows(get_eden_depths(eden_path = eden_path,
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level="wcas",
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years=years)) %>%
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dplyr::mutate(date=as.Date(date))
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depth_data <- dplyr::filter(depth_data, !date %in% new_depths$date) %>%
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return(cat("...No new data..."))
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} else {
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69-
write.table(data$covariate_data, "Water/eden_covariates.csv", row.names = FALSE, col.names = TRUE,
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write.table(data$covariate_data, file = file.path(eden_path,"eden_covariates.csv"), row.names = FALSE, col.names = TRUE,
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na="", sep = ",", quote = FALSE)
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72-
write.table(data$depth_data, file = "Water/eden_depth.csv",
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write.table(data$depth_data, file = file.path(eden_path,"eden_depth.csv"),
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row.names = FALSE, col.names = TRUE, na = "", sep = ",", quote = FALSE)
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}
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}

‎R/utils-pipe.R‎

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#' Pipe operator
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#'
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#' See \code{magrittr::\link[magrittr]{\%>\%}} for details.
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#'
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#' @name %>%
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#' @rdname pipe
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#' @keywords internal
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#' @export
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#' @importFrom magrittr %>%
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#' @usage lhs \%>\% rhs
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NULL

‎man/available_years.Rd‎

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‎man/download_eden_depths.Rd‎

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‎man/get_eden_covariates.Rd‎

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‎man/get_eden_data.Rd‎

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