update code and GHCNh download

NIEHS · Sep 19, 2024 · 106c6ce · 106c6ce
1 parent ebbec9f
commit 106c6ce
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Showing 3 changed files with 5 additions and 25 deletions.
diff --git a/R/download_ghcnh.R b/R/download_ghcnh.R
@@ -26,7 +26,8 @@ find_ghcnh_polygon <- function(polygon) {
     "hcnflag",
     "wmoid"
   )
-  inv <- inv |> sf::st_as_sf(coords = c("lon", "lat"), crs = 4326)
+  inv <- inv |>
+    sf::st_as_sf(coords = c("lon", "lat"), crs = 4326, na.fail = FALSE)
   inv_in_poly <- sf::st_filter(inv, poly)
   return(inv_in_poly)
 }

diff --git a/R/format_observations.R b/R/format_observations.R
@@ -150,10 +150,7 @@ format_wu <- function(raw,
 #' @export
 format_ghcnh <- function(raw) {
   ghcnh_cols <- c(
-    "Year",
-    "Month",
-    "Day",
-    "Hour",
+    "DATE",
     "temperature",
     "Latitude",
     "Longitude",
@@ -166,25 +163,7 @@ format_ghcnh <- function(raw) {
       all(ghcnh_cols %in% colnames(raw))
   )
   x <- raw
-  # note: as.POSIXct return a double when called through apply.
-  # this is why it is called after the apply
-  x$time <- apply(
-    x[, c("Year", "Month", "Day", "Hour")],
-    1,
-    function(x) {
-      paste0(
-        x[1],
-        "-",
-        x[2],
-        "-",
-        x[3],
-        " ",
-        x[4],
-        ":00:00"
-      )
-    }
-  ) |>
-    as.POSIXct(format = "%Y-%m-%d %H:%M:%S", tz = "UTC")
+  x$time <- as.POSIXct(x$DATE, format = "%Y-%m-%dT%H:%M:%S", tz = "UTC")
   x <- x |>
     summarize_hourly_temp(
       "time",

diff --git a/vignettes/case_study_triangle_area.Rmd b/vignettes/case_study_triangle_area.Rmd
@@ -57,7 +57,7 @@ cws_final <- readRDS(paste0(
 ### Timeseries at each step of brassens pipeline
 
 ```{r}
-timeseries(cws_raw, ts = ts, te = te, var = temp)
+timeseries(cws_raw2, ts = ts, te = te, var = temp)
 timeseries(cws_qc, ts = ts, te = te, var = temp)
 timeseries(cws_final, ts = ts, te = te, var = temp)
 ```