package removed gbm.auto alias. factorplot add ggplot2 replace, attem…

…pt to address no visible binding for Category and ycentred, add automatic ordering of integer variables

.Rhistory

@@ -1,54 +1,3 @@
-axis.title = ggplot2::element_text(size = rel(ggplot2axistitle)),
-legend.text = ggplot2::element_text(size = rel(ggplot2legendtext)),
-legend.title = ggplot2::element_text(size = rel(ggplot2legendtitle)),
-legend.title.align = ggplot2legendtitlealign, # otherwise effect type title centre aligned for some reason
-plot.background = ggplot2::element_rect(fill = ggplot2plotbackgroundfill,
-colour = ggplot2plotbackgroundcolour), # white background
-strip.text.x = ggplot2::element_text(size = rel(ggplot2striptextx)),
-panel.border = ggplot2::element_rect(colour = ggplot2panelbordercolour,
-fill = ggplot2panelborderfill,
-linewidth = ggplot2panelborderlinewidth),
-legend.spacing.x = ggplot2legendspacingx, # compress spacing between legend items, this is min
-legend.background = ggplot2legendbackground,
-panel.background = ggplot2::element_rect(fill = ggplot2panelbackgroundfill,
-colour = ggplot2panelbackgroundcolour),
-panel.grid = ggplot2::element_line(colour = ggplot2panelgridcolour),
-legend.key = ggplot2legendkey)
-ggplot2labsx = "",
-ggplot2labsx = ""
-ggplot2labsy = "Marginal Effect"
-ggplot2axistext = 1.5
-ggplot2axistitle = 2
-ggplot2legendtext = 1
-ggplot2legendtitle = 1.5
-ggplot2legendtitlealign = 0
-ggplot2plotbackgroundfill = "white"
-ggplot2plotbackgroundcolour = "grey50"
-ggplot2striptextx = 2
-ggplot2panelbordercolour = "black"
-ggplot2panelborderfill = NA
-ggplot2panelborderlinewidth = 1
-ggplot2legendspacingx = unit(0, "cm")
-ggplot2legendbackground = ggplot2::element_blank()
-ggplot2panelbackgroundfill = "white"
-ggplot2panelbackgroundcolour = "grey50"
-ggplot2panelgridcolour = "grey90"
-ggplot2legendkey = ggplot2::element_blank()
-ggsavefilename = paste0(saveloc, lubridate::today(), "_SankeyAlluvial_EMT.SoEv-EfTyp_Col-EfSz.png")
-ggsaveplot = last_plot()
-ggsavedevice = "png"
-ggsavepath = ""
-ggsavescale = 2
-ggsavewidth = 10
-ggsaveheight = 4
-ggsaveunits = "in"
-ggsavedpi = 300
-ggsavelimitsize = TRUE
-ggplot2::ggplot(x) +
-ggplot2::geom_col(aes(x = Category,
-y = ycentred)) +
-# alter axis labels
-ggplot2::labs(x = "",
 y = "Marginal Effect") +
 ggplot2::scale_x_discrete(guides(x =  guide_axis(angle = 90))) +
 ggplot2::theme_minimal() %+replace% ggplot2::theme(
@@ -510,3 +459,54 @@ legendposition = c(0.05, 0.18),
 savedir = "/home/simon/Documents/Si Work/PostDoc Work/Gbmauto help/2022-12-06 Cat Wells/CPUESpawnVS/gbmmapsftest"
 )
 devtools::document()
+devtools::check()
+?rename
+data("iris")
+tmp <- iris |> dplyr::rename("MYSPECIES" = "Species")
+devtools::document()
+devtools::check()
+View(iris)
+tmp <- iris |> dplyr::arrange("Sepal.Length")
+View(tmp)
+tmp <- iris |> dplyr::arrange(Sepal.Length)
+View(tmp)
+tmp <- iris |> dplyr::arrange("Petal.Length")
+View(tmp)
+tmp <- iris |> dplyr::mutate(Petal.Length = ordered("Petal.Length"))
+View(tmp)
+?ordered
+x <- readr@@read_csv("/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Mesh.Inch.csv")
+x <- readr::read_csv("/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Mesh.Inch.csv")
+x <- x |>
+# dplyr::mutate(ycentred = y - mean(y)) |> # make mean column
+# The above exists already in gbm.auto L843
+# Also it uses preset colname y produced by gbm.auto.
+dplyr::rename("Category" = tidyselect::last_col(offset = 2), # no first_col option
+"ycentred" = tidyselect::last_col()) |>
+# 2023-08-30 quoted Category to hopefully address gbm.factorplot: no visible binding for global variable ‘Category’
+# also need to do for ycentred
+dplyr::arrange(ycentred) # re-order the x axis for categorical variables in order from high to low value
+View(x)
+x <- readr::read_csv("/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year.csv")
+View(x)
+x <- x |>
+# dplyr::mutate(ycentred = y - mean(y)) |> # make mean column
+# The above exists already in gbm.auto L843
+# Also it uses preset colname y produced by gbm.auto.
+dplyr::rename("Category" = tidyselect::last_col(offset = 2), # no first_col option
+"ycentred" = tidyselect::last_col()) |> # attempt to address no visible binding for global variable ‘Category’
+# 2023-08-30 quoted Category to hopefully address gbm.factorplot: no visible binding for global variable ‘Category’
+# also need to do for ycentred
+dplyr::arrange("ycentred") # re-order the x axis for categorical variables in order from high to low value
+View(x)
+x <- x |>
+# dplyr::mutate(ycentred = y - mean(y)) |> # make mean column
+# The above exists already in gbm.auto L843
+# Also it uses preset colname y produced by gbm.auto.
+dplyr::rename("Category" = tidyselect::last_col(offset = 2), # no first_col option
+"ycentred" = tidyselect::last_col()) |> # attempt to address no visible binding for global variable ‘Category’
+# 2023-08-30 quoted Category to hopefully address gbm.factorplot: no visible binding for global variable ‘Category’
+# also need to do for ycentred
+dplyr::arrange(ycentred) # re-order the x axis for categorical variables in order from high to low value
+devtools::document()
+devtools::check()

NAMESPACE

@@ -30,6 +30,7 @@ importFrom(gbm,predict.gbm)
 importFrom(ggmap,get_map)
 importFrom(ggmap,ggmap)
 importFrom(ggmap,register_google)
+importFrom(ggplot2,"%+replace%")
 importFrom(ggplot2,aes)
 importFrom(ggplot2,element_blank)
 importFrom(ggplot2,element_line)

R/gbm.auto-package.R

@@ -1,7 +1,7 @@
 #' @keywords internal
-"_PACKAGE"
 #' @aliases gbm.auto-package
-#'
+"_PACKAGE"
+
 ## usethis namespace: start
 #' @importFrom lifecycle deprecated
 ## usethis namespace: end

R/gbm.factorplot.R

@@ -49,7 +49,7 @@
 #'
 #' @export
 #' @importFrom dplyr arrange mutate rename
-#' @importFrom ggplot2 aes element_blank element_line element_rect element_text geom_col ggplot ggsave guide_axis guides labs last_plot rel theme theme_minimal
+#' @importFrom ggplot2 aes element_blank element_line element_rect element_text geom_col ggplot ggsave guide_axis guides labs last_plot rel theme theme_minimal %+replace%
 #' @importFrom grid unit
 #' @importFrom lubridate today
 #' @importFrom readr read_csv
@@ -112,24 +112,29 @@ gbm.factorplot <- function(x,
     # dplyr::mutate(ycentred = y - mean(y)) |> # make mean column
     # The above exists already in gbm.auto L843
     # Also it uses preset colname y produced by gbm.auto.
-    dplyr::rename(Category = tidyselect::last_col(offset = 2)) |> # no first_col option
+    dplyr::rename("Category" = tidyselect::last_col(offset = 2), # no first_col option
+                  "ycentred" = tidyselect::last_col()) |> # attempt to address no visible binding for global variable ‘Category’
+    # 2023-08-30 quoted Category to hopefully address gbm.factorplot: no visible binding for global variable ‘Category’
+    # also need to do for ycentred
     dplyr::arrange(ycentred) # re-order the x axis for categorical variables in order from high to low value
 
   # re-reorder by factorplotlevels if present
   if (!is.null(factorplotlevels)) {
     # check level number matches x categories
-    if (length(factorplotlevels) != length(x$Category)) stop("number of factorplotlevels doesn't match number of categories in x")
+    if (length(factorplotlevels) != length(x[, "Category"])) stop("number of factorplotlevels doesn't match number of categories in x") # x$Category
     # check names match
-    if (!all(factorplotlevels %in% x$Category)) stop(paste0("The following level names not present in categories in x: ",
-                                                            factorplotlevels[!factorplotlevels %in% x$Category]))
+    if (!all(factorplotlevels %in% x[, "Category"])) stop(paste0("The following level names not present in categories in x: ", # x$Category
+                                                            factorplotlevels[!factorplotlevels %in% x[, "Category"]])) # x$Category
     x <- x |>
-      dplyr::mutate(Category = ordered(Category, factorplotlevels = factorplotlevels)) |> # recreate Category as ordered factor with factorplotlevels
-      dplyr::arrange(Category) # arrange by labels (implicit)
+      dplyr::mutate(Category = ordered(Category, levels = factorplotlevels)) |> # recreate Category as ordered factor with factorplotlevels. Can't quote "Category" in ordered
+      dplyr::arrange(Category) # arrange by labels (implicit). Can't quote "Category"
+  } else {
+    if (is.integer(x$Category)) x <- x |> dplyr::mutate(Category = ordered(Category)) # make integers ordered factor to avoid defaulting to continuous
   }
 
   ggplot2::ggplot(x) +
-    ggplot2::geom_col(ggplot2::aes(x = Category,
-                                   y = ycentred)) +
+    ggplot2::geom_col(ggplot2::aes(x = Category, # x[, "Category"]
+                                   y = ycentred)) + # x[, "ycentred"]
     # rotate x axis labels
     ggplot2::guides(x =  ggplot2::guide_axis(angle = ggplot2guideaxisangle)) +
     # alter axis labels