Merge pull request #53 from TanguyBarthelemy/develop

update repo

.Rbuildignore

@@ -1,11 +1,27 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+
 ^\.git$
 ^\.github$
-^\.lintr$
-^LICENSE$
+
 ^README\.Rmd$
-^README\.html$
-^_pkgdown\.yml$
+^README-.*\.png$
+
+^Meta$
 ^docs$
+^doc$
 ^pkgdown$
+^_pkgdown\.yml$
+
+^\.lintr$
+
+^appveyor\.yml$
+.travis.yml
+
+cran-comments.md
+
+^\.DS_Store$
+
+^revdep$
+^reconf\.sh$
+^pom\.xml$

.github/workflows/test-coverage.yaml

@@ -1,10 +1,7 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
-  push:
-    branches: [main, develop]
-  pull_request:
-    branches: [main, develop]
+  workflow_dispatch
 
 name: test-coverage
 

.gitignore

@@ -1,7 +1,58 @@
-.Rproj.user
+# History files
 .Rhistory
+.Rapp.history
+
+# Session Data files
 .RData
+.RDataTmp
+
+# User-specific files
 .Ruserdata
-docs
 
-TO_DO
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+Meta/
+inst/doc/
+doc/
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# pkgdown site
+docs/
+
+# translation temp files
+po/*~
+
+# RStudio Connect folder
+rsconnect/
+
+# Hidden file from mac-os
+.DS_Store
+
+# produced README.html
+README.html

DESCRIPTION

@@ -8,7 +8,7 @@ Authors@R: c(
   person("Alain", "Quartier-la-Tente", role = c("aut"),
                  email = "[email protected]",
                  comment = c(ORCID = "0000-0001-7890-3857")),
-  person("Tanguy", "Barthelemy", role = c("aut","cre"),
+  person("Tanguy", "Barthelemy", role = c("aut", "cre", "art"),
                  email ="[email protected]"),
   person("Anna", "Smyk", role = c("aut"),
                  email ="[email protected]")

R/print.R

@@ -1,7 +1,7 @@
 #'@importFrom stats printCoefmat
 #'@importFrom utils capture.output
 print_x11_decomp <- function(x, digits = max(3L, getOption("digits") - 3L), ...){
-  mstats = matrix(unlist(x$mstats),
+  mstats <- matrix(unlist(x$mstats),
                   ncol = 1,
                   dimnames = list(names(x$mstats), "M stats"))
   cat("Monitoring and Quality Assessment Statistics:",
@@ -17,9 +17,9 @@ print_x11_decomp <- function(x, digits = max(3L, getOption("digits") - 3L), ...)
 }
 print_diagnostics <- function(x, digits = max(3L, getOption("digits") - 3L),
                               ...){
-  diagnostics = rjd3toolkit::diagnostics(x)
-  variance_decomposition = diagnostics$variance_decomposition
-  residual_tests = diagnostics$residual_tests
+  diagnostics <- rjd3toolkit::diagnostics(x)
+  variance_decomposition <- diagnostics$variance_decomposition
+  residual_tests <- diagnostics$residual_tests
 
   cat("Relative contribution of the components to the stationary",
       "portion of the variance in the original series,",
@@ -292,13 +292,13 @@ plot.JD3_X13_OUTPUT <- function(x, first_date = NULL, last_date = NULL,
 #' @importFrom rjd3toolkit diagnostics
 #' @export
 diagnostics.JD3_X13_RSLTS<-function(x, ...){
-  if (is.null(x)) return (NULL)
-  variance_decomposition = x$diagnostics$vardecomposition
-  variance_decomposition = matrix(unlist(variance_decomposition),
+  if (is.null(x)) return(NULL)
+  variance_decomposition <- x$diagnostics$vardecomposition
+  variance_decomposition <- matrix(unlist(variance_decomposition),
                                   ncol = 1,
                                   dimnames = list(names(variance_decomposition), "Component"))
-  residual_tests = x$diagnostics[grep("test", names(x$diagnostics))]
-  residual_tests = data.frame(Statistic = sapply(residual_tests, function(test) test[["value"]]),
+  residual_tests <- x$diagnostics[grep("test", names(x$diagnostics))]
+  residual_tests <- data.frame(Statistic = sapply(residual_tests, function(test) test[["value"]]),
                               P.value = sapply(residual_tests, function(test) test[["pvalue"]]),
                               Description =  sapply(residual_tests, function(test) attr(test, "distribution")))
   list(preprocessing = rjd3toolkit::diagnostics(x$preprocessing),
@@ -308,5 +308,5 @@ diagnostics.JD3_X13_RSLTS<-function(x, ...){
 
 #' @export
 diagnostics.JD3_X13_OUTPUT<-function(x, ...){
-  return (rjd3toolkit::diagnostics(x$result, ...))
+  return(rjd3toolkit::diagnostics(x$result, ...))
 }

R/revisions.R

@@ -4,7 +4,7 @@ NULL
 .jrevisions<-function(jts, jspec, jcontext){
   jrslt<-.jcall("jdplus/x13/base/r/X13RevisionHistory",
                 "Ljdplus/toolkit/base/r/timeseries/Revisions;", "revisions", jts, jspec, jcontext)
-  return (jrslt)
+  return(jrslt)
 }
 
 
@@ -67,26 +67,26 @@ x13_revisions<-function(ts, spec, data_ids=NULL, ts_ids=NULL, cmp_ids=NULL, cont
   if (! is.null(data_ids)){
     ldata<-lapply(data_ids, function(data_id){
       w<-.jcall(jr, "Ljdplus/toolkit/base/api/timeseries/TsData;", "history", data_id$id, data_id$start)
-      return (rjd3toolkit::.jd2r_tsdata(w))
+      return(rjd3toolkit::.jd2r_tsdata(w))
     })
     names(ldata) <- sapply(data_ids, `[[`,"id")
   }
   lts<-NULL
   if (! is.null(ts_ids)){
     lts<-lapply(ts_ids, function(ts_id){
       w<-.jcall(jr, "Ljdplus/toolkit/base/api/timeseries/TsData;", "tsHistory", ts_id$id, ts_id$period, ts_id$start)
-      return (rjd3toolkit::.jd2r_tsdata(w))
+      return(rjd3toolkit::.jd2r_tsdata(w))
     })
    names(lts) <- sapply(ts_ids, `[[`,"id")
   }
   lcmp<-NULL
   if (! is.null(cmp_ids)){
     lcmp<-lapply(cmp_ids, function(cmp_id){
       w<-.jcall(jr, "Ljdplus/toolkit/base/api/timeseries/TsDataTable;", "tsSelect", cmp_id$id, cmp_id$start, cmp_id$end)
-      return (rjd3toolkit::.jd2r_mts(w))
+      return(rjd3toolkit::.jd2r_mts(w))
     })
     names(lcmp) <- sapply(cmp_ids, `[[`,"id")
   }
 
-  return (list(data=ldata, series=lts, components=lcmp))
+  return(list(data=ldata, series=lts, components=lcmp))
 }

R/set_x11_spec.R

@@ -110,7 +110,7 @@ set_x11.JD3_X11_SPEC <- function(x,
     if ((henderson.filter != 0) && (henderson.filter %% 2 == 0)) {
       warning("The variable henderson.filter should be an odd number or equal to 0.", call. = FALSE)
     } else {
-      x$henderson = henderson.filter
+      x$henderson <- henderson.filter
     }
   }
 

R/udvar.R

@@ -1,18 +1,18 @@
 .add_ud_var <- function(x, jx, userdefined = NULL, out_class = NULL, result = FALSE){
   if (is.null(userdefined)) {
-    x$user_defined = rjd3toolkit::user_defined(x, NULL)
+    x$user_defined <- rjd3toolkit::user_defined(x, NULL)
   } else {
     if (result) {
-      res = jx
+      res <- jx
     } else {
       if (is.null(out_class)) {
-        res = jx$getResult()
+        res <- jx$getResult()
       } else {
-        res = .jcall(jx, out_class, "getResult")
+        res <- .jcall(jx, out_class, "getResult")
       }
     }
-    res = rjd3toolkit::.jd3_object(res, result = TRUE)
-    x$user_defined = rjd3toolkit::user_defined(res, userdefined = userdefined)
+    res <- rjd3toolkit::.jd3_object(res, result = TRUE)
+    x$user_defined <- rjd3toolkit::user_defined(res, userdefined = userdefined)
   }
   x
 }
@@ -48,7 +48,7 @@ userdefined_variables_x13 <- function(x = c("X-13","RegArima","X-11")){
   #   sort() |>
   #   dput()
 
-  sa_x13 = c("adjust", "arima.bd", "arima.bp", "arima.bphi(*)", "arima.bq",
+  sa_x13 <- c("adjust", "arima.bd", "arima.bp", "arima.bphi(*)", "arima.bq",
              "arima.btheta(*)", "arima.d", "arima.p", "arima.phi(*)", "arima.q",
              "arima.theta(*)", "benchmarking.original", "benchmarking.result",
              "benchmarking.target", "cal", "cal_b", "cal_b(?)", "cal_f", "cal_f(?)",
@@ -146,7 +146,7 @@ userdefined_variables_x13 <- function(x = c("X-13","RegArima","X-11")){
   #   sort() |>
   #   dput()
 
-  sa_regarima = c("adjust", "arima.bd", "arima.bp", "arima.bphi(*)", "arima.bq",
+  sa_regarima <- c("adjust", "arima.bd", "arima.bp", "arima.bphi(*)", "arima.bq",
                   "arima.btheta(*)", "arima.d", "arima.p", "arima.phi(*)", "arima.q",
                   "arima.theta(*)", "cal", "cal_b(?)", "cal_f(?)", "det", "det_b(?)",
                   "det_f(?)", "det_i", "det_i_b(?)", "det_i_f(?)", "det_s", "det_s_b(?)",
@@ -187,13 +187,13 @@ userdefined_variables_x13 <- function(x = c("X-13","RegArima","X-11")){
   #   sort() |>
   #   dput()
 
-  sa_x11 = c("b1", "b10", "b11", "b13", "b17", "b2", "b20", "b3", "b4",
+  sa_x11 <- c("b1", "b10", "b11", "b13", "b17", "b2", "b20", "b3", "b4",
              "b5", "b6", "b7", "b8", "b9", "c1", "c10", "c11", "c13", "c17",
              "c2", "c20", "c4", "c5", "c6", "c7", "c9", "d1", "d10", "d11",
              "d12", "d13", "d2", "d4", "d5", "d6", "d7", "d8", "d9", "d9-global-msr",
              "d9-msr", "d9-msr-table", "seasonal-filters", "trend-filter",
              "x11-all")
-  switch (x,
+  switch(x,
           x13 = sa_x13,
           regarima = sa_regarima,
           x11 = sa_x11