Merge pull request #183 from CeresBarros/columnNames_and_DT

Refer to columns by name, not index + using `data.table`
bcgov · Jan 26, 2024 · 395ae06 · 395ae06
2 parents 1fe1307 + 1116a20
commit 395ae06
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -22,14 +22,14 @@ jobs:
       matrix:
         config:
           - {os: macOS-latest,   r: 'release'}
-          - {os: windows-latest, r: 'devel'}
+          # - {os: windows-latest, r: 'devel'}
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: 'oldrel'}
-          - {os: windows-latest, r: '4.1'}
-          - {os: ubuntu-20.04,   r: 'devel'}
+          # - {os: windows-latest, r: 'oldrel'}
+          # - {os: windows-latest, r: '4.1'}
+          # - {os: ubuntu-20.04,   r: 'devel'}
           - {os: ubuntu-20.04,   r: 'release'}
-          - {os: ubuntu-20.04,   r: 'oldrel'}
-          - {os: ubuntu-20.04,   r: '4.1'}
+          # - {os: ubuntu-20.04,   r: 'oldrel'}
+          # - {os: ubuntu-20.04,   r: '4.1'}
 
     env:
       _SP_EVOLUTION_STATUS_: 2

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,13 +1,15 @@
 Package: climr
 Title: Downscaling of global climate data
-Version: 0.0.1.9000
-Date: 16-01-2024
+Version: 0.0.1.9001
+Date: 25-01-2024
 Authors@R: c(
     person("Kiri","Daust", email = "[email protected]", role = "aut"),
     person("Colin", "Mahony", email = "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-6111-5675")),
     person("Bruno", "Tremblay", email = "[email protected]", role = c("aut"),
            comment = c(ORCID = "0000-0002-2945-356X")),
+    person("Ceres", "Barros", email = "[email protected]", role = c("aut"),
+           comment = c(ORCID = "0000-0003-4036-977X")),       
     person("Francois", "Bornais", email = "[email protected]", role = c("aut")),
     person(family = "Province of British Columbia", role = c("cph", "fnd")))
 Description: This package replicate the basic approach of ClimateNA (climatena.ca),

diff --git a/NAMESPACE b/NAMESPACE
@@ -49,6 +49,7 @@ importFrom(pool,dbPool)
 importFrom(pool,poolClose)
 importFrom(sf,st_as_sf)
 importFrom(sf,st_join)
+importFrom(stats,as.formula)
 importFrom(stats,complete.cases)
 importFrom(terra,"crs<-")
 importFrom(terra,as.list)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,17 @@
+# `climr` 0.0.2
+## Enhancements
+* new tests comparing to reference outputs
+* code further streamlined
+* new messages warn user about meaningless `downscale`/`climr_downscale` argument combinations
+* argument options in `climr_downscale(..., which_normal)` now match the options of `normal_input(..., normal)`
+
+## Behaviour changes
+* `xyz` (argument to `climr_downscale` and `downscale`) must now be a 4 column `data.table` (or coercible class) with `lon`, `lat`, `elev` and `id` columns. All other columns are ignored and NOT returned.
+
+## Bugfixes
+* fixed temperature values of composite anomalies
+* name of composite anomalies changed to "normal_composite" in `normal_input(..., normal)`.
+
 # `climr` 0.0.1
 
 ## Enhancements

diff --git a/R/append_clim_vars.R b/R/append_clim_vars.R
@@ -113,40 +113,40 @@ append_clim_vars <- function(dt, vars) {
       set(dt, j = "Tave12", value = (v("Tmax12") + v("Tmin12")) / 2)
     },
     "PET01" = function() {
-      set(dt, j = "PET01", value = calc_PET(v("Tave01"), v("Tmin01"), v("Tmax01"), v("Elev")))
+      set(dt, j = "PET01", value = calc_PET(v("Tave01"), v("Tmin01"), v("Tmax01"), v("elev")))
     },
     "PET02" = function() {
-      set(dt, j = "PET02", value = calc_PET(v("Tave02"), v("Tmin02"), v("Tmax02"), v("Elev")))
+      set(dt, j = "PET02", value = calc_PET(v("Tave02"), v("Tmin02"), v("Tmax02"), v("elev")))
     },
     "PET03" = function() {
-      set(dt, j = "PET03", value = calc_PET(v("Tave03"), v("Tmin03"), v("Tmax03"), v("Elev")))
+      set(dt, j = "PET03", value = calc_PET(v("Tave03"), v("Tmin03"), v("Tmax03"), v("elev")))
     },
     "PET04" = function() {
-      set(dt, j = "PET04", value = calc_PET(v("Tave04"), v("Tmin04"), v("Tmax04"), v("Elev")))
+      set(dt, j = "PET04", value = calc_PET(v("Tave04"), v("Tmin04"), v("Tmax04"), v("elev")))
     },
     "PET05" = function() {
-      set(dt, j = "PET05", value = calc_PET(v("Tave05"), v("Tmin05"), v("Tmax05"), v("Elev")))
+      set(dt, j = "PET05", value = calc_PET(v("Tave05"), v("Tmin05"), v("Tmax05"), v("elev")))
     },
     "PET06" = function() {
-      set(dt, j = "PET06", value = calc_PET(v("Tave06"), v("Tmin06"), v("Tmax06"), v("Elev")))
+      set(dt, j = "PET06", value = calc_PET(v("Tave06"), v("Tmin06"), v("Tmax06"), v("elev")))
     },
     "PET07" = function() {
-      set(dt, j = "PET07", value = calc_PET(v("Tave07"), v("Tmin07"), v("Tmax07"), v("Elev")))
+      set(dt, j = "PET07", value = calc_PET(v("Tave07"), v("Tmin07"), v("Tmax07"), v("elev")))
     },
     "PET08" = function() {
-      set(dt, j = "PET08", value = calc_PET(v("Tave08"), v("Tmin08"), v("Tmax08"), v("Elev")))
+      set(dt, j = "PET08", value = calc_PET(v("Tave08"), v("Tmin08"), v("Tmax08"), v("elev")))
     },
     "PET09" = function() {
-      set(dt, j = "PET09", value = calc_PET(v("Tave09"), v("Tmin09"), v("Tmax09"), v("Elev")))
+      set(dt, j = "PET09", value = calc_PET(v("Tave09"), v("Tmin09"), v("Tmax09"), v("elev")))
     },
     "PET10" = function() {
-      set(dt, j = "PET10", value = calc_PET(v("Tave10"), v("Tmin10"), v("Tmax10"), v("Elev")))
+      set(dt, j = "PET10", value = calc_PET(v("Tave10"), v("Tmin10"), v("Tmax10"), v("elev")))
     },
     "PET11" = function() {
-      set(dt, j = "PET11", value = calc_PET(v("Tave11"), v("Tmin11"), v("Tmax11"), v("Elev")))
+      set(dt, j = "PET11", value = calc_PET(v("Tave11"), v("Tmin11"), v("Tmax11"), v("elev")))
     },
     "PET12" = function() {
-      set(dt, j = "PET12", value = calc_PET(v("Tave12"), v("Tmin12"), v("Tmax12"), v("Elev")))
+      set(dt, j = "PET12", value = calc_PET(v("Tave12"), v("Tmin12"), v("Tmax12"), v("elev")))
     },
     "CMI" = function() {
       set(dt, j = "CMI", value = v("PPT") - (v("PET01") + v("PET02") + v("PET03") + v("PET04") + v("PET05") + v("PET06") + v("PET07") + v("PET08") + v("PET09") + v("PET10") + v("PET11") + v("PET12")))
@@ -260,40 +260,40 @@ append_clim_vars <- function(dt, vars) {
       set(dt, j = "RH12", value = calc_RH(v("Tmin12"), v("Tmax12")))
     },
     "Eref01" = function() {
-      set(dt, j = "Eref01", value = calc_Eref(1, v("Tmin01"), v("Tmax01"), v("Lat")))
+      set(dt, j = "Eref01", value = calc_Eref(1, v("Tmin01"), v("Tmax01"), v("lat")))
     },
     "Eref02" = function() {
-      set(dt, j = "Eref02", value = calc_Eref(2, v("Tmin02"), v("Tmax02"), v("Lat")))
+      set(dt, j = "Eref02", value = calc_Eref(2, v("Tmin02"), v("Tmax02"), v("lat")))
     },
     "Eref03" = function() {
-      set(dt, j = "Eref03", value = calc_Eref(3, v("Tmin03"), v("Tmax03"), v("Lat")))
+      set(dt, j = "Eref03", value = calc_Eref(3, v("Tmin03"), v("Tmax03"), v("lat")))
     },
     "Eref04" = function() {
-      set(dt, j = "Eref04", value = calc_Eref(4, v("Tmin04"), v("Tmax04"), v("Lat")))
+      set(dt, j = "Eref04", value = calc_Eref(4, v("Tmin04"), v("Tmax04"), v("lat")))
     },
     "Eref05" = function() {
-      set(dt, j = "Eref05", value = calc_Eref(5, v("Tmin05"), v("Tmax05"), v("Lat")))
+      set(dt, j = "Eref05", value = calc_Eref(5, v("Tmin05"), v("Tmax05"), v("lat")))
     },
     "Eref06" = function() {
-      set(dt, j = "Eref06", value = calc_Eref(6, v("Tmin06"), v("Tmax06"), v("Lat")))
+      set(dt, j = "Eref06", value = calc_Eref(6, v("Tmin06"), v("Tmax06"), v("lat")))
     },
     "Eref07" = function() {
-      set(dt, j = "Eref07", value = calc_Eref(7, v("Tmin07"), v("Tmax07"), v("Lat")))
+      set(dt, j = "Eref07", value = calc_Eref(7, v("Tmin07"), v("Tmax07"), v("lat")))
     },
     "Eref08" = function() {
-      set(dt, j = "Eref08", value = calc_Eref(8, v("Tmin08"), v("Tmax08"), v("Lat")))
+      set(dt, j = "Eref08", value = calc_Eref(8, v("Tmin08"), v("Tmax08"), v("lat")))
     },
     "Eref09" = function() {
-      set(dt, j = "Eref09", value = calc_Eref(9, v("Tmin09"), v("Tmax09"), v("Lat")))
+      set(dt, j = "Eref09", value = calc_Eref(9, v("Tmin09"), v("Tmax09"), v("lat")))
     },
     "Eref10" = function() {
-      set(dt, j = "Eref10", value = calc_Eref(10, v("Tmin10"), v("Tmax10"), v("Lat")))
+      set(dt, j = "Eref10", value = calc_Eref(10, v("Tmin10"), v("Tmax10"), v("lat")))
     },
     "Eref11" = function() {
-      set(dt, j = "Eref11", value = calc_Eref(11, v("Tmin11"), v("Tmax11"), v("Lat")))
+      set(dt, j = "Eref11", value = calc_Eref(11, v("Tmin11"), v("Tmax11"), v("lat")))
     },
     "Eref12" = function() {
-      set(dt, j = "Eref12", value = calc_Eref(12, v("Tmin12"), v("Tmax12"), v("Lat")))
+      set(dt, j = "Eref12", value = calc_Eref(12, v("Tmin12"), v("Tmax12"), v("lat")))
     },
     "CMD01" = function() {
       set(dt, j = "CMD01", value = calc_CMD(v("Eref01"), v("PPT01")))
@@ -674,11 +674,11 @@ append_clim_vars <- function(dt, vars) {
   }
 
   # Remove unwanted variables
-  j_out <- names(dt)[!names(dt) %in% c("ID", "GCM", "SSP", "RUN", "PERIOD", vars)]
+  j_out <- names(dt)[!names(dt) %in% c("id", "GCM", "SSP", "RUN", "PERIOD", vars)]
   if (length(j_out)) {
     set(dt, j = j_out, value = NULL)
   }
 
   # Reorder to match vars
-  setcolorder(dt, c(names(dt)[names(dt) %in% c("ID", "GCM", "SSP", "RUN", "PERIOD")], vars))
+  setcolorder(dt, c(names(dt)[names(dt) %in% c("id", "GCM", "SSP", "RUN", "PERIOD")], vars))
 }
diff --git a/R/data-lists.R b/R/data-lists.R
@@ -54,14 +54,14 @@ list_run <- function(dbCon, gcm) {
 #' Currently available normals (`list_normal()`) are:
 #'   * "normal_na" for Climate NA derived normals
 #'   * "normal_bc" for British Columbia PRISM climatologies derived normals
-#'   * "composite_normal" for a composite of BC PRISM, adjusted US PRISM and 
+#'   * "normal_composite" for a composite of BC PRISM, adjusted US PRISM and 
 #'     DAYMET (Alberta and Saskatchewan), covering western Canada and western
 #'     US.
 #' 
 #' @rdname data-option-lists
 #' @export
 list_normal <- function() {
-  c("normal_na", "normal_bc","normal_composite")
+  c("normal_na", "normal_bc", "normal_composite")
 }