use shape as first parameter for consistency

R/agg_upload_f.R

@@ -3,8 +3,8 @@
 #' This function is called by the agg_upload module and loads a
 #'  raster image.
 #'
-#' @param path character. The location of the file to be loaded.
 #' @param shape sf. sf object containing the area of interest
+#' @param path character. The location of the file to be loaded.
 #' @param logger Stores all notification messages to be displayed in the Log
 #' Window. Insert the logger reactive list here for running in
 #' shiny, otherwise leave the default NULL
@@ -16,11 +16,11 @@
 #' shp_file <- list.files(system.file("extdata/shapes",
 #'         package="disagapp"), pattern = ".shp", full.names = TRUE)
 #' shape <- sf::st_read(shp_file, quiet = TRUE)
-#' raster <- agg_upload(path = path, shape = shape)
+#' raster <- agg_upload(shape = shape, path = path)
 #'
 #' @export
 
-agg_upload <- function(path, shape, logger = NULL) {
+agg_upload <- function(shape, path, logger = NULL) {
 
   if (!inherits(path, "character")){
     logger |> writeLog(type = "error", "path must be a character string")

R/cov_bioclim_f.R

@@ -31,9 +31,10 @@
 #' poly <- sf::st_polygon(list(poly_matrix))
 #' shape <- sf::st_sf(1, geometry = list(poly))
 #' sf::st_crs(shape) = 4326
-#' raster <- cov_bioclim(country_code = "LIE",
-#'                       variables = c("Mean temperature", "Mean diurnal range"),
-#'                       shape = shape)
+#' raster <- cov_bioclim(shape = shape,
+#'                       country_code = "LIE",
+#'                       variables = c("Mean temperature", "Mean diurnal range"))
+#'
 #'
 #' @export
 

R/cov_upload_f.R

@@ -5,9 +5,9 @@
 #' overlap with the area of interest and crops and masks them to the area of
 #' interest.
 #'
+#' @param shape sf. sf object containing the area of interest
 #' @param path_df data.frame. Containing `datapath` and `name` columns of the
 #' file(s) to be uploaded.
-#' @param shape sf. sf object containing the area of interest
 #' @param logger Stores all notification messages to be displayed in the Log
 #' Window. Insert the logger reactive list here for running in
 #' shiny, otherwise leave the default NULL
@@ -21,10 +21,10 @@
 #' shp_file <- list.files(system.file("extdata", "shapes", package="disagapp"),
 #'                        pattern = ".shp", full.names = TRUE)
 #' shape <- sf::st_read(shp_file, quiet = TRUE)
-#' rasters <- cov_upload(path_df = cov_df, shape = shape)
+#' rasters <- cov_upload(shape = shape, path_df = cov_df)
 #' @export
 
- cov_upload <- function(path_df, shape, logger = NULL) {
+ cov_upload <- function(shape, path_df, logger = NULL) {
 
    # check inputs
    if (!("data.frame" %in% class(path_df))){

inst/shiny/modules/agg_upload.R

@@ -45,7 +45,7 @@ agg_upload_module_server <- function(id, common, parent_session, map) {
                         name = list.files(system.file("extdata", "aggregation", package="disagapp")))
     }
     # FUNCTION CALL ####
-    agg_raster <- agg_upload(aggdf$datapath, common$shape, common$logger)
+    agg_raster <- agg_upload(common$shape, aggdf$datapath, common$logger)
     if (is.null(agg_raster)){
       return()
     }

inst/shiny/modules/agg_upload.Rmd

@@ -7,7 +7,7 @@ Upload an aggregation raster. You need to specify the directory where the file i
 aggregation_directory <- ""
 aggregation_files <- "{{agg_upload_path}}"
 aggregation_file_path <- file.path(aggregation_directory, aggregation_files)
-aggregation <- disagapp::agg_upload(aggregation_file_path)
+aggregation <- disagapp::agg_upload(shape, aggregation_file_path)
 names(aggregation) <- "{{agg_upload_name}}"
     
 ```

inst/shiny/modules/cov_upload.R

@@ -41,7 +41,7 @@ cov_upload_module_server <- function(id, common, parent_session, map) {
 
     # FUNCTION CALL ####
 
-    cov_list <- cov_upload(covdf, common$shape, common$logger)
+    cov_list <- cov_upload(common$shape, covdf, common$logger)
 
     if (is.null(cov_list)){
       return()

inst/shiny/modules/cov_upload.Rmd

@@ -7,7 +7,7 @@ covariate_directory <- ""
 covariate_files <- {{cov_upload_path}}
 covariate_file_paths <- file.path(covariate_directory, covariate_files)
 covariate_file_df <- data.frame(datapath = covariate_file_paths, name = covariate_files)
-uploaded_covariates <- disagapp::cov_upload(covariate_file_df)
+uploaded_covariates <- disagapp::cov_upload(shape, covariate_file_df)
 covariates <- append(covariates, uploaded_covariates)
 ```
 

tests/testthat/test-agg_upload.R

@@ -1,7 +1,7 @@
 
 test_that("Check agg_upload function works as expected", {
   mdg_shape <- resp_shape(shpdf)
-  result <- agg_upload(aggdf$datapath, mdg_shape)
+  result <- agg_upload(mdg_shape, aggdf$datapath)
   expect_is(result, "SpatRaster")
 })
 

tests/testthat/test-cov_upload.R

@@ -3,7 +3,7 @@ mad_shape <- resp_shape(shpdf)
 lie_shape <- resp_download(df, area_column, resp_column, country_code[1], admin_level)
 
 test_that("Check cov_upload function works as expected", {
-  result <- cov_upload(covdf, mad_shape)
+  result <- cov_upload(mad_shape, covdf)
   expect_is(result, "list")
   expect_is(result[[1]], "SpatRaster")
   expect_equal(length(result), 4)
@@ -14,16 +14,16 @@ test_that("Check cov_upload handles CRS issues", {
   covdf_nocrs <- data.frame(datapath = system.file("extdata", "test_data", "no_crs.tif", package="disagapp"),
                       name = "no_crs.tif")
 
-  expect_error(cov_upload(covdf_nocrs, mad_shape), "Some files do not have a coordinate reference system")
+  expect_error(cov_upload(mad_shape, covdf_nocrs), "Some files do not have a coordinate reference system")
 
   covdf_difcrs <- data.frame(datapath = system.file("extdata", "test_data", "different_projection.tif", package="disagapp"),
                             name = "different_projection.tif")
 
-  result <- cov_upload(covdf_difcrs, mad_shape)
+  result <- cov_upload(mad_shape, covdf_difcrs)
   result_crs <- terra::crs(result[[1]], describe = TRUE)
   expect_equal(result_crs$code, "4326")
 
-  expect_error(cov_upload(covdf, lie_shape), "Some files do not overlap with the response data")
+  expect_error(cov_upload(lie_shape, covdf), "Some files do not overlap with the response data")
 
 })