Remove unused ellipsis parameters

Unused arguments were being passed in calls through ignored ellipsis. These previously silent and inconsequential bugs started triggering warnings. They are now fixed and if reintroduced, will trigger errors.
aphalo · Sep 12, 2024 · 35eea81 · 35eea81
1 parent 0199cb2
commit 35eea81
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Showing 29 changed files with 68 additions and 1,796 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: ggspectra
 Type: Package
 Title: Extensions to 'ggplot2' for Radiation Spectra
 Version: 0.3.12.9002
-Date: 2024-08-04
+Date: 2024-09-12
 Authors@R:
    c(
     person("Pedro J.", "Aphalo", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3385-972X")),

diff --git a/R/autoplot-cps-spct.r b/R/autoplot-cps-spct.r
@@ -38,7 +38,6 @@
 #'   long form.
 #' @param ylim numeric y axis limits,
 #' @param na.rm logical.
-#' @param ... currently ignored.
 #'
 #' @return a \code{ggplot} object.
 #'
@@ -58,8 +57,7 @@ cps_plot <- function(spct,
                      facets,
                      ylim,
                      object.label,
-                     na.rm,
-                     ...) {
+                     na.rm) {
   if (!is.cps_spct(spct)) {
     stop("cps_plot() can only plot cps_spct objects.")
   }
@@ -335,7 +333,6 @@ autoplot.cps_spct <-
     cps_plot(spct = object,
              w.band = w.band,
              range = range,
-             norm = norm,
              pc.out = pc.out,
              label.qty = label.qty,
              span = span,
@@ -347,8 +344,7 @@ autoplot.cps_spct <-
              facets = facets,
              ylim = ylim,
              object.label = object.label,
-             na.rm = na.rm,
-             ...) +
+             na.rm = na.rm) +
       autotitle(object = object,
                 time.format = time.format,
                 tz = tz,

diff --git a/R/autoplot-filter-spct.r b/R/autoplot-filter-spct.r
@@ -917,7 +917,6 @@ R_plot <- function(spct,
 #'   (color coordinates) or a \code{\link[photobiology]{chroma_spct}} object.
 #' @param na.rm logical.
 #' @param ylim numeric y axis limits,
-#' @param ... currently ignored.
 #'
 #' @return a \code{ggplot} object.
 #'
@@ -937,8 +936,7 @@ O_plot <- function(spct,
                    chroma.type,
                    facets,
                    na.rm,
-                   ylim,
-                   ...) {
+                   ylim) {
   if (!is.object_spct(spct)) {
     stop("O_plot() can only plot object_spct objects.")
   }
@@ -1297,8 +1295,7 @@ autoplot.filter_spct <-
                            idfactor = idfactor,
                            facets = facets,
                            ylim = ylim,
-                           na.rm = na.rm,
-                           ...)
+                           na.rm = na.rm)
     } else if (plot.qty == "absorbance") {
       out.ggplot <- A_plot(spct = object,
                            w.band = w.band,
@@ -1313,8 +1310,7 @@ autoplot.filter_spct <-
                            idfactor = idfactor,
                            facets = facets,
                            ylim = ylim,
-                           na.rm = na.rm,
-                           ...)
+                           na.rm = na.rm)
     } else if (plot.qty == "absorptance") {
       out.ggplot <- Afr_plot(spct = object,
                              w.band = w.band,
@@ -1330,8 +1326,7 @@ autoplot.filter_spct <-
                              idfactor = idfactor,
                              facets = facets,
                              ylim = ylim,
-                             na.rm = na.rm,
-                             ...)
+                             na.rm = na.rm)
     } else {
       stop("Invalid 'plot.qty' argument value: '", plot.qty, "'")
     }
@@ -1822,8 +1817,7 @@ autoplot.object_spct <-
                            chroma.type = chroma.type,
                            facets = facets,
                            ylim = ylim,
-                           na.rm = na.rm,
-                           ...)
+                           na.rm = na.rm)
       out.ggplot +
         autotitle(object = object,
                   time.format = time.format,
@@ -1841,7 +1835,6 @@ autoplot.object_spct <-
         stop("Invalid 'plot.qty' argument value: '", plot.qty, "'")
       }
       autoplot(object = object,
-               ...,
                w.band = w.band,
                range = range,
                norm = norm,

diff --git a/R/autoplot-generic-spct.R b/R/autoplot-generic-spct.R
@@ -37,7 +37,6 @@
 #'   long form.
 #' @param ylim numeric y axis limits,
 #' @param na.rm logical.
-#' @param ... currently ignored.
 #'
 #' @return a \code{ggplot} object.
 #'
@@ -58,8 +57,7 @@ generic_plot <- function(spct,
                          idfactor,
                          facets,
                          ylim,
-                         na.rm,
-                         ...) {
+                         na.rm) {
   if (!photobiology::is.generic_spct(spct)) {
     stop("generic_plot() can only plot generic_spct objects.")
   }
@@ -274,8 +272,7 @@ autoplot.generic_spct <-
                    idfactor = idfactor,
                    facets = facets,
                    ylim = ylim,
-                   na.rm = na.rm,
-                   ...) +
+                   na.rm = na.rm) +
         autotitle(object = object,
                   time.format = time.format,
                   tz = tz,

diff --git a/R/autoplot-raw-spct.r b/R/autoplot-raw-spct.r
@@ -40,7 +40,6 @@
 #'   long form.
 #' @param ylim numeric y axis limits,
 #' @param na.rm logical.
-#' @param ... currently ignored.
 #'
 #' @return a \code{ggplot} object.
 #'
@@ -60,8 +59,7 @@ raw_plot <- function(spct,
                      idfactor,
                      facets,
                      ylim,
-                     na.rm,
-                     ...) {
+                     na.rm) {
   if (!is.raw_spct(spct)) {
     stop("raw_plot() can only plot response_spct objects.")
   }
@@ -374,13 +372,11 @@ autoplot.raw_spct <-
              pc.out = pc.out,
              annotations = annotations,
              geom = geom,
-             norm = norm,
              text.size = text.size,
              idfactor = idfactor,
              facets = facets,
              ylim = ylim,
-             na.rm = na.rm,
-             ...) +
+             na.rm = na.rm) +
       autotitle(object = object,
                 time.format = time.format,
                 tz = tz,

diff --git a/R/autoplot-response-spct.r b/R/autoplot-response-spct.r
@@ -37,7 +37,6 @@
 #'   long form.
 #' @param na.rm logical.
 #' @param ylim numeric y axis limits,
-#' @param ... currently ignored.
 #'
 #' @return a \code{ggplot} object.
 #'
@@ -56,8 +55,7 @@ e_rsp_plot <- function(spct,
                        idfactor,
                        facets,
                        ylim,
-                       na.rm,
-                       ...) {
+                       na.rm) {
   if (!is.response_spct(spct)) {
     stop("e_Rsp_plot() can only plot response_spct objects.")
   }
@@ -280,7 +278,6 @@ e_rsp_plot <- function(spct,
 #'   long form.
 #' @param ylim numeric y axis limits,
 #' @param na.rm logical.
-#' @param ... currently ignored.
 #'
 #' @return a \code{ggplot} object.
 #'
@@ -299,8 +296,7 @@ q_rsp_plot <- function(spct,
                        idfactor,
                        facets,
                        ylim,
-                       na.rm,
-                       ...) {
+                       na.rm) {
   if (!is.response_spct(spct)) {
     stop("q_Rsp_plot() can only plot response_spct objects.")
   }
@@ -643,13 +639,11 @@ autoplot.response_spct <-
                                wls.target = wls.target,
                                annotations = annotations,
                                geom = geom,
-                               norm = norm,              # read from object
                                text.size = text.size,
                                idfactor = idfactor,
                                facets = facets,
                                ylim = ylim,
-                               na.rm = na.rm,
-                               ...)
+                               na.rm = na.rm)
     } else if (unit.out=="energy") {
       out.ggplot <- e_rsp_plot(spct = object,
                                w.band = w.band,
@@ -660,13 +654,11 @@ autoplot.response_spct <-
                                wls.target = wls.target,
                                annotations = annotations,
                                geom = geom,
-                               norm = norm,
                                text.size = text.size,
                                idfactor = idfactor,
                                facets = facets,
                                ylim = ylim,
-                               na.rm = na.rm,
-                               ...)
+                               na.rm = na.rm)
     } else {
       stop("Invalid 'unit.out' argument: '", unit.out, "'")
     }

diff --git a/R/autoplot-source-spct.r b/R/autoplot-source-spct.r
@@ -41,7 +41,6 @@
 #'   long form.
 #' @param ylim numeric y axis limits,
 #' @param na.rm logical.
-#' @param ... currently ignored.
 #'
 #' @return a \code{ggplot} object.
 #'
@@ -61,8 +60,7 @@ e_plot <- function(spct,
                    idfactor,
                    facets,
                    ylim,
-                   na.rm,
-                   ...) {
+                   na.rm) {
   if (!is.source_spct(spct)) {
     stop("e_plot() can only plot source_spct objects.")
   }
@@ -331,7 +329,6 @@ e_plot <- function(spct,
 #'   form.
 #' @param ylim numeric y axis limits,
 #' @param na.rm logical.
-#' @param ... currently ignored.
 #'
 #' @return a \code{ggplot} object.
 #'
@@ -351,8 +348,7 @@ q_plot <- function(spct,
                    idfactor,
                    facets,
                    ylim,
-                   na.rm,
-                   ...) {
+                   na.rm) {
   if (!is.source_spct(spct)) {
     stop("q_plot() can only plot source_spct objects.")
   }
@@ -825,8 +821,7 @@ autoplot.source_spct <-
                            idfactor = idfactor,
                            facets = facets,
                            ylim = ylim,
-                           na.rm = na.rm,
-                           ...)
+                           na.rm = na.rm)
     } else if (unit.out == "energy") {
       out.ggplot <- e_plot(spct = object,
                            w.band = w.band,
@@ -842,8 +837,7 @@ autoplot.source_spct <-
                            idfactor = idfactor,
                            facets = facets,
                            ylim = ylim,
-                           na.rm = na.rm,
-                           ...)
+                           na.rm = na.rm)
     } else {
       stop("Invalid 'radiation.unit' argument value: '", unit.out, "'")
     }

diff --git a/R/axis-utils-calibration-spct.R b/R/axis-utils-calibration-spct.R
@@ -4,7 +4,7 @@
 #' as character, expression (R default devices) or LaTeX (for tikz device).
 #'
 #' @param unit.exponent integer
-#' @param format character string, "R", "R.expresion", "R.character", or
+#' @param format character string, "R", "R.expression", "R.character", or
 #'   "LaTeX".
 #' @param label.text character Textual portion of the labels.
 #' @param scaled logical If \code{TRUE} relative units are assumed.

diff --git a/R/ggplot-methods.R b/R/ggplot-methods.R
@@ -118,7 +118,7 @@ ggplot.source_spct <-
     # private (not exported) method or function from 'ggplot2'
     data.tb <- data
     removed <- photobiology::rmDerivedSpct(data.tb)
-    p <- ggplot2::ggplot(data = data.tb, mapping = mapping, ...,
+    p <- ggplot2::ggplot(data = data.tb, mapping = mapping,
                          environment = environment)
     class(p[["data"]]) <- c(removed, class(p[["data"]]))
 
@@ -162,7 +162,7 @@ ggplot.response_spct <-
     # private (not exported) method or function from 'ggplot2'
     data.tb <- data
     removed <- photobiology::rmDerivedSpct(data.tb)
-    p <- ggplot2::ggplot(data = data.tb, mapping = mapping, ...,
+    p <- ggplot2::ggplot(data = data.tb, mapping = mapping,
                          environment = environment)
     class(p[["data"]]) <- c(removed, class(p[["data"]]))
 
@@ -209,7 +209,7 @@ ggplot.filter_spct <-
     # private (not exported) method or function from 'ggplot2'
     data.tb <- data
     removed <- photobiology::rmDerivedSpct(data.tb)
-    p <- ggplot2::ggplot(data = data.tb, mapping = mapping, ...,
+    p <- ggplot2::ggplot(data = data.tb, mapping = mapping,
                          environment = environment)
     class(p[["data"]]) <- c(removed, class(p[["data"]]))
 
@@ -247,7 +247,7 @@ ggplot.reflector_spct <-
     # private (not exported) method or function from 'ggplot2'
     data.tb <- data
     removed <- photobiology::rmDerivedSpct(data.tb)
-    p <- ggplot2::ggplot(data = data.tb, mapping = mapping, ...,
+    p <- ggplot2::ggplot(data = data.tb, mapping = mapping,
                          environment = environment)
     class(p[["data"]]) <- c(removed, class(p[["data"]]))
 
@@ -286,7 +286,7 @@ ggplot.cps_spct <-
     # private (not exported) method or function from 'ggplot2'
     data.tb <- data
     removed <- photobiology::rmDerivedSpct(data.tb)
-    p <- ggplot2::ggplot(data = data.tb, mapping = mapping, ...,
+    p <- ggplot2::ggplot(data = data.tb, mapping = mapping,
                          environment = environment)
     class(p[["data"]]) <- c(removed, class(p[["data"]]))
 
@@ -325,7 +325,7 @@ ggplot.calibration_spct <-
     # private (not exported) method or function from 'ggplot2'
     data.tb <- data
     removed <- photobiology::rmDerivedSpct(data.tb)
-    p <- ggplot2::ggplot(data = data.tb, mapping = mapping, ...,
+    p <- ggplot2::ggplot(data = data.tb, mapping = mapping,
                          environment = environment)
     class(p[["data"]]) <- c(removed, class(p[["data"]]))
 
@@ -364,7 +364,7 @@ ggplot.raw_spct <-
     # private (not exported) method or function from 'ggplot2'
     data.tb <- data
     removed <- photobiology::rmDerivedSpct(data.tb)
-    p <- ggplot2::ggplot(data = data.tb, mapping = mapping, ...,
+    p <- ggplot2::ggplot(data = data.tb, mapping = mapping,
                          environment = environment)
     class(p[["data"]]) <- c(removed, class(p[["data"]]))
 
@@ -416,7 +416,7 @@ ggplot.object_spct <-
     if (plot.qty == "as.is") {
       data.class <- class(data)
       photobiology::rmDerivedSpct(data)
-      p <- ggplot2::ggplot(data = data, mapping = mapping, ...,
+      p <- ggplot2::ggplot(data = data, mapping = mapping,
                            environment = environment)
       class(p[["data"]]) <- data.class
     } else {
@@ -479,7 +479,8 @@ ggplot.generic_spct <-
                  tibble = tibble::as_tibble)
     spct <- funs[[spct_class]](data, ...)
 
-    ggplot2::ggplot(data = spct, mapping = mapping, ..., range = range,
+    # dispatched to one of the methods defined above
+    ggplot2::ggplot(data = spct, mapping = mapping, range = range,
                     environment = environment)
   }
 

diff --git a/README.Rmd b/README.Rmd
@@ -15,9 +15,10 @@ knitr::opts_chunk$set(
 
 # ggspectra <img src="man/figures/logo.png" align="right" width="120" />
 
-[![cran version](https://www.r-pkg.org/badges/version/ggspectra)](https://cran.r-project.org/package=ggspectra) 
+[![cran version](https://www.r-pkg.org/badges/version-last-release/ggspectra)](https://cran.r-project.org/package=ggspectra) 
 [![cran checks](https://badges.cranchecks.info/worst/ggspectra.svg)](https://cran.r-project.org/web/checks/check_results_ggspectra.html)
-[![R build status](https://github.com/aphalo/ggspectra/workflows/R-CMD-check/badge.svg)](https://github.com/aphalo/ggspectra/actions)
+[![photobiology status badge](https://aphalo.r-universe.dev/badges/ggspectra)](https://aphalo.r-universe.dev/ggspectra)
+[![R-CMD-check](https://github.com/aphalo/ggspectra/workflows/R-CMD-check/badge.svg)](https://github.com/aphalo/ggspectra/actions)
 [![Documentation](https://img.shields.io/badge/documentation-ggspectra-informational.svg)](https://docs.r4photobiology.info/ggspectra/)
 [![doi](https://img.shields.io/badge/doi-10.32614/CRAN.package.ggspectra-blue.svg)](https://doi.org/10.32614/CRAN.package.ggspectra)