Merge pull request #64 from stineb/master

Update to terra
geco-bern · Jul 18, 2024 · e2c5ac3 · e2c5ac3
2 parents 24998cb + b24ff93
commit e2c5ac3
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Showing 3 changed files with 15 additions and 7 deletions.
diff --git a/R/ingest.R b/R/ingest.R
@@ -868,8 +868,9 @@ ingest <- function(
 
 	} else if (source == "hwsd"){
 
-	  # Get HWSD soil data. year_start and year_end not required
 
+	  # https://github.com/bluegreen-labs/hwsdr
+	  # Get HWSD soil data. year_start and year_end not required
 
 	  # TODO replace with {hwsdr} call
 	  # con <- rhwsd::get_hwsd_con()

diff --git a/R/ingest_globalfields.R b/R/ingest_globalfields.R
@@ -467,8 +467,10 @@ ingest_globalfields <- function(
     df_out_top <- extract_pointdata_allsites( paste0(dir, "/", filename), df_lonlat, get_time = FALSE ) %>%
       dplyr::select(-lon, -lat) %>%
       tidyr::unnest(data) %>%
-      dplyr::rename(!!layer := V1) %>%
-      dplyr::select(sitename, !!layer)
+      tidyr::pivot_longer(cols = starts_with("PBR_depth")) %>% 
+      dplyr::rename(!!layer := value, depth = name) %>%
+      dplyr::mutate(depth = as.numeric(str_remove(depth, "PBR_depth="))) %>% 
+      dplyr::select(sitename, !!layer, depth)
 
     # bottom soil layers
     filename <- list.files(dir, pattern = paste0(layer, "2.nc"))
@@ -477,8 +479,10 @@ ingest_globalfields <- function(
     df_out_bottom <- extract_pointdata_allsites( paste0(dir, "/", filename), df_lonlat, get_time = FALSE ) %>%
       dplyr::select(-lon, -lat) %>%
       tidyr::unnest(data) %>%
-      dplyr::rename(!!layer := V1) %>%
-      dplyr::select(sitename, !!layer)
+      tidyr::pivot_longer(cols = starts_with("PBR_depth")) %>% 
+      dplyr::rename(!!layer := value, depth = name) %>%
+      dplyr::mutate(depth = as.numeric(str_remove(depth, "PBR_depth="))) %>% 
+      dplyr::select(sitename, !!layer, depth)
 
     # combine for layers read from each file
     df_out <- bind_rows(df_out_top, df_out_bottom) %>% 
@@ -497,7 +501,8 @@ ingest_globalfields <- function(
       rename(value = !!layer) %>% 
 
       # interpret missing values
-      na_if(-999) %>% 
+      ungroup() %>% 
+      mutate(value = ifelse(value == -999, NA, value)) %>% 
       mutate(value = ifelse(varnam %in% c("PHH2O", "PHK", "PHCA") & value == 100,
                             NA,
                             value)) %>% 

diff --git a/vignettes/example.Rmd b/vignettes/example.Rmd
@@ -1049,6 +1049,8 @@ Four steps are required before you can use `ingest()` to get HWSD data:
 ```{r warning=FALSE, eval = FALSE}
 if(!require(devtools)){install.packages(devtools)}
 devtools::install_github("stineb/rhwsd")
+
+# XXX to change to https://github.com/bluegreen-labs/hwsdr
 ```
 
 2.  Install additionally required packages: DBI and RSQLite.
@@ -1190,7 +1192,7 @@ df_gsde <- ingest(
   siteinfo_fluxnet2015 %>% slice(1:2),
   source    = "gsde",
   settings  = settings_gsde,
-  dir       = "~/data/soil/shangguan"
+  dir       = "/data/archive/soil_shangguan_2014/data/"
   )
 ```