Merge pull request #26 from TanguyBarthelemy/develop

Update repo

.Rbuildignore

@@ -1,19 +1,27 @@
-^appveyor\.yml$
-^docs$
-^_pkgdown\.yml$
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^.lintr$
-^README.Rmd$
+
+^\.git$
+^\.github$
+
+^README\.Rmd$
 ^README-.*\.png$
-.travis.yml
-^pkgdown$
+
+^Meta$
+^docs$
 ^doc$
+^pkgdown$
+^_pkgdown\.yml$
+
+^\.lintr$
+
+^appveyor\.yml$
+.travis.yml
+
 cran-comments.md
-TODO.R
+
+^\.DS_Store$
+
 ^revdep$
-workspace
-workspace.xml
-R/test_X11.R
-^\.github$
-^LICENSE$
+^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

@@ -1,9 +1,58 @@
-.Rproj.user
+# History files
 .Rhistory
+.Rapp.history
+
+# Session Data files
 .RData
+.RDataTmp
+
+# User-specific files
 .Ruserdata
+
+# 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
-workspace
-workspace.xml
-inst/doc
-docs
+
+# produced README.html
+README.html

NEWS.md

@@ -36,6 +36,6 @@ to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 * New Jars
 
 
-[Unreleased]: https://github.com/rjdemetra/rjd3filters/compare/v2.0.0...HEAD
-[2.0.0]: https://github.com/rjdemetra/rjd3filters/releases/tag/v1.0.0...v2.0.0
-[1.0.0]: https://github.com/rjdemetra/rjd3filters/releases/tag/v1.0.0
+[Unreleased]: https://github.com/rjdverse/rjd3filters/compare/v2.0.0...HEAD
+[2.0.0]: https://github.com/rjdverse/rjd3filters/releases/tag/v1.0.0...v2.0.0
+[1.0.0]: https://github.com/rjdverse/rjd3filters/releases/tag/v1.0.0

R/2_finite_filters.R

@@ -106,7 +106,7 @@ is.finite_filters <- function(x){
           rfilters <- rev(rfilters)
         }
       } else {
-        if(first_to_last) {
+        if (first_to_last) {
           lfilters <- rev(lfilters)
           rfilters <- rev(rfilters)
         }

R/filter.R

@@ -122,7 +122,7 @@ ff_ma <- function(x, coefs, remove_missing = TRUE) {
     result <- c(rep(NA, data_clean$leading), result,
                rep(NA, data_clean$trailing))
   }
-  if(is.ts(x))
+  if (is.ts(x))
     result <- ts(result,start = start(x), frequency = frequency(x))
   result
 }

R/fst_filters.R

@@ -176,7 +176,7 @@ mse.default<-function(aweights, sweights, density=c("uniform", "rw"), passband =
     } else {
       sweights <- coef(sweights)
     }
-  } else if(length(sweights)>length(aweights)){
+  } else if (length(sweights)>length(aweights)){
     # we asume sweights were specify from [-n to n] instead of [0,n]
     n <- (length(sweights)-1)/2
     sweights <- sweights[-seq_len(n)]

R/get_properties_function.R

@@ -131,7 +131,7 @@ diagnostic_matrix <- function(x, lags, passband = pi/6,
   results <- c(sum(x)-1, sum(coef(x) * seq(lower_bound(x), upper_bound(x), by = 1)),
                sum(coef(x) * seq(lower_bound(x), upper_bound(x), by = 1)^2),
                fst(x, lags, passband = passband))
-  if(!missing(sweights)){
+  if (!missing(sweights)){
     results <- c(results,
                  mse(x,
                      sweights,

R/kernels.R

@@ -21,10 +21,10 @@ get_kernel <- function(kernel = c("Henderson","Uniform", "Triangular",
                      choices = c("henderson", "uniform", "triangular", "epanechnikov", "parabolic",
                                  "biweight", "triweight", "tricube", "trapezoidal", "gaussian"
                      ))
-  if(kernel == "parabolic")
+  if (kernel == "parabolic")
     kernel <- "epanechnikov"
   h <- as.integer(horizon)
-  if(kernel == "gaussian"){
+  if (kernel == "gaussian"){
     jkernel <- .jcall("jdplus/toolkit/base/core/data/analysis/DiscreteKernel",
                       "Ljava/util/function/IntToDoubleFunction;",
                       tolower(kernel), h, sd_gauss)

R/lp_filters.R

@@ -28,7 +28,7 @@ localpolynomials<-function(x,
                            endpoints = c("LC", "QL", "CQ", "CC", "DAF"),
                            ic = 4.5,
                            tweight = 0, passband = pi/12){
-  if(2*horizon < degree)
+  if (2*horizon < degree)
     stop("You need more observation (2 * horizon + 1) than variables (degree + 1) to estimate the filter.")
 
   d <- 2 / (sqrt(pi) * ic)
@@ -78,7 +78,7 @@ lp_filter <- function(horizon = 6, degree = 3,
                       endpoints = c("LC", "QL", "CQ", "CC", "DAF", "CN"),
                       ic = 4.5,
                       tweight = 0, passband = pi/12){
-  if(2*horizon < degree)
+  if (2*horizon < degree)
     stop("You need more observation (2 * horizon + 1) than variables (degree + 1) to estimate the filter.")
 
   d <- 2 / (sqrt(pi) * ic)

R/plots.R

@@ -31,13 +31,13 @@ plot_coef <- function(x, nxlab = 7, add = FALSE, ...){
 plot_coef.default <- function(x, nxlab = 7, add = FALSE,
                               zero_as_na = TRUE, q = 0, legend = FALSE,
                               legend.pos = "topright", ...){
-  if(zero_as_na)
+  if (zero_as_na)
     x  <- apply(x,2, trailingzero_as_na)
   col_to_plot <- sprintf("q=%i",q)
   col_to_plot <- col_to_plot[col_to_plot %in% colnames(x)]
   horizon <- (nrow(x)-1)/2
   if (length(col_to_plot) == 0) {
-    if(!add){
+    if (!add){
       plot(1, type="n",xaxt = "n", xlab = "",
            ylab = "coefficient", xlim=c(-horizon, horizon), ylim=c(0, 1),
            ...)
@@ -48,10 +48,10 @@ plot_coef.default <- function(x, nxlab = 7, add = FALSE,
   matplot(seq(-horizon, horizon, by = 1),x[,col_to_plot],
           xaxt = "n", xlab = "", type = "o", pch = 20,
           ylab = "coefficient", add = add, ...)
-  if(legend)
+  if (legend)
     legend(legend.pos,col_to_plot,
            col = seq_along(col_to_plot), lty=seq_along(col_to_plot), lwd=2)
-  if(!add)
+  if (!add)
     axis(1, at=seq(-horizon, horizon, by = 1), labels = rownames(x))
 }
 
@@ -62,7 +62,7 @@ plot_coef.moving_average <- function(x, nxlab = 7, add = FALSE, ...){
   matplot(seq(lower_bound(x), upper_bound(x), by = 1), x_plot,
           xaxt = "n", xlab = "", type = "o", pch = 20,
           ylab = "coefficient", add = add, ...)
-  if(!add)
+  if (!add)
     axis(1, at=seq(lower_bound(x), upper_bound(x), by = 1), labels = names(x_plot))
 }
 
@@ -91,7 +91,7 @@ plot_gain.moving_average<- function(x, nxlab = 7, add = FALSE,
   plot(g, type = "l",
        xaxt = "n", xlab = "",
        ylab = "gain", add = add, xlim = xlim, ...)
-  if(!add){
+  if (!add){
     x_lab_at <- seq(xlim[1]/pi, xlim[2]/pi, length.out = nxlab)
     axis(1, at = x_lab_at * pi, labels = xlabel(x_lab_at))
   }
@@ -112,7 +112,7 @@ plot_gain.finite_filters <- function(x, nxlab = 7, add = FALSE,
   all_g_f <- all_g_f[col_to_plot]
   y_val <- sapply(all_g_f, function(f) f(x_values))
   if (length(col_to_plot) == 0) {
-    if(!add){
+    if (!add){
       plot(1, type="n",xaxt = "n", xlab = "",
            ylab = "gain", xlim=xlim, ylim=c(0, 1),
            ...)
@@ -157,7 +157,7 @@ plot_phase.moving_average<- function(x, nxlab = 7, add = FALSE,
   plot(p_plot, type = "l",
        xaxt = "n", xlab = "",
        ylab = "phase", add = add, xlim = xlim, ...)
-  if(!add){
+  if (!add){
     x_lab_at <- seq(xlim[1]/pi, xlim[2]/pi, length.out = nxlab)
     axis(1, at = x_lab_at * pi, labels = xlabel(x_lab_at))
   }
@@ -180,11 +180,11 @@ plot_phase.finite_filters <- function(x, nxlab = 7, add = FALSE,
   all_p_f <- all_p_f[col_to_plot]
   y_val <- sapply(all_p_f, function(f) f(x_values))
 
-  if(normalized){
+  if (normalized){
     y_val[-1,] <- y_val[-1,] / x_values[-1]
   }
   if (length(col_to_plot) == 0) {
-    if(!add){
+    if (!add){
       plot(1, type="n",xaxt = "n", xlab = "",
            ylab = "phase", xlim=xlim, ylim=c(0, 1),
            ...)
@@ -222,7 +222,7 @@ trailingzero_as_na <- function(x){
     i <- i - 1
   }
   x
-  # if(x[length(x)]==0)
+  # if (x[length(x)]==0)
   #   x [seq(from = tail(which(!sapply(x, function(y) isTRUE(all.equal(y,0)))),1)+1,
   #          to = length(x),
   #          by = 1)] <- NA
@@ -237,7 +237,7 @@ rm_leading_zero_or_na <- function(x){
     remove_i <- c(i, remove_i)
     i <- i + 1
   }
-  if(is.null(remove_i)){
+  if (is.null(remove_i)){
     x
   } else{
     x[-remove_i]
@@ -252,7 +252,7 @@ rm_trailing_zero_or_na <- function(x){
     remove_i <- c(i, remove_i)
     i <- i - 1
   }
-  if(is.null(remove_i)){
+  if (is.null(remove_i)){
     x
   } else{
     x[-remove_i]
@@ -267,7 +267,7 @@ rm_trailing_zero <- function(x){
     remove_i <- c(i, remove_i)
     i <- i - 1
   }
-  if(is.null(remove_i)){
+  if (is.null(remove_i)){
     x
   } else{
     x[-remove_i]
@@ -288,7 +288,7 @@ remove_bound_NA <- function(x) {
     j <- j + 1
   }
 
-  if(is.null(remove_i_first) & is.null(remove_i_last)){
+  if (is.null(remove_i_first) & is.null(remove_i_last)){
     # list(data = x, leading = 0,
     #      trailing = 0)
   } else{

R/zzz.R

@@ -5,7 +5,7 @@
 NULL
 
 .onLoad <- function(libname, pkgname) {
-  if (! requireNamespace("rjd3toolkit", quietly = TRUE)) stop("Loading rjd3 libraries failed")
+  if (!requireNamespace("rjd3toolkit", quietly = TRUE)) stop("Loading rjd3 libraries failed")
   # For debugts_ging: to see if Jars are effectively loaded
   # options(java.parameters = "-verbose:class")
 

README.Rmd

@@ -10,8 +10,9 @@ knitr::opts_chunk$set(
   comment = "#>", 
   fig.path = "man/figures/README-", 
   fig.align="center", 
-  fig.width = 8
+  fig.width = 8L
 )
+options(max.print = 1000L)
 ```
 
 # rjd3filters
@@ -127,13 +128,16 @@ legend("topleft", legend = c("y", "Musgrave", "FST", "RKHS"),
 ### Comparison of the filters
 
 Different quality criteria from Grun-Rehomme *et al* (2018) and Wildi and McElroy(2019) can also be computed with the function `diagnostic_matrix()`:
+
 ```{r diagnostic-table, eval = TRUE}
 q_0_coefs <- list(Musgrave = musgrave[, "q=0"], 
                   fst_notimeliness = fst_notimeliness[, "q=0"], 
                   rkhs_timeliness = rkhs_timeliness[, "q=0"])
 
-sapply(q_0_coefs, diagnostic_matrix, 
-       lags = 6, sweight = musgrave[, "q=6"])
+sapply(X = q_0_coefs, 
+       FUN = diagnostic_matrix, 
+       lags = 6, 
+       sweights = musgrave[, "q=6"])
 ```
 
 The filters can also be compared by plotting there coefficients (`plot_coef`), gain function (`plot_gain`) and phase function (`plot_phase`):
@@ -244,4 +248,4 @@ pull requests should include **updated tests** and **updated documentation**. If
 
 ## Licensing
 
-The code of this project is licensed under the [European Union Public Licence (EUPL)](https://joinup.ec.europa.eu/page/eupl-text-11-12).
+The code of this project is licensed under the [European Union Public Licence (EUPL)](https://joinup.ec.europa.eu/collection/eupl/eupl-text-eupl-12).

README.md

@@ -142,8 +142,10 @@ q_0_coefs <- list(Musgrave = musgrave[, "q=0"],
                   fst_notimeliness = fst_notimeliness[, "q=0"], 
                   rkhs_timeliness = rkhs_timeliness[, "q=0"])
 
-sapply(q_0_coefs, diagnostic_matrix, 
-       lags = 6, sweight = musgrave[, "q=6"])
+sapply(X = q_0_coefs, 
+       FUN = diagnostic_matrix, 
+       lags = 6, 
+       sweights = musgrave[, "q=6"])
 #>         Musgrave fst_notimeliness rkhs_timeliness
 #> b_c  0.000000000     2.220446e-16     0.000000000
 #> b_l -0.575984377    -1.554312e-15    -0.611459167
@@ -361,4 +363,5 @@ should be added or updated.
 ## Licensing
 
 The code of this project is licensed under the [European Union Public
-Licence (EUPL)](https://joinup.ec.europa.eu/page/eupl-text-11-12).
+Licence
+(EUPL)](https://joinup.ec.europa.eu/collection/eupl/eupl-text-eupl-12).

_pkgdown.yml

@@ -1,4 +1,4 @@
-url: https://rjdemetra.github.io/rjd3filters/
+url: https://rjdverse.github.io/rjd3filters/
 template:
   bootstrap: 5