improve file handling

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '555688'
+ValidationKey: '576143'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
@@ -8,5 +8,6 @@ AcceptedNotes:
 - no visible binding for global variable
 - Found the following hidden files and directories: ~
 - All declared Imports should be used.
+- Non-standard file/directory found at top level: output
 allowLinterWarnings: yes
 enforceVersionUpdate: no

CITATION.cff

@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'piamValidation: Validation Tools for PIK-PIAM'
-version: 0.2.8
-date-released: '2024-05-03'
+version: 0.2.9
+date-released: '2024-05-24'
 abstract: The piamValidation package provides validation tools for the Potsdam Integrated
   Assessment Modelling environment.
 authors:

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: piamValidation
 Title: Validation Tools for PIK-PIAM
-Version: 0.2.8
-Date: 2024-05-03
+Version: 0.2.9
+Date: 2024-05-24
 Authors@R:
     c(person("Pascal", "Weigmann",, "pascal.weigmann@pik-potsdam.de", role = c("aut", "cre")),
       person("Oliver", "Richters",, role = "aut"))
@@ -16,6 +16,7 @@ Imports:
     ggthemes,
     htmltools,
     knitr,
+    piamutils,
     plotly,
     quitte (>= 0.3123.0),
     readxl,

NAMESPACE

@@ -9,10 +9,12 @@ import(ggplot2)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
+importFrom(dplyr,lag)
 importFrom(dplyr,mutate)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(ggthemes,theme_tufte)
+importFrom(piamutils,getSystemFile)
 importFrom(plotly,ggplotly)
 importFrom(readxl,excel_sheets)
 importFrom(readxl,read_excel)

R/combineData.R

@@ -14,7 +14,7 @@ combineData <- function(data, cfgRow, histData = NULL) {
   all_reg <- unique(data$region)
   all_per <- unique(data$period)  # not a factor, convert?
   all_per <- all_per[all_per <= 2100]
-  # TODO: take ref_per from ref_data for current var
+  # TODO: check if this works well
   ref_per <- c(2005, 2010, 2015, 2020)
 
 

R/importFunctions.R

@@ -28,7 +28,8 @@ getConfig <- function(configName) {
     path <- normalizePath(configName)
   }
   if (path == "") stop("Config not found, please provide either full path to a
-                       config file or choose a config from 'inst/config'.")
+  config file or select a config from 'inst/config' by choosing its
+  name ('validationConfig_<name>.csv'.\n")
 
   # config can be .xlsx or .csv, use "config" sheet in .xlsx if available
   if (grepl("\\.xlsx$", path)) {

R/validationReport.R

@@ -2,36 +2,59 @@
 #'
 #' @param dataPath one or multiple path(s) to scenario data in .mif or .csv
 #'        format
-#' @param config name of a config from inst/config
-#' @param report specify which .Rmd file should be used to create report
+#' @param config name a config from inst/config ("validationConfig_<name>.csv")
+#'        or give a full path to a separate configuration file
+#' @param report name a .Rmd from inst/markdown ("validationReport_<name>.Rmd")
+#'        to be rendered or give a full path to a separate .Rmd file
+#'
+#' @importFrom piamutils getSystemFile
 #'
 #' @export
 
 validationReport <- function(dataPath, config, report = "default") {
 
-
   # convert relative to absolute paths
   dataPath <- normalizePath(dataPath)
 
-  # for config only if no config in inst/config was chosen
+  # user has the option to enter name of files that are shipped with package
+  # or provide full paths to manually created files for config and report
+
   if (file.exists(normalizePath(config, mustWork = F))) {
+    # full path to config given
     config <- normalizePath(config)
+    config_name <- "Custom"
+  } else {
+    # name of config file in inst/config given
+    config_name <- config
   }
 
-  yamlParams <- list(mif = dataPath, cfg = config)
-
-  report_name <- paste0("validation_", report)
+  if (file.exists(normalizePath(report, mustWork = F))) {
+    # full path to report given
+    report_path <- normalizePath(report)
+    report_name <- "Custom"
+  } else {
+    # name of report file in inst/markdown given
+    report_path <- piamutils::getSystemFile(
+      paste0("markdown/validationReport_", report, ".Rmd"),
+      package = "piamValidation")
+    report_name <- report
+  }
 
+  # put rendered reports in output folder in working directory
   output_path <- paste0(getwd(), "/output")
   if (!dir.exists(output_path)) dir.create(output_path)
 
-  # create default report for given data
-  rmarkdown::render(paste0(path.package("piamValidation"),
-                           "/markdown/", report_name, ".Rmd"),
+  # include chosen config and report name in output file except if it is default
+  infix <- ""
+  if (config_name != "default") infix <- paste0(infix, "_cfg", config_name)
+  if (report_name != "default") infix <- paste0(infix, "_rep", report_name)
+
+  # create specified report for given data and config
+  yamlParams <- list(mif = dataPath, cfg = config)
+  rmarkdown::render(input = report_path,
                     params = yamlParams,
-                    output_file = paste0(output_path, "/", report_name,
+                    output_file = paste0(output_path, "/validation", infix,
                                          format(Sys.time(), "_%Y%m%d-%H%M%S"),
                                          ".html"))
-
 }
 

README.md

@@ -1,6 +1,6 @@
 # Validation Tools for PIK-PIAM
 
-R package **piamValidation**, version **0.2.8**
+R package **piamValidation**, version **0.2.9**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/piamValidation)](https://cran.r-project.org/package=piamValidation)  [![R build status](https://github.com/pik-piam/piamValidation/workflows/check/badge.svg)](https://github.com/pik-piam/piamValidation/actions) [![codecov](https://codecov.io/gh/pik-piam/piamValidation/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/piamValidation) [![r-universe](https://pik-piam.r-universe.dev/badges/piamValidation)](https://pik-piam.r-universe.dev/builds)
 
@@ -46,7 +46,7 @@ In case of questions / problems please contact Pascal Weigmann <pascal.weigmann@
 
 To cite package **piamValidation** in publications use:
 
-Weigmann P, Richters O (2024). _piamValidation: Validation Tools for PIK-PIAM_. R package version 0.2.8, <URL: https://github.com/pik-piam/piamValidation>.
+Weigmann P, Richters O (2024). _piamValidation: Validation Tools for PIK-PIAM_. R package version 0.2.9, <https://github.com/pik-piam/piamValidation>.
 
 A BibTeX entry for LaTeX users is
 
@@ -55,7 +55,7 @@ A BibTeX entry for LaTeX users is
   title = {piamValidation: Validation Tools for PIK-PIAM},
   author = {Pascal Weigmann and Oliver Richters},
   year = {2024},
-  note = {R package version 0.2.8},
+  note = {R package version 0.2.9},
   url = {https://github.com/pik-piam/piamValidation},
 }
 ```

inst/markdown/validation_COMMITTED.Rmd → inst/markdown/validationReport_NGFS.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "piamValidation: COMMITTED"
+title: "piamValidation: NGFS"
 date: "`r format(Sys.Date())`"
 output:
   html_document:
@@ -32,12 +32,25 @@ knitr::opts_chunk$set(
 
 ## Import and Prepare Data
 
+Loading data from:
+
+```{r}
+for (m in params$mif) cat(paste0(normalizePath(m), "\n"))
+```
+
+Using config:
+
+```{r}
+cat(params$cfg, "\n")
+```
+
 
 ```{r, message = FALSE}
 # Data Preparation
 df <- validateScenarios(params$mif, params$cfg)
 df <- appendTooltips(df)
 ```
+
 ## Validation
 
 ### Summary