Refactor climdex.r into modular R scripts

.github/workflows/R-CMD-check-on-PR.yaml

@@ -16,7 +16,7 @@ jobs:
  fail-fast: false
  matrix:
  config:
- - {os: macos-latest, r: 'release'}
+ # - {os: macos-latest, r: 'release'}
  - {os: windows-latest, r: 'release'}
  - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
  - {os: ubuntu-latest, r: 'release'}

DESCRIPTION

@@ -8,9 +8,12 @@ Maintainer: James Hiebert <[email protected]>
 Depends:
  R (>= 2.12.0),
  PCICt (>= 0.5-4)
+Encoding: UTF-8
 Imports:
  methods,
- Rcpp (>= 0.11.4)
+ Rcpp (>= 0.11.4),
+ stats,
+ utils
 Suggests:
  compiler,
  RUnit
@@ -23,4 +26,18 @@ License: GPL-3
 URL: https://www.r-project.org
 LazyData: yes
 BugReports: https:/pacificclimate/climdex.pcic/issues/
-RoxygenNote: 7.2.3
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2
+Collate:
+ 'input_utils.R'
+ 'climdexInput_class.R'
+ 'climdex.pcic-package.R'
+ 'constants.R'
+ 'date_utils.R'
+ 'precipitation_indices.R'
+ 'series_utils.R'
+ 'stats_utils.R'
+ 'temperature_indices.R'
+ 'threshold_indices.R'
+ 'threshold_utils.R'
+

NAMESPACE

@@ -1,3 +1,6 @@
+# Generated by roxygen2: do not edit by hand
+
+export(climdex.bootstrap.idx.list)
 export(climdex.cdd)
 export(climdex.csdi)
 export(climdex.cwd)
@@ -9,6 +12,8 @@ export(climdex.mean.idx.list)
 export(climdex.bootstrap.idx.list)
 export(climdex.gsl)
 export(climdex.id)
+export(climdex.mean.idx.list)
+export(climdex.min.max.idx.list)
 export(climdex.prcptot)
 export(climdex.quantile)
 export(climdex.r10mm)
@@ -48,6 +53,7 @@ exportClasses(climdexInput)
 import(PCICt)
 import(Rcpp)
 import(methods)
-importFrom("stats", "quantile")
-importFrom("utils", "head", "read.csv")
+importFrom(stats,quantile)
+importFrom(utils,head)
+importFrom(utils,read.csv)
 useDynLib(climdex.pcic, .registration = TRUE)

R/climdex.pcic-package.R

@@ -27,7 +27,8 @@
 #' 
 #' @name climdex.pcic
 #' @aliases climdex.pcic-package
-#' @docType package
+#' @keywords internal
+"_PACKAGE"
 #' @seealso \code{\link{climdexInput.raw}}, \code{\link{climdexInput.csv}},
 #' \code{\link{climdexInput-class}}.
 #' @references \url{http://etccdi.pacificclimate.org/list_27_indices.shtml}
@@ -43,7 +44,7 @@
 #' Zhang, X., 2005: Avoiding inhomogeneity in percentile-based indices of
 #' temperature extremes. Journal of Climate 18.11 (2005):1641-.
 #' @keywords climate ts
-#' @useDynLib climdex.pcic
+#' @useDynLib climdex.pcic, .registration = TRUE
 #' @import PCICt Rcpp methods
 NULL