fix problems on open_prediction_grid.R (function + test + vignette)

R/open_data_heatmodel.R → R/open_prediction_grid.R

@@ -1,29 +1,23 @@
 #' Open prediction grid for a given period
 #'
 #' @param period A vector of "Date" objects
+#' @param data_path a character to data folder
 #' @returns a data.table of prediction points
 #' (each row corresponds to a lat, lon, date)
-open_pred_period <- function(period) {
+open_pred_period <- function(period, data_path) {
   if (class(period) != "Date") {
     stop("period is not a Date")
   }
   period <- as.character(period)
   for (d in period) {
-    file <- paste0(
-      "../input/prediction-grid/",
-      "prediction_grid_points_urb_rur_space_time_covariates_",
-      d,
-      ".csv"
-    )
+    file <- paste0(data_path, "pred_grid_", d, ".tif")
     if (!file.exists(file)) {
       stop(paste0("date ", d, " is not in files"))
     }
   }
   list_pred <- list()
   for (d in period) {
-    pred_d <- fread(file)
-    list_pred <- append(list_pred, list(pred_d))
+    list_pred[[d]] <- terra::rast(file)
   }
-  pred_p <- rbindlist(list_pred, fill = TRUE)
-  return(pred_p = pred_p)
+  return(list_pred = list_pred)
 }

tests/testthat/test-open_prediction_grid.R

@@ -0,0 +1,20 @@
+test_that("Check open_pred_period works", {
+  data_path <- "../testdata/"
+
+  # -- 1st example: period is not a Date object
+  p <- c("2022-06-01", "2022-06-03")
+  expect_error(open_pred_period(period = p, data_path = data_path),
+               "period is not a Date")
+
+  # -- 2nd example: date is not in files
+  p <- c(as.Date("2022-08-01"), as.Date("2100-06-03"))
+  expect_error(open_pred_period(period = p, data_path = data_path),
+               "date 2100-06-03 is not in files")
+
+  # -- 3rd example: should work
+  p <- c(as.Date("2022-08-01"), as.Date("2022-08-02"))
+  expect_no_error(open_pred_period(period = p, data_path = data_path))
+  output <- open_pred_period(period = p, data_path = data_path)
+  expect_equal(class(output), "list")
+  expect_equal(names(output), as.character(p))
+})

vignettes/prediction_grid.Rmd

@@ -0,0 +1,24 @@
+---
+title: "Prediction grid creation"
+output: html_document
+date: "2023-12-18"
+---
+
+# Create and store prediction grid
+
+```{r}
+getwd()
+cfl <- list_covar_testdata(covar_folder = "../tests/testdata/")
+create_pred_rds(borders_path = "../tests/testdata/rtp_counties.shp",
+                covar_files_list = cfl,
+                output_path = "../tests/testdata/")
+```
+
+# Open prediction grid
+
+```{r}
+data_path <- "../tests/testdata/"
+period <- seq(as.Date("2022-08-01"), as.Date("2022-08-02"), by = "1 day")
+grid <- open_pred_period(period = period, data_path = data_path)
+```
+