Merge branch 'develop-0.6.1'

aphalo · Nov 13, 2024 · dcfe179 · dcfe179
2 parents 2955961 + 089f4e6
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: ggpmisc
 Type: Package
 Title: Miscellaneous Extensions to 'ggplot2'
-Version: 0.6.0-1
-Date: 2024-06-26
+Version: 0.6.1
+Date: 2024-11-13
 Authors@R:
     c(
     person("Pedro J.", "Aphalo", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3385-972X")),
@@ -59,5 +59,5 @@ URL: https://docs.r4photobiology.info/ggpmisc/,
      https://github.com/aphalo/ggpmisc
 BugReports: https://github.com/aphalo/ggpmisc/issues
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr
diff --git a/NEWS.md b/NEWS.md
@@ -4,6 +4,11 @@ editor_options:
     wrap: 72
 ---
 
+# ggpmisc 0.6.1
+
+-   Fix warning with current 'broom' and upcoming 'ggplot2'.
+-   Make order of formal parameters in stats consistent with that in current 'ggplot2'.
+
 # ggpmisc 0.6.0-1
 
 -   Add ellipsis parameter (`...`) to `use_label()` so that in addition to a character vector of label names passed to parameter `labels`, separate strings for each name are now also accepted.

diff --git a/R/stat-fit-broom-tb.R b/R/stat-fit-broom-tb.R
@@ -317,6 +317,8 @@
 stat_fit_tb <- function(mapping = NULL,
                         data = NULL,
                         geom = "table_npc",
+                        position = "identity",
+                        ...,
                         method = "lm",
                         method.args = list(formula = y ~ x),
                         n.min = 2L,
@@ -328,16 +330,14 @@ stat_fit_tb <- function(mapping = NULL,
                         p.digits = digits,
                         label.x = "center",
                         label.y = "top",
-                        position = "identity",
                         table.theme = NULL,
                         table.rownames = FALSE,
                         table.colnames = TRUE,
                         table.hjust = 1,
                         parse = FALSE,
                         na.rm = FALSE,
                         show.legend = FALSE,
-                        inherit.aes = TRUE,
-                        ...) {
+                        inherit.aes = TRUE) {
   ggplot2::layer(
     stat = StatFitTb, data = data, mapping = mapping, geom = geom,
     position = position, show.legend = show.legend, inherit.aes = inherit.aes,

diff --git a/R/stat-fit-broom.R b/R/stat-fit-broom.R
@@ -196,6 +196,8 @@
 stat_fit_glance <- function(mapping = NULL,
                             data = NULL,
                             geom = "text_npc",
+                            position = "identity",
+                            ...,
                             method = "lm",
                             method.args = list(formula = y ~ x),
                             n.min = 2L,
@@ -204,9 +206,9 @@ stat_fit_glance <- function(mapping = NULL,
                             label.y = "top",
                             hstep = 0,
                             vstep = 0.075,
-                            position = "identity",
-                            na.rm = FALSE, show.legend = FALSE,
-                            inherit.aes = TRUE, ...) {
+                            na.rm = FALSE,
+                            show.legend = FALSE,
+                            inherit.aes = TRUE) {
   ggplot2::layer(
     stat = StatFitGlance, data = data, mapping = mapping, geom = geom,
     position = position, show.legend = show.legend, inherit.aes = inherit.aes,
@@ -483,7 +485,8 @@ StatFitGlance <-
 #'   passed to [generics::augment()] whether they are silently ignored or obeyed
 #'   depends on each specialization of [augment()], so do carefully read the
 #'   documentation for the version of [augment()] corresponding to the `method`
-#'   used to fit the model.
+#'   used to fit the model. Be aware that `se_fit = FALSE` is the default in
+#'   these methods even when supported.
 #'
 #' @family ggplot statistics for model fits
 #'
@@ -526,6 +529,13 @@ StatFitGlance <-
 #'     stat_fit_augment(method = "lm",
 #'                      method.args = list(formula = y ~ x))
 #'
+#' if (broom.installed)
+#'   ggplot(mtcars, aes(x = disp, y = mpg)) +
+#'     geom_point(aes(colour = factor(cyl))) +
+#'     stat_fit_augment(method = "lm",
+#'                      augment.args = list(se_fit = TRUE),
+#'                      method.args = list(formula = y ~ x + I(x^2)))
+#'
 #' # Residuals from regression by panel example
 #' if (broom.installed)
 #'   ggplot(mtcars, aes(x = disp, y = mpg)) +
@@ -540,6 +550,7 @@ StatFitGlance <-
 #'   ggplot(mtcars, aes(x = disp, y = mpg, colour = factor(cyl))) +
 #'     geom_point() +
 #'     stat_fit_augment(method = "lm",
+#'                      augment.args = list(se_fit = TRUE),
 #'                      method.args = list(formula = y ~ x))
 #'
 #' # Residuals from regression by group example
@@ -574,16 +585,20 @@ StatFitGlance <-
 #'     stat_fit_augment(method = "rq")
 #'
 #'
-stat_fit_augment <- function(mapping = NULL, data = NULL, geom = "smooth",
+stat_fit_augment <- function(mapping = NULL,
+                             data = NULL,
+                             geom = "smooth",
+                             position = "identity",
+                             ...,
                              method = "lm",
                              method.args = list(formula = y ~ x),
                              n.min = 2L,
                              augment.args = list(),
                              level = 0.95,
                              y.out = ".fitted",
-                             position = "identity",
-                             na.rm = FALSE, show.legend = FALSE,
-                             inherit.aes = TRUE, ...) {
+                             na.rm = FALSE,
+                             show.legend = FALSE,
+                             inherit.aes = TRUE) {
   ggplot2::layer(
     stat = StatFitAugment, data = data, mapping = mapping, geom = geom,
     position = position, show.legend = show.legend, inherit.aes = inherit.aes,
@@ -607,14 +622,14 @@ stat_fit_augment <- function(mapping = NULL, data = NULL, geom = "smooth",
 #' @usage NULL
 #'
 fit_augment_compute_group_fun <- function(data,
-                                    scales,
-                                    method,
-                                    method.args,
-                                    n.min,
-                                    augment.args,
-                                    level,
-                                    y.out,
-                                    ...) {
+                                          scales,
+                                          method,
+                                          method.args,
+                                          n.min,
+                                          augment.args,
+                                          level,
+                                          y.out,
+                                          ...) {
   unAsIs <- function(X) {
     if ("AsIs" %in% class(X)) {
       class(X) <- class(X)[-match("AsIs", class(X))]
@@ -670,7 +685,8 @@ fit_augment_compute_group_fun <- function(data,
     z[["t.value"]] <- rep_len(NA_real_, nrow(z))
   }
   if (!exists(".se.fit", z)) {
-    z[[".se.fit"]] <- rep_len(NA_real_, nrow(z))
+#    z[[".se.fit"]] <- rep_len(NA_real_, nrow(z)) # triggered warning!
+    z[[".se.fit"]] <- rep_len(0, nrow(z))
   }
   z[["fm.class"]] <- rep_len(fm.class[1], nrow(z))
   z[["fm.method"]] <- rep_len(method.name, nrow(z))
@@ -894,18 +910,23 @@ StatFitAugment <-
 #'                                                 after_stat(x_estimate),
 #'                                                 after_stat(x_p.value))))
 #'
-stat_fit_tidy <- function(mapping = NULL, data = NULL, geom = "text_npc",
+stat_fit_tidy <- function(mapping = NULL,
+                          data = NULL,
+                          geom = "text_npc",
+                          position = "identity",
+                          ...,
                           method = "lm",
                           method.args = list(formula = y ~ x),
                           n.min = 2L,
                           tidy.args = list(),
-                          label.x = "left", label.y = "top",
+                          label.x = "left",
+                          label.y = "top",
                           hstep = 0,
                           vstep = NULL,
                           sanitize.names = FALSE,
-                          position = "identity",
-                          na.rm = FALSE, show.legend = FALSE,
-                          inherit.aes = TRUE, ...) {
+                          na.rm = FALSE,
+                          show.legend = FALSE,
+                          inherit.aes = TRUE) {
   ggplot2::layer(
     stat = StatFitTidy, data = data, mapping = mapping, geom = geom,
     position = position, show.legend = show.legend, inherit.aes = inherit.aes,

diff --git a/R/stat-fit-deviations.R b/R/stat-fit-deviations.R
@@ -171,16 +171,19 @@
 #'
 #' @export
 #'
-stat_fit_deviations <- function(mapping = NULL, data = NULL, geom = "segment",
-                               method = "lm",
-                               method.args = list(),
-                               n.min = 2L,
-                               formula = NULL,
-                               position = "identity",
-                               na.rm = FALSE,
-                               orientation = NA,
-                               show.legend = FALSE,
-                               inherit.aes = TRUE, ...) {
+stat_fit_deviations <- function(mapping = NULL,
+                                data = NULL,
+                                geom = "segment",
+                                position = "identity",
+                                ...,
+                                method = "lm",
+                                method.args = list(),
+                                n.min = 2L,
+                                formula = NULL,
+                                na.rm = FALSE,
+                                orientation = NA,
+                                show.legend = FALSE,
+                                inherit.aes = TRUE) {
   ggplot2::layer(
     stat = StatFitDeviations, data = data, mapping = mapping, geom = geom,
     position = position, show.legend = show.legend, inherit.aes = inherit.aes,

diff --git a/R/stat-fit-residuals.R b/R/stat-fit-residuals.R
@@ -171,17 +171,18 @@
 stat_fit_residuals <- function(mapping = NULL,
                                data = NULL,
                                geom = "point",
+                               position = "identity",
+                               ...,
                                method = "lm",
                                method.args = list(),
                                n.min = 2L,
                                formula = NULL,
                                resid.type = NULL,
                                weighted = FALSE,
-                               position = "identity",
                                na.rm = FALSE,
                                orientation = NA,
                                show.legend = FALSE,
-                               inherit.aes = TRUE, ...) {
+                               inherit.aes = TRUE) {
   ggplot2::layer(
     stat = StatFitResiduals, data = data, mapping = mapping, geom = geom,
     position = position, show.legend = show.legend, inherit.aes = inherit.aes,

diff --git a/R/stat-ma-eq.R b/R/stat-ma-eq.R
@@ -305,7 +305,8 @@
 #'
 #' @export
 #'
-stat_ma_eq <- function(mapping = NULL, data = NULL,
+stat_ma_eq <- function(mapping = NULL,
+                       data = NULL,
                        geom = "text_npc",
                        position = "identity",
                        ...,

diff --git a/R/stat-multcomp.R b/R/stat-multcomp.R
@@ -323,7 +323,8 @@
 #'
 #' @export
 #'
-stat_multcomp <- function(mapping = NULL, data = NULL,
+stat_multcomp <- function(mapping = NULL,
+                          data = NULL,
                           geom = NULL,
                           position = "identity",
                           ...,

diff --git a/R/stat-peaks.R b/R/stat-peaks.R
@@ -265,18 +265,18 @@ find_peaks <-
 stat_peaks <- function(mapping = NULL,
                        data = NULL,
                        geom = "point",
+                       position = "identity",
+                       ...,
                        span = 5,
                        ignore_threshold = 0,
                        strict = FALSE,
                        label.fmt = NULL,
                        x.label.fmt = NULL,
                        y.label.fmt = NULL,
                        orientation = "x",
-                       position = "identity",
                        na.rm = FALSE,
                        show.legend = FALSE,
-                       inherit.aes = TRUE,
-                       ...) {
+                       inherit.aes = TRUE) {
   ggplot2::layer(
     stat = StatPeaks,
     data = data,
@@ -507,18 +507,18 @@ StatPeaks <-
 stat_valleys <- function(mapping = NULL,
                          data = NULL,
                          geom = "point",
+                         position = "identity",
+                         ...,
                          span = 5,
                          ignore_threshold = 0,
                          strict = FALSE,
                          label.fmt = NULL,
                          x.label.fmt = NULL,
                          y.label.fmt = NULL,
                          orientation = "x",
-                         position = "identity",
                          na.rm = FALSE,
                          show.legend = FALSE,
-                         inherit.aes = TRUE,
-                         ...) {
+                         inherit.aes = TRUE) {
   ggplot2::layer(
     stat = StatValleys,
     data = data,

diff --git a/R/stat-poly-eq.R b/R/stat-poly-eq.R
@@ -482,7 +482,8 @@
 #'
 #' @export
 #'
-stat_poly_eq <- function(mapping = NULL, data = NULL,
+stat_poly_eq <- function(mapping = NULL,
+                         data = NULL,
                          geom = "text_npc",
                          position = "identity",
                          ...,

diff --git a/R/stat-poly-line.R b/R/stat-poly-line.R
@@ -169,8 +169,10 @@
 #'
 #' @export
 #'
-stat_poly_line <- function(mapping = NULL, data = NULL,
-                           geom = "smooth", position = "identity",
+stat_poly_line <- function(mapping = NULL,
+                           data = NULL,
+                           geom = "smooth",
+                           position = "identity",
                            ...,
                            method = "lm",
                            formula = NULL,

diff --git a/R/stat-quant-eq.R b/R/stat-quant-eq.R
@@ -436,30 +436,31 @@
 #'
 #' @export
 #'
-stat_quant_eq <- function(mapping = NULL, data = NULL,
-                         geom = "text_npc",
-                         position = "identity",
-                         ...,
-                         formula = NULL,
-                         quantiles = c(0.25, 0.5, 0.75),
-                         method = "rq:br",
-                         method.args = list(),
-                         n.min = 3L,
-                         eq.with.lhs = TRUE,
-                         eq.x.rhs = NULL,
-                         coef.digits = 3,
-                         coef.keep.zeros = TRUE,
-                         decreasing = getOption("ggpmisc.decreasing.poly.eq", FALSE),
-                         rho.digits = 4,
-                         label.x = "left", label.y = "top",
-                         hstep = 0,
-                         vstep = NULL,
-                         output.type = NULL,
-                         na.rm = FALSE,
-                         orientation = NA,
-                         parse = NULL,
-                         show.legend = FALSE,
-                         inherit.aes = TRUE) {
+stat_quant_eq <- function(mapping = NULL,
+                          data = NULL,
+                          geom = "text_npc",
+                          position = "identity",
+                          ...,
+                          formula = NULL,
+                          quantiles = c(0.25, 0.5, 0.75),
+                          method = "rq:br",
+                          method.args = list(),
+                          n.min = 3L,
+                          eq.with.lhs = TRUE,
+                          eq.x.rhs = NULL,
+                          coef.digits = 3,
+                          coef.keep.zeros = TRUE,
+                          decreasing = getOption("ggpmisc.decreasing.poly.eq", FALSE),
+                          rho.digits = 4,
+                          label.x = "left", label.y = "top",
+                          hstep = 0,
+                          vstep = NULL,
+                          output.type = NULL,
+                          na.rm = FALSE,
+                          orientation = NA,
+                          parse = NULL,
+                          show.legend = FALSE,
+                          inherit.aes = TRUE) {
   # we guess formula from orientation
   if (is.null(formula)) {
     if (is.na(orientation) || orientation == "x") {