Merge branch 'develop'

.gitignore

@@ -27,6 +27,8 @@ vignettes/*.pdf
 Meta/
 inst/doc/
 doc/
+/doc/
+/Meta/
 
 # OAuth2 token, see https:/hadley/httr/releases/tag/v0.3
 .httr-oauth

.lintr

@@ -3,6 +3,8 @@ linters: linters_with_defaults(
  object_usage_linter = NULL,
  object_name_linter = NULL,
  line_length_linter = NULL,
- commented_code_linter = NULL
+ commented_code_linter = NULL,
+ cyclocomp_linter = NULL,
+ brace_linter = NULL
  )
 encoding: "UTF-8"

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rjd3revisions
 Type: Package
 Title: Revision analysis with 'JDemetra+ 3.x'
-Version: 1.3.2
+Version: 1.4.0
 Authors@R: c(
  person(given = "Corentin", family = "Lemasson",
  email = "[email protected]", role = c("aut", "cre")), 
@@ -12,6 +12,10 @@ Description: Revision analysis tool part of 'JDemetra+ 3.x' (<https:
  with the results. The various tests enable the users to detect
  potential bias and sources of inefficiency in preliminary 
  estimates.
+License: EUPL | file LICENSE
+URL: https:/rjdverse/rjd3revisions, https://rjdverse.github.io/rjd3revisions/
+BugReports: https:/rjdverse/rjd3revisions/issues
+SystemRequirements: Java (>= 17)
 Depends:
  R (>= 4.1.0)
 Imports:
@@ -22,32 +26,32 @@ Imports:
  utils,
  stats,
  grDevices,
- graphics
+ graphics,
+ methods
 Suggests: 
  kableExtra,
  testthat (>= 3.0.0),
  knitr,
  rmarkdown,
  readxl,
- formattable
+ flextable
 Remotes:
- github::rjdverse/rjd3toolkit@*release
-SystemRequirements: Java (>= 17)
-License: EUPL | file LICENSE
-Encoding: UTF-8
+ github::rjdverse/rjd3toolkit
 Collate: 
  'rjd3revisions-package.R'
  'check.R'
  'conversion.R'
+ 'format_table.R'
  'report.R'
  'revisions.R'
  'revision_analysis.R'
  'simulate.R'
  'tests.R'
+ 'thresholds.R'
  'vintages.R'
  'zzz.R'
-RoxygenNote: 7.3.2
-URL: https:/rjdverse/rjd3revisions, https://rjdverse.github.io/rjd3revisions/
-BugReports: https:/rjdverse/rjd3revisions/issues
 Config/testthat/edition: 3
+Encoding: UTF-8
+RoxygenNote: 7.3.2
+Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(View,default)
+S3method(View,rjd3rev_rslts)
 S3method(View,rjd3rev_vintages)
 S3method(check_horizontal,data.frame)
 S3method(check_horizontal,default)
@@ -20,6 +22,7 @@ S3method(print,rjd3rev_vintages)
 S3method(summary,rjd3rev_revisions)
 S3method(summary,rjd3rev_rslts)
 S3method(summary,rjd3rev_vintages)
+export(View)
 export(bias)
 export(check_date_month)
 export(check_date_quarter)
@@ -40,7 +43,10 @@ export(orthogonallyModel1)
 export(orthogonallyModel2)
 export(render_report)
 export(revision_analysis)
+export(set_all_thresholds_to_default)
+export(set_thresholds_to_default)
 export(signalnoise)
+export(simulate_long)
 export(slope_and_drift)
 export(theil)
 export(theil2)
@@ -52,6 +58,8 @@ importFrom(grDevices,palette.colors)
 importFrom(graphics,legend)
 importFrom(graphics,par)
 importFrom(graphics,title)
+importFrom(methods,hasArg)
+importFrom(stats,as.formula)
 importFrom(stats,end)
 importFrom(stats,frequency)
 importFrom(stats,median)
@@ -60,6 +68,7 @@ importFrom(stats,quantile)
 importFrom(stats,reshape)
 importFrom(stats,rnorm)
 importFrom(stats,start)
+importFrom(stats,time)
 importFrom(stats,ts)
 importFrom(stats,ts.plot)
 importFrom(tools,file_ext)

NEWS.md

@@ -9,6 +9,24 @@ to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 ## [Unreleased]
 
 
+## [1.4.0] - 2024-08-21 
+
+### Added
+
+* user-defined thresholds for tests assessment
+* possibility to add plot of revisions in report
+* New `View()`, `summary()` and `print()` method to visualize the revision analysis
+
+### Changed
+
+* pivot from {formattable} dependency to {flextable} to build the tables
+* `simulate_long()` is now an exported function to construct datasets example
+
+### Fixed
+
+* solve a display glitch in diagonal view of functions print.rjd3rev_vintages() and print.rjd3rev_revisions() 
+
+
 ## [1.3.2] - 2024-07-10
 
 ### Added
@@ -92,7 +110,8 @@ to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 * Release based on JD+_main : v3.0.2
 
-[Unreleased]: https:/rjdverse/rjd3revisions/compare/v1.3.2...HEAD
+[Unreleased]: https:/rjdverse/rjd3revisions/compare/v1.4.0...HEAD
+[1.4.0]: https:/rjdverse/rjd3revisions/releases/tag/v1.3.2...v1.4.0
 [1.3.2]: https:/rjdverse/rjd3revisions/releases/tag/v1.3.1...v1.3.2
 [1.3.1]: https:/rjdverse/rjd3revisions/releases/tag/v1.3.0...v1.3.1
 [1.3.0]: https:/rjdverse/rjd3revisions/releases/tag/v1.2.1...v1.3.0

R/check.R

@@ -246,7 +246,7 @@ check_long <- function(x, date_format = "%Y-%m-%d") {
 #' Check vertical format
 #'
 #' @param x a formatted \code{data.frame} containing the input in the vertical format
-#' @param periodicity periodicity of the time period (12, 4 or 1 for resp.
+#' @param periodicity Integer. Periodicity of the time period (12, 4 or 1 for resp.
 #' monthly, quarterly or annual data)
 #' @param date_format \code{character} string corresponding to the format used in
 #' the input data.frame for the revision dates.

R/format_table.R

@@ -0,0 +1,45 @@
+theme_design <- function(x) {
+ x <- flextable::border_remove(x)
+ std_border <- flextable::fp_border_default(width = 4, color = "white")
+ # x <- fontsize(x, size = 10, part = "all")
+ x <- flextable::font(x, fontname = "Helvetica Neue", part = "all")
+ x <- flextable::align(x, align = "center", part = "all")
+
+ x <- flextable::bg(x, bg = "gray94", part = "body")
+ x <- flextable::bg(x, bg = "gray74", part = "header")
+ x <- flextable::bg(x, bg = "#7ca2ff", part = "footer")
+ x <- flextable::color(x, color = "black", part = "all")
+
+ x <- flextable::bg(x, j = 1L, bg = "gray74")
+ x <- flextable::color(x, j = 1L, color = "black")
+
+ x <- flextable::padding(x, padding = 6, part = "all")
+ x <- flextable::border_outer(x, part = "all", border = std_border)
+ x <- flextable::border_inner_h(x, border = std_border, part = "all")
+ x <- flextable::border_inner_v(x, border = std_border, part = "all")
+ x <- flextable::set_table_properties(x, layout = "autofit")
+ return(x)
+}
+
+create_formula <- function(col, status) {
+ return(as.formula(sprintf("~ grepl(x = `%s`, pattern = \"%s\")", col, status)))
+}
+
+format_column <- function(x, col) {
+ x <- flextable::bg(x, create_formula(col, "Good"), col, bg = "#4CAF50")
+ x <- flextable::bg(x, create_formula(col, "Uncertain"), col, bg = "#FFEB3B")
+ x <- flextable::bg(x, create_formula(col, "Bad"), col, bg = "#ff3737")
+ x <- flextable::bg(x, create_formula(col, "Severe"), col, bg = "#c10000")
+ x <- flextable::bold(x, create_formula(col, "Severe"), col)
+ x <- flextable::color(x, create_formula(col, "Severe"), col, color = "white")
+ return(x)
+}
+
+format_table <- function(x, col = "Tests") {
+ formatted_table <- cbind(
+ data.frame(Tests = rownames(x)),
+ as.data.frame(x)
+ )
+ colnames(formatted_table)[1] <- col
+ return(formatted_table)
+}

R/report.R

@@ -1,10 +1,13 @@
 #' Generate report on Revision Analysis
 #'
-#' @param rslt an object of class `"rjd3rev_vintages"` which is the output
+#' @param rslt an object of class `"rjd3rev_rslts"` which is the output
 #' of the function `revision_analysis()`
 #' @param output_file path or name of the output file containing the report
 #' @param output_dir path of the dir containing the output file (Optional)
-#' @param output_format either an HTML document (default) or a PDF document
+#' @param output_format either an HTML document (default), a PDF document or a
+#' Word document
+#' @param plot_revisions Boolean. Default is FALSE meaning that a plot with the
+#' revisions will not be added to the report.
 #' @param open_report Boolean. Default is TRUE meaning that the report will
 #' open automatically after being generated.
 #' @param ... Arguments to be passed to `rmarkdown::render()`, for example:
@@ -18,33 +21,36 @@
 #' @examples
 #'
 #' ## Simulated data
-#'
-#' long_format <- rjd3revisions:::simulate_long(
-#' start_period = as.Date("2020-01-01"),
-#' n_period = 24,
-#' n_revision = 6,
-#' periodicity = 12L
+#' df_long <- simulate_long(
+#' n_period = 10L * 4L,
+#' n_revision = 5L,
+#' periodicity = 4L,
+#' start_period = as.Date("2010-01-01")
 #' )
 #'
 #' ## Make analysis and generate the report
 #'
-#' vintages <- create_vintages(long_format, periodicity = 12L)
+#' vintages <- create_vintages(df_long, periodicity = 4L, type = "long")
 #' rslt <- revision_analysis(vintages, view = "diagonal")
+#'
 #' \dontrun{
 #' render_report(
 #' rslt,
 #' output_file = "my_report",
 #' output_dir = "C:/Users/xxx",
-#' output_format = "pdf_document"
+#' output_format = "pdf_document",
+#' plot_revisions = TRUE
 #' )
 #' }
 #'
-render_report <- function(rslt,
- output_file,
- output_dir,
- output_format = c("html_document", "pdf_document"),
- open_report = TRUE,
- ...) {
+render_report <- function(
+ rslt,
+ output_file,
+ output_dir,
+ output_format = c("html_document", "pdf_document", "word_document"),
+ plot_revisions = FALSE,
+ open_report = TRUE,
+ ...) {
 
  # Check input
  checkmate::assert_class(rslt, "rjd3rev_rslts")
@@ -68,6 +74,8 @@ render_report <- function(rslt,
  ext <- "html"
  } else if (output_format == "pdf_document") {
  ext <- "pdf"
+ } else if (output_format == "word_document") {
+ ext <- "docx"
  }
  }
  output_file <- tools::file_path_sans_ext(output_file)
@@ -82,8 +90,11 @@ render_report <- function(rslt,
  }
 
  e <- list2env(list(
+ rslt = rslt,
  descriptive_statistics = rslt$descriptive.statistics,
- main_results = rslt$summary
+ main_results = rslt$summary,
+ add_plot = plot_revisions,
+ revisions = rslt$revisions
  ))
 
  rmarkdown::render(