Refrain from recomputing VPD for CRU based on potentially non-existin…

…g column 'vapr'

This fixes VPD for CRU, when vapr was not requested.
This commit moves computation of vpd with calc_vpd() inside of ingest_globalfields() for CRU, watch_wfdei, and wfde5. This results in consistent code between these 3 sources and also irrespective of the user calling ingest() or ingest_bysite(). Hence, this reduces code replication.
Furthermore, calc_vpd() is now re-computed (in ingest() or ingest_bysite()) only in cases when there is bias correction of `vapr` with WorldClim data. This code is still repeated across ingest() and ingest_bysite().

R/ingest.R

@@ -647,35 +647,11 @@ ingest <- function(
       }
 
     } else {
-
-      # Calculate vapour pressure deficit from specific humidity
-      # this calculates this variable for cases where there is
-      # no bias correction
-
       if ("vpd" %in% getvars){
-
-        if (source == "watch_wfdei" || source == "wfde5"){
-          # use daily mean temperature
-          ddf <- ddf %>%
-            rowwise() %>%
-            dplyr::mutate(
-              vapr = calc_vp(qair = qair, patm = patm),
-              vpd = calc_vpd(eact = vapr, tc = temp)
-              ) %>% 
-            ungroup()
-
-        } else if (source == "cru"){
-          # use daily minimum and maximum temperatures
-          ddf <- ddf %>%
-            rowwise() %>%
-            dplyr::mutate(
-              vpd = calc_vpd(eact = vapr, tmin = tmin, tmax = tmax)
-              ) %>% 
-            ungroup()
-        }
-
+        # For cases where there is no bias correction,
+        # (of sources cru, watch_wfdei, wfde5; but not ndep)
+        # vapour pressure deficit has already been computed within `ingest_globalfields()`
       }
-
     }
 
 	} else if (source == "gee"){

R/ingest_bysite.R

@@ -448,46 +448,10 @@ ingest_bysite <- function(
       }
 
     } else {
-
-      # Calculate vapour pressure deficit from specific humidity
-      # this calculates this variable for cases where there is
-      # no bias correction
-
       if ("vpd" %in% getvars){
-
-        # xxxxxxx
-        if (!("vapr" %in% names(df_tmp))){
-          # calculate vapour pressure from specific humidity - needed for bias correction with worldclim data
-          if (source == "watch_wfdei"){
-            # specific humidity (qair, g g-1) is read, convert to vapour pressure (vapr, Pa)
-            df_tmp <- df_tmp %>% 
-              rowwise() %>% 
-              dplyr::mutate(vapr = calc_vp(qair = qair, patm = patm)) %>% 
-              ungroup()
-
-          } else if (source == "cru"){
-            # vapour pressure is read from file, convert from hPa to Pa
-            df_tmp <- df_tmp %>% 
-              dplyr::mutate(vapr = 1e2 * vap) %>% 
-              dplyr::select(-vap)
-
-          }
-        }
-
-        if (source == "watch_wfdei"){
-          # use daily mean temperature
-          df_tmp <- df_tmp %>%
-            rowwise() %>%
-            dplyr::mutate(vpd = calc_vpd(eact = vapr, tc = temp)) %>% 
-            ungroup()
-
-        } else if (source == "cru"){
-          # use daily minimum and maximum temperatures
-          df_tmp <- df_tmp %>%
-            rowwise() %>%
-            dplyr::mutate(vpd = calc_vpd(eact = vapr, tmin = tmin, tmax = tmax)) %>% 
-            ungroup()
-        }
+        # For cases where there is no bias correction,
+        # (of sources cru, watch_wfdei, wfde5; but not ndep)
+        # vapour pressure deficit has already been computed within `ingest_globalfields()`
       }
     }
 

R/ingest_globalfields.R

@@ -92,6 +92,13 @@ ingest_globalfields <- function(
             dplyr::rename(patm = myvar),
           by = c("sitename", "date")
         )
+
+      # calculate VPD based on humidity, air temperature, and atmospheric pressure
+      df_out <- df_out %>%
+        rowwise() %>%
+        mutate(vapr = calc_vp(qair = qair, patm = patm)) %>%
+        mutate(vpd  = calc_vpd(eact = vapr, tc = temp)) %>%
+        ungroup()
     }
 
     # precipitation
@@ -163,6 +170,13 @@ ingest_globalfields <- function(
             dplyr::rename(patm = myvar),
           by = c("sitename", "date")
         )
+
+      # calculate VPD based on humidity, air temperature, and atmospheric pressure
+      df_out <- df_out %>%
+        rowwise() %>%
+        mutate(vapr = calc_vp(qair = qair, patm = patm)) %>%
+        mutate(vpd  = calc_vpd(eact = vapr, tc = temp)) %>%
+        ungroup()
     }
 
     # precipitation