Merge pull request #34 from TanguyBarthelemy/develop

Some linting
rjdverse · Jan 28, 2025 · 3e2718e · 3e2718e
2 parents eb2e8e5 + 77eebca
commit 3e2718e
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Showing 34 changed files with 874 additions and 804 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,3 +1,4 @@
+
 ^.*\.Rproj$
 ^\.Rproj\.user$
 
@@ -6,6 +7,7 @@
 
 ^README\.Rmd$
 ^README-.*\.png$
+^README\.html$
 
 ^Meta$
 ^docs$
@@ -24,4 +26,19 @@ cran-comments.md
 
 ^revdep$
 ^reconf\.sh$
+
 ^pom\.xml$
+
+^CITATION\.cff$
+^LICENSE.md$
+
+^\.httr-oauth$
+^\.zenodo\.json$
+
+^checklist.yml$
+^codecov\.yml$
+^data-raw$
+^dev$
+
+^man-roxygen$
+^organisation.yml$
diff --git a/.lintr b/.lintr
@@ -1,26 +1,48 @@
-linters: linters_with_defaults(
+linters: lintr::all_linters(
         indentation_linter = NULL,
-        trailing_blank_lines_linter = NULL,
-        trailing_whitespace_linter = NULL,
-        assignment_linter = NULL,
-        whitespace_linter = NULL,
-        brace_linter = NULL,
+        # line_length_linter = lintr::line_length_linter(80L),
+        line_length_linter = lintr::line_length_linter(200L),
         infix_spaces_linter = NULL,
-        paren_body_linter = NULL,
+        #paren_body_linter = NULL,
         indentation_linter = NULL,
-        function_left_parentheses_linter = NULL,
-        spaces_left_parentheses_linter = NULL,
+        #function_left_parentheses_linter = NULL,
         commas_linter = NULL,
         quotes_linter = NULL,
         spaces_inside_linter = NULL,
-        vector_logic_linter = NULL,
-        seq_linter = NULL,
+        #vector_logic_linter = NULL,
+        #seq_linter = NULL,
         object_length_linter = NULL,
         semicolon_linter = NULL,
         cyclocomp_linter = NULL,
         object_usage_linter = NULL,
         object_name_linter = NULL,
-        line_length_linter = NULL,
-        commented_code_linter = NULL
+        commented_code_linter = NULL,
+        extraction_operator_linter = NULL,
+        undesirable_function_linter = NULL,
+        nonportable_path_linter = NULL,
+        implicit_integer_linter = NULL,
+        numeric_leading_zero_linter = NULL,
+        fixed_regex_linter = NULL,
+        unused_import_linter = NULL,
+        #absolute_path_linter = NULL,
+        library_call_linter = NULL,
+        keyword_quote_linter = NULL,
+        missing_package_linter = NULL,
+        unnecessary_concatenation_linter = NULL,
+        strings_as_factors_linter = NULL,
+        #class_equals_linter = NULL,
+        namespace_linter = NULL,
+        inner_combine_linter = NULL,
+        #paste_linter = NULL,
+        unnecessary_lambda_linter = NULL,
+        function_argument_linter = NULL,
+        if_not_else_linter = NULL,
+        unnecessary_lambda_linter = NULL,
+        boolean_arithmetic_linter = NULL,
+        condition_message_linter = NULL,
+        undesirable_operator_linter = NULL,
+        #nested_ifelse_linter = NULL,
+        unnecessary_nested_if_linter = NULL,
+        todo_comment_linter = NULL
     )
 encoding: "UTF-8"
diff --git a/NEWS.md b/NEWS.md
@@ -5,6 +5,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this project adheres
 to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+
 ## [Unreleased]
 
 ### Added
@@ -16,9 +17,9 @@ to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 ### Changed
 
 * `filter()` correction when the length of the series equals the length of the filter.
-
 * `confint_filter()` uses by default a Student distribution instead of a Normal distribution.
 
+
 ## [2.1.1] - 2024-07-12
 
 ### Changed
@@ -31,9 +32,7 @@ to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 * New functions to compute functions to compute diagnostics and goodness of fit of filtered series: cross validation (`cv()`) and cross validate estimate (`cve()`), leave-one-out cross validation estimate (`loocve`), CP statistic (`cp()`) and Rice's T statistics (`rt()`).
 
 * New function `confint_filter()` to compute confidence intervals for filtered series.
-
 * New function `is.finite_filters()`.
-
 * New parameter `zero_as_na` in `cbind.moving_average`, boolean indicating if trealing and leading zeros added to have a matrix form should be replaced by `NA`.
 
 

diff --git a/R/1_moving_average.R b/R/1_moving_average.R
@@ -73,13 +73,13 @@ NULL
 #' s <- y * s_mm
 #' plot(s)
 #' @export
-moving_average <- function(x, lags = -length(x), trailing_zero = FALSE, leading_zero = FALSE){
+moving_average <- function(x, lags = -length(x), trailing_zero = FALSE, leading_zero = FALSE) {
   if (inherits(x, "moving_average"))
     return(x)
   x <- as.numeric(x)
   if (trailing_zero)
     x <- rm_trailing_zero_or_na(x)
-  if (leading_zero){
+  if (leading_zero) {
     new_x <- rm_leading_zero_or_na(x)
     lags <- lags - (length(new_x) - length(x))
     x <- new_x
@@ -95,15 +95,15 @@ moving_average <- function(x, lags = -length(x), trailing_zero = FALSE, leading_
              upper_bound = upper_bound)
   res
 }
-.jd2ma <- function(jobj, trailing_zero = FALSE){
+.jd2ma <- function(jobj, trailing_zero = FALSE) {
   x <- .jcall(jobj, "[D", "weightsToArray")
   lags <- .jcall(jobj, "I", "getLowerBound")
   moving_average(x, lags, trailing_zero = trailing_zero)
 }
-.ma2jd <- function(x){
+.ma2jd <- function(x) {
   lags <- lower_bound(x)
   coefs <- as.numeric(coef(x))
-  if (length(x) == 1){
+  if (length(x) == 1) {
     coefs <- .jarray(coefs)
   }
   .jcall("jdplus/toolkit/base/core/math/linearfilters/FiniteFilter",
@@ -113,60 +113,60 @@ moving_average <- function(x, lags = -length(x), trailing_zero = FALSE, leading_
 }
 #' @rdname moving_average
 #' @export
-is.moving_average <- function(x){
+is.moving_average <- function(x) {
   is(x, "moving_average")
 }
 #' @importFrom stats coef coefficients end qnorm qt ts.union
 #' @export
-coef.moving_average <- function(object, ...){
+coef.moving_average <- function(object, ...) {
   coefs <- object@coefficients
   return(coefs)
 }
 #' @rdname moving_average
 #' @export
-is_symmetric <- function(x){
+is_symmetric <- function(x) {
   # .jcall(.ma2jd(x), "Z", "isSymmetric")
   (upper_bound(x) == (-lower_bound(x))) &&
     isTRUE(all.equal(coef(x), rev(coef(x)), check.attributes = FALSE))
 }
 #' @rdname moving_average
 #' @export
-upper_bound <- function(x){
+upper_bound <- function(x) {
   x@upper_bound
 }
 #' @rdname moving_average
 #' @export
-lower_bound <- function(x){
+lower_bound <- function(x) {
   x@lower_bound
 }
 #' @rdname moving_average
 #' @export
-mirror <- function(x){
+mirror <- function(x) {
   .jd2ma(.jcall(.ma2jd(x), "Ljdplus/toolkit/base/core/math/linearfilters/FiniteFilter;", "mirror"))
 }
 #' @method rev moving_average
 #' @rdname moving_average
 #' @export
-rev.moving_average <- function(x){
+rev.moving_average <- function(x) {
   mirror(x)
 }
 #' @rdname moving_average
 #' @export
-length.moving_average <- function(x){
+length.moving_average <- function(x) {
   length(coef(x))
 }
 #' @rdname moving_average
 #' @export
-to_seasonal <- function(x, s){
+to_seasonal <- function(x, s) {
   UseMethod("to_seasonal", x)
 }
 #' @export
-to_seasonal.default <- function(x, s){
+to_seasonal.default <- function(x, s) {
   lb <- lower_bound(x)
   up <- upper_bound(x)
   coefs <- coef(x)
   new_coefs <- c(unlist(lapply(coefs[-length(x)],
-                               function(x){
+                               function(x) {
                                  c(x, rep(0, s - 1))
                                })),
                  coefs[length(x)])
@@ -175,7 +175,7 @@ to_seasonal.default <- function(x, s){
 
 #' @rdname filters_operations
 #' @export
-sum.moving_average <- function(..., na.rm = FALSE){
+sum.moving_average <- function(..., na.rm = FALSE) {
   sum(
     unlist(lapply(list(...),
                   function(x) sum(coef(x),na.rm = na.rm)
@@ -223,7 +223,7 @@ setReplaceMethod("[",
                  })
 #' @rdname filters_operations
 #' @export
-cbind.moving_average <- function(..., zero_as_na = FALSE){
+cbind.moving_average <- function(..., zero_as_na = FALSE) {
   all_mm <- list(...)
   new_lb <- min(sapply(all_mm, lower_bound))
   new_ub <- max(sapply(all_mm, upper_bound))
@@ -233,7 +233,7 @@ cbind.moving_average <- function(..., zero_as_na = FALSE){
   } else {
       blank_value <- 0
   }
-  new_mm <- lapply(all_mm, function(x){
+  new_mm <- lapply(all_mm, function(x) {
     c(rep(blank_value, abs(new_lb - lower_bound(x))),
       coef(x),
       rep(blank_value, abs(nb_uterms - (lower_bound(x) + length(x))))
@@ -245,7 +245,7 @@ cbind.moving_average <- function(..., zero_as_na = FALSE){
 }
 #' @rdname filters_operations
 #' @export
-rbind.moving_average <- function(...){
+rbind.moving_average <- function(...) {
   t(cbind(...))
 }
 #' @rdname filters_operations