Style(#44): air formatting of functions

.github/workflows/format-check.yaml

@@ -0,0 +1,23 @@
+# Workflow derived from https://github.com/posit-dev/setup-air/tree/main/examples
+
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+
+name: format-check.yaml
+
+permissions: read-all
+
+jobs:
+  format-check:
+    name: format-check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Install
+        uses: posit-dev/setup-air@v1
+
+      - name: Check
+        run: air format . --check

R/agg_custom.R

@@ -6,25 +6,33 @@
 #'
 #' @noRd
 
-
-agg_custom  <-  function(data, groups, fun, agg.scale){
+agg_custom <- function(data, groups, fun, agg.scale) {
   out = atlantistools::agg_data(data = data, groups = groups, fun = fun) %>%
-    mutate(date = as.POSIXct(time*365*86400, origin = '1964-01-01 00:00:00',tz = 'UTC'))
+    mutate(
+      date = as.POSIXct(
+        time * 365 * 86400,
+        origin = '1964-01-01 00:00:00',
+        tz = 'UTC'
+      )
+    )
 
-  if(agg.scale == 'month') {
-    out$time.agg = as.numeric(factor(format(out$date,format = '%m')))
-  }else if(agg.scale == 'year'){
+  if (agg.scale == 'month') {
+    out$time.agg = as.numeric(factor(format(out$date, format = '%m')))
+  } else if (agg.scale == 'year') {
     out$time.agg = as.numeric(factor(format(out$date, format = '%Y')))
-  }else{
-    out$time.agg = out$time*365
+  } else {
+    out$time.agg = out$time * 365
   }
 
-  match.cols = c(groups[-which(groups == 'time')],'time.agg')
+  match.cols = c(groups[-which(groups == 'time')], 'time.agg')
   out.agg = out %>%
     group_by_at(match.cols) %>%
-    dplyr::summarise(time = floor(min(time)),
-              atoutput = mean(atoutput,na.rm=T),.groups="drop")
-    dplyr::select(all_of(c(groups,'atoutput')))
+    dplyr::summarise(
+      time = floor(min(time)),
+      atoutput = mean(atoutput, na.rm = T),
+      .groups = "drop"
+    )
+  dplyr::select(all_of(c(groups, 'atoutput')))
 
   return(out.agg)
 }

R/calc_mef.R

@@ -11,21 +11,18 @@
 #'
 #'@noRd
 
-
-
 calc_mef <- function(observed, expected) {
-
   #remove NAs. Exist only in observed data
   expected <- expected[!is.na(observed)]
   observed <- observed[!is.na(observed)]
 
-  oo <- sum((observed-mean(observed))^2)
+  oo <- sum((observed - mean(observed))^2)
   po <- sum((expected - observed)^2)
 
-  mef <- (oo-po)/oo
+  mef <- (oo - po) / oo
 
   # number of data point used in calculation
   n <- length(expected)
 
-  return(list(mef=mef,n=n))
+  return(list(mef = mef, n = n))
 }

R/check_species_codes.R

@@ -11,27 +11,29 @@
 #'
 #' @noRd
 
-check_species_codes <- function(modelBiomass,speciesCodes){
-
+check_species_codes <- function(modelBiomass, speciesCodes) {
   # use default options
   atlantisCodes <- modelBiomass %>%
     dplyr::filter(!is.na(.data$code)) %>%
     dplyr::distinct(.data$code) %>%
     dplyr::pull()
   # use default options
-  if (is.null(speciesCodes)) { # select all species
+  if (is.null(speciesCodes)) {
+    # select all species
     speciesCodes <- atlantisCodes
   } else {
     # remove NA's check for codes not in atlantis
     speciesCodes <- speciesCodes[!is.na(speciesCodes)]
     # check to make sure no non atlantis codes
-    invalidCodes <- base::setdiff(speciesCodes,atlantisCodes)
+    invalidCodes <- base::setdiff(speciesCodes, atlantisCodes)
 
-    if (!(length(invalidCodes)==0)){
-      stop("Invalid Atlantis group codes: ",paste0(invalidCodes,collapse=", "))
+    if (!(length(invalidCodes) == 0)) {
+      stop(
+        "Invalid Atlantis group codes: ",
+        paste0(invalidCodes, collapse = ", ")
+      )
     }
   }
 
   return(speciesCodes)
-
 }