Merge pull request #30 from NorwegianVeterinaryInstitute/dev

OKplan v0.8.0

.gitignore

@@ -39,3 +39,5 @@ vignettes/*.pdf
 .Renviron
 
 inst/doc
+!vignettes/OKplan.pdf
+

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: OKplan
 Title: Tools to facilitate the Planning of the annual Surveillance Programmes
-Version: 0.7.1
-Date: 2024-11-12
+Version: 0.8.0
+Date: 2024-12-19
 Authors@R: 
   c(person(given = "Petter",
            family = "Hopp",
@@ -26,9 +26,9 @@ Imports:
     stats,
     NVIbatch (>= 0.4.0),
     NVIcheckmate (>= 0.7.3),
-    NVIdb,
+    NVIdb (>= 0.13.1),
     NVIpjsr,
-    NVIpretty (>= 0.4.0),
+    NVIpretty (>= 0.4.2),
     OKcheck
 Suggests:
     covr,
@@ -38,6 +38,7 @@ Suggests:
     knitr,
     purrr,
     rmarkdown,
+    R.rsp,
     testthat,
     usethis,
     utils,
@@ -53,5 +54,5 @@ Remotes:
     NorwegianVeterinaryInstitute/NVIrpackages,
     NorwegianVeterinaryInstitute/OKcheck
 RoxygenNote: 7.3.1
-VignetteBuilder: knitr
+VignetteBuilder: knitr, R.rsp
 Language: en-GB

NAMESPACE

@@ -8,6 +8,7 @@ export(check_ok_selection)
 export(get_holiday)
 export(get_tested_herds)
 export(make_random)
+export(save_okplan)
 export(style_sum_line)
 export(write_ok_selection_list)
 importFrom(rlang,.data)

NEWS.md

@@ -1,3 +1,19 @@
+# OKplan 0.8.0 - (2024-12-19)
+
+## New features:
+
+- created `save_okplan` to save the selection information in a standard format.
+
+- `write_ok_selection_list` now accepts `data.frame`, `list` and csv-file as input to the argument `column_standards`.
+
+
+## Other changes:
+
+- `OK_column_standards` is updated with column standards used in 2025, i.e. including orgnr in selection lists and generating  "ok_ai_art_fjorfe".
+
+- created pdf reference manual "OKplan.pdf" as a vignette.
+
+
 # OKplan 0.7.1 - (2024-11-12)
 
 ## Bug fixes

R/check_ok_selection.R

@@ -43,8 +43,8 @@
 #'     Set "browser" for the default browser or "viewer" for the R studio
 #'      viewer. `TRUE` equals "browser". If `FALSE`, don't display
 #'      the results file. Defaults to "browser".
-#' @param \dots Other arguments to be passed to
-#'     \ifelse{html}{\code{\link[NVIbatch]{output_rendered}}}{\code{NVIbatch::output_rendered}}.
+#' @param \dots	Other arguments to be passed to
+#'     \ifelse{html}{\code{\link[NVIbatch:output_rendered]{NVIbatch::output_rendered}}}{\code{NVIbatch::output_rendered}}.
 #'
 #' @return Generates an html-file with the results of the checks to be displayed in the browser.
 #'

R/save_okplan.R

@@ -0,0 +1,88 @@
+#' @title Writes the surveillance selection to a standardised file.
+#'
+#' @description The surveillance selection is written to a standardised file.
+#'     The file is standardised to include a standard set of columns and have
+#'     the records in a standard order.
+#' @details The data is saved as an "okplan" file that will be used the source
+#'     file when the selection list is generated.
+#'
+#'     The function uses
+#'     \ifelse{html}{\code{\link[NVIdb:standardize_columns]{NVIdb::standardize_columns}}}{\code{NVIdb::standardize_columns}}.
+#'     to select and order the columns. The formatting information is taken from
+#'     \code{\link{OK_column_standards}}.
+#'
+#' @param data [\code{data.frame}]\cr
+#'     The sampling plan with the units to be reported.
+#' @param filename [\code{character(1)}]\cr
+#'     The name of the csv file including extension.
+#' @param filepath [\code{character(1)}]\cr
+#'     The path to the csv file.
+#' @param sortvar [\code{character}]\cr
+#'     The sort order for the records in the csv-file. Defaults to
+#'     c("ok_hensiktkode", "ok_driftsformkode", "statuskode",
+#'       "prioritet_av_reserve", "eier_lokalitetnr")
+#' @param \dots	Other arguments to be passed to
+#'     \ifelse{html}{\code{\link[utils:write.csv2]{utils::write.csv2}}}{\code{utils::write.csv2}}.
+#'
+#' @return None. Saves a data frame with the selection in a standard csv file.
+#'
+#' @author Petter Hopp Petter.Hopp@@vetinst.no
+#' @export
+#' @examples
+#' \dontrun{
+#' library(OKplan)
+#' td <- tempdir()
+#' okplan <- as.data.frame(list("ok_hensiktkode" = c("01002", "01002"),
+#'                              "ok_driftsformkode" = c("010202", "010202"),
+#'                              "statuskode" = c(1, 1),
+#'                              "prioritet_av_reserve" = c(NA, NA),
+#'                              "eier_lokalitetnr" = c("1101123456", "1102123456")))
+#' write_okplan(data = okplan,
+#'              filename = "okplan_species_disease",
+#'              filepath = td)
+#' }
+save_okplan <- function(data,
+                         filename,
+                         filepath,
+                         sortvar = c("ok_hensiktkode", "ok_driftsformkode",
+                                     "statuskode", "prioritet_av_reserve",
+                                     "eier_lokalitetnr"),
+                         ...) {
+
+  # PREPARE ARGUMENTS BEFORE ARGUMENT CHECKING ----
+  ## Remove trailing backslash or slash before testing path
+  filepath <- sub("\\\\{1,2}$|/{1,2}$", "", filepath)
+
+  # ARGUMENT CHECKING ----
+  ## Object to store check-results
+  checks <- checkmate::makeAssertCollection()
+  ## Perform checks
+  ### data
+  checkmate::assert_data_frame(data, add = checks)
+  checkmate::assert_character(filename, min.chars = 1, len = 1, add = checks)
+  ### filename and filepath
+  checkmate::assert_character(filename, min.chars = 1, len = 1, add = checks)
+  checkmate::assert_directory_exists(filepath)
+  ### order
+  checkmate::assert_subset(sortvar, choices = colnames(data), add = checks)
+  ## Report check-results
+  checkmate::reportAssertions(checks)
+
+
+  # STANDARDISE AND SAVE DATA TO csv-FILE ----
+  ## Standardise column order, exclude columns
+  data <- NVIdb::standardize_columns(data,
+                                     dbsource = "okplan",
+                                     standards = OKplan::OK_column_standards,
+                                     property = "colorder",
+                                     exclude = TRUE)
+
+  ## Sort data in the order given by sortvar
+  data <- data[do.call(base::order, data[, sortvar]), ]
+
+  ## write the data to the csv-file
+  utils::write.csv2(data,
+                    file = file.path(filepath, filename),
+                    row.names = FALSE,
+                    ...)
+}

R/write_ok_selection_list.R

@@ -5,20 +5,21 @@
 #'     without further formatting.
 #' @details The data must originate from an "okplan" file and
 #'     the function uses
-#'     \ifelse{html}{\code{\link[NVIdb]{standardize_columns}}}{\code{NVIdb::standardize_columns}}
-#'     to  select, order, format and style the columns. The formatting
+#'     \ifelse{html}{\code{\link[NVIdb:standardize_columns]{NVIdb::standardize_columns}}}{\code{NVIdb::standardize_columns}}.
+#'     to select, order, format and style the columns. The formatting
 #'     information is either taken from \code{\link{OK_column_standards}} or
-#'     can be input as a list.
+#'     can be input as a \code{list}
 #'
 #' When using \code{\link{OK_column_standards}}, the formatting information is
 #'     taken in accord with the argument \code{dbsource}. If the formatting
 #'     needs to be edited, it must be edited in the general source file for
 #'     column standards and thereafter, build it into a new version of \code{OKplan}.
 #'     As this can be a tedious process, there is a possibility to input the
-#'     formatting information as a list.
+#'     formatting information as a \code{list} or as a csv-file that can be transformed
+#'     to a \code{data.frame} with the same columns as \code{\link{OK_column_standards}}.
 #'
 #' The list input to column_standards must follow a specific format.
-#'     It is a list with at least three named vectors:
+#'     It is a \code{list} with at least three named vectors:
 #' \itemize{
 #' \item \code{colname}: a vector of all columns in in the source file that
 #'     should be included in the Excel report with the selection list.
@@ -61,11 +62,15 @@
 #'     The name of the Excel file.
 #' @param filepath [\code{character(1)}]\cr
 #'     The path to the Excel file.
-#' @param column_standards [\code{data.frame} | \code{list}]\cr
-#'     The column standards to be used as input for
+#' @param column_standards [\code{data.frame} | \code{list} | \code{character(1)}]\cr
+#' The column standards to be used as input for
 #'     \ifelse{html}{\code{\link[NVIdb]{standardize_columns}}}{\code{NVIdb::standardize_columns}}
-#'     when formatting the sampling plan for
-#'     output, see details. Defaults to \code{\link{OK_column_standards}}.
+#'     when formatting the sampling plan for output, see details. Defaults to
+#'     \code{\link{OK_column_standards}}.
+#' For giving alternatives to the standard table for column_standards using
+#'     different formats, see details. Defaults to
+#'     file.path(NVIdb::set_dir_NVI("ProgrammeringR", slash = FALSE),
+#'               "standardization", "colnames", "column_standards.csv").
 #' @param calculate_sum [\code{logical(1)}]\cr
 #'     Should a line with the sum be appended? Defaults to \code{TRUE}.
 #' @param footnote [\code{character(1)}]\cr
@@ -103,33 +108,52 @@ write_ok_selection_list <- function(data,
   checks <- checkmate::makeAssertCollection()
 
   # Perform checks
-  # for (i in 1:length(data)) {
+  # data
   checkmate::assert_data_frame(data, max.rows = (1048576 - 1), max.cols = 16384, add = checks)
-  # }
+  # filename and filepath
   checkmate::assert_character(sheet, min.chars = 1, min.len = 1, max.len = length(data), unique = TRUE, add = checks)
   checkmate::assert_character(filename, min.chars = 1, len = 1, add = checks)
   checkmate::assert_directory_exists(filepath, add = checks)
   if (isTRUE(add_worksheet)) {
-    checkmate::assert_file_exists(file.path(filepath, filename), access = "r")
+    checkmate::assert_file_exists(file.path(filepath, filename), access = "r", add = checks)
   }
   # column_standards
+  # checkmate::assert(checkmate::check_class(column_standards, classes = c("data.frame")),
+  #                   checkmate::check_class(column_standards, classes = c("list")),
+  #                   add = checks)
+  # if (inherits(column_standards, what = "list")) {
+  #   lengths_standard <- lengths(column_standards)
+  #   NVIcheckmate::assert_integer(lengths_standard, lower = lengths_standard[1], upper = lengths_standard[1],
+  #                                min.len = 3, max.len = 6,
+  #                                comment = "When input as a list, all elements must have the same length",
+  #                                add = checks)
+  #
+  #   checkmate::assert_subset(names(column_standards), choices = c("table_db", "colname_db", "colname", "collabel", "colwidth", "colorder"),
+  #                            add = checks)
+  # }
+  # if (inherits(column_standards, what = "data.frame")) {
+  #   checkmate::assert_data_frame(column_standards, min.rows = 1, min.cols = 6, add = checks)
+  # }
   checkmate::assert(checkmate::check_class(column_standards, classes = c("data.frame")),
                     checkmate::check_class(column_standards, classes = c("list")),
+                    checkmate::check_class(column_standards, classes = c("character")),
                     add = checks)
+  if (inherits(column_standards, what = "character")) {
+    checkmate::assert_file_exists(column_standards, add = checks)
+  }
   if (inherits(column_standards, what = "list")) {
     lengths_standard <- lengths(column_standards)
     NVIcheckmate::assert_integer(lengths_standard, lower = lengths_standard[1], upper = lengths_standard[1],
                                  min.len = 3, max.len = 6,
                                  comment = "When input as a list, all elements must have the same length",
                                  add = checks)
-
     checkmate::assert_subset(names(column_standards), choices = c("table_db", "colname_db", "colname", "collabel", "colwidth", "colorder"),
                              add = checks)
   }
   if (inherits(column_standards, what = "data.frame")) {
     checkmate::assert_data_frame(column_standards, min.rows = 1, min.cols = 6, add = checks)
   }
-
+  # calculate_sum
   checkmate::assert_flag(calculate_sum, add = checks)
   checkmate::assert_string(footnote, min.chars = 1, null.ok = TRUE, add = checks)
   checkmate::assert_character(dbsource, min.len = 1, add = checks)
@@ -144,27 +168,23 @@ write_ok_selection_list <- function(data,
   checkmate::reportAssertions(checks)
 
   # TRANSFORM column_standards FROM list TO data.frame
-  # column_standards = list("colname" = c("mt_region", "mt_avdeling"),
-  #                 "collabel" = c("MT region", "MT avdeling"),
-  #                 "colwidth" = c(35, 35))
-
-  if (inherits(column_standards, what = "list")) {
-    column_standards <- as.data.frame((column_standards))
-
-    if (!"table_db" %in% colnames(column_standards)) {
-      column_standards$table_db <- dbsource
-    }
-
-    if (!"colname_db" %in% colnames(column_standards)) {
-      column_standards$colname_db <- column_standards$colname
-    }
-
-    if (!"colorder" %in% colnames(column_standards)) {
-      column_standards$colorder <- c(1:dim(column_standards)[1])
-    }
-    colnames(column_standards)[which(colnames(column_standards) == "collabel")] <- "label_1_no"
-    colnames(column_standards)[which(colnames(column_standards) == "colwidth")] <- "colwidth_Excel"
-  }
+  # if (inherits(column_standards, what = "list")) {
+  #   column_standards <- as.data.frame((column_standards))
+  #
+  #   if (!"table_db" %in% colnames(column_standards)) {
+  #     column_standards$table_db <- dbsource
+  #   }
+  #
+  #   if (!"colname_db" %in% colnames(column_standards)) {
+  #     column_standards$colname_db <- column_standards$colname
+  #   }
+  #
+  #   if (!"colorder" %in% colnames(column_standards)) {
+  #     column_standards$colorder <- c(1:dim(column_standards)[1])
+  #   }
+  #   colnames(column_standards)[which(colnames(column_standards) == "collabel")] <- "label_1_no"
+  #   colnames(column_standards)[which(colnames(column_standards) == "colwidth")] <- "colwidth_Excel"
+  # }
 
   # GENERATE EXCEL WORKBOOK ----
   # create or load workbook