CRAN presubmit tweaks

NAMESPACE

@@ -99,6 +99,7 @@ importFrom(stats,poisson)
 importFrom(stats,ppoints)
 importFrom(stats,runif)
 importFrom(stats,sd)
+importFrom(stats,setNames)
 importFrom(stats,var)
 importFrom(stringi,stri_split_fixed)
 importFrom(tidyselect,last_col)

R/gbm.auto.R

@@ -106,12 +106,12 @@
 #' For Linux/*buntu systems, in terminal, type: 'sudo apt install libgeos-dev', 'sudo apt install
 #' libproj-dev', 'sudo apt install libgdal-dev'.
 #'
-#' 2. Error in FUN(X[[i]], ...) : only defined on a data frame with all numeric
+#' 2. Error in FUN(X\[\[i\]\], ...) : only defined on a data frame with all numeric
 #' variables. Check your variable types are correct, e.g. numerics haven't been imported
 #' as factors because there's an errant first row of text information before the
 #' data. Remove NA rows from the response variable if present: convert blank
 #' cells to NA on import with read.csv(x, na.strings = "") then
-#' samples2 <- samples1[-which(is.na(samples[,resvar_column_number])),]
+#' samples2 <- samples1\[-which(is.na(samples\[,resvar_column_number\])),\]
 #'
 #' 3. At bf=0.5, if nrows <= 42 gbm.step will crash. Use gbm.bfcheck to determine optimal viable bf
 #' size
@@ -142,7 +142,7 @@
 #'  samples to run BRT modelling. Run gbm.bfcheck to check recommended minimum BF size. Similarly:
 #'  glm.fit: fitted probabilities numerically 0 or 1 occurred, and glm.fit: algorithm did not
 #'  converge. Similarly: Error in if (get(paste0("Gaus_BRT", ".tc", j, ".lr", k, ".bf",
-#'  l))$self.statistics$correlation[[1]]: argument is of length zero. See also: Error 15.
+#'  l))$self.statistics$correlation\[\[1\]\]: argument is of length zero. See also: Error 15.
 #'
 #' 10. Anomalous values can obfuscate clarity in line plots e.g. salinity range 32:35ppm but dataset
 #'  has errant 0 value: plot axis will be 0:35, and 99.99% of the data will be in the tiny bit at
@@ -151,7 +151,7 @@
 #' 11. Error in plot.new() : figure margins too large: In RStudio, adjust plot frame (usually bottom
 #'  right) to increase its size. Still fails? Set multiplot=FALSE.
 #'
-#' 12. Error in dev.print(file = paste0("./", names(samples[i]), "/pred_dev_bin.jpeg"): can only
+#' 12. Error in dev.print(file = paste0("./", names(samples\[i\]), "/pred_dev_bin.jpeg"): can only
 #' print from a screen device. An earlier failed run (e.g. LR/BF too low) left a plotting device
 #' open. Close it with: 'dev.off()'.
 #'
@@ -168,7 +168,7 @@
 #' 16. If lineplots of factorial variables include empty columns be sure to remove unused levels
 #' with samples %<>% droplevels() before the gbm.auto run
 #'
-#' 17. Error in seq.default(from = min(x$var.levels[[i.var[i]]]), to = max(x$var.levels[[i.var[i]]])
+#' 17. Error in seq.default(from = min(x$var.levels\[\[i.var\[i\]\]\]), to = max(x$var.levels\[\[i.var\[i\]\]\])
 #' :'from' must be a finite number. If you logged any expvars with log() and they has zeroes in them
 #' , those zeroes became imaginary numbers. Use log1p() instead.
 #'

R/gbm.map.R

@@ -9,10 +9,10 @@
 #'
 #' @param x Vector of longitudes, from make.grid in mapplots; x. Order by this
 #' (descending) SECOND.
-#' @param y Vector of latitudes, from make.grid in mapplots; grids[,gridslat].
+#' @param y Vector of latitudes, from make.grid in mapplots; grids\[,gridslat\].
 #' Order by this (descending) first.
 #' @param z Vector of abundances generated by gbm.predict.grids, from make.grid
-#' in mapplots; grids[,predabund].
+#' in mapplots; grids\[,predabund\].
 #' @param byx Longitudinal width of grid cell, from make.grid in mapplots.
 #' Autogenerated if left blank.
 #' @param byy Latitudinal height of grid cell, from make.grid in mapplots.
@@ -22,7 +22,7 @@
 #' @param mapmain Plot title, has species value appended. Default "Predicted
 #' CPUE (numbers per hour): ".
 #' @param species Response variable name, from basemap in mapplots;
-#' names(samples[i]). Defaults to "Response Variable".
+#' names(samples\[i\]). Defaults to "Response Variable".
 #' @param heatcolours Vector for abundance colour scale, defaults to the heatcol from
 #' legend.grid and draw.grid in mapplots which is c("white", "yellow", "orange"
 #' , "red", "brown4").
@@ -56,13 +56,13 @@
 #'
 #' @details Errors and their origins:
 #'
-#' Error in seq.default(xlim[1], xlim[2], by = byx):wrong sign in 'by' argument
+#' Error in seq.default(xlim\[1\], xlim\[2\], by = byx):wrong sign in 'by' argument
 #' Check that your lat & long columns are the right way around. Ensure grids
 #' data are gridded, i.e. they are in a regular pattern of same/similar lines of lat/lon, even if
 #' they're missing sections.
 #'
 #' Suggested parameter values:
-#' z = rsbdf[,"Unrepresentativeness"]
+#' z = rsbdf\[,"Unrepresentativeness"\]
 #'
 #' mapmain = "Unrepresentativeness: "
 #'

R/gbm.mapsf.R

@@ -11,6 +11,7 @@
 #' @importFrom ggspatial layer_spatial
 #' @importFrom lubridate today
 #' @importFrom stars geom_stars st_as_stars
+#' @importFrom stats setNames
 #' @importFrom sf st_set_crs st_bbox st_transform st_as_sfc st_as_sf st_buffer
 #' @importFrom starsExtra trim2
 #' @importFrom viridis scale_fill_viridis
@@ -101,13 +102,13 @@
 #'
 #' @details
 #'
-#' Error in seq.default(xlim[1], xlim[2], by = byx):wrong sign in 'by' argument
+#' Error in seq.default(xlim\[1\], xlim\[2\], by = byx):wrong sign in 'by' argument
 #' Check that your lat & long columns are the right way around. Ensure grids (predabund) data are
 #' gridded, i.e. they are in a regular pattern of same/similar lines of lat/lon, even if they're
 #' missing sections.
 #'
 #' Suggested parameter values:
-#' z = rsbdf[,"Unrepresentativeness"]
+#' z = rsbdf\[,"Unrepresentativeness"\]
 #'
 #' mapmain = "Unrepresentativeness: "
 #'
@@ -261,7 +262,7 @@ gbm.mapsf <- function(
       if (!inherits(map, "ggmap")) stop("map must be a ggmap object")
       # Extract the bounding box (in lat/lon) from the ggmap to a numeric vector,
       # and set the names to what sf::st_bbox expects:
-      map_bbox <- setNames(unlist(attr(map, "bb")), c("ymin", "xmin", "ymax", "xmax"))
+      map_bbox <- stats::setNames(unlist(attr(map, "bb")), c("ymin", "xmin", "ymax", "xmax"))
       # Convert the bbox to an sf polygon, transform it to 3857,
       # and convert back to a bbox (convoluted, but it works)
       bbox_3857 <- sf::st_bbox(sf::st_transform(sf::st_as_sfc(sf::st_bbox(map_bbox, crs = 4326)), 3857))

cran-comments.md

@@ -1,7 +1,7 @@
 ---
 title: "cran-comments"
 author: "Simon Dedman"
-date: "25 May 2023"
+date: "23 August 2023"
 output: html_document
 ---
 
@@ -19,10 +19,16 @@ knitr::opts_chunk$set(echo = TRUE)
 
 ## R CMD check results
 
-0 errors | 0 warnings | 1 note
+0 errors | 1 warnings | 2 notes
+
+Warnings:
+
+* "Rd files with duplicated alias 'gbm.auto': ‘gbm.auto-package.Rd’ ‘gbm.auto.Rd’". Have found no way to remove this, caused by lifecycle and usethis autogeneration of gbm.auto-package.R and Rd.
 
 Notes:
 
+* Possible code problems: no visible binding for global variables: named variables are column names in a csv exported by another function.
+
 * Non-standard things, png file created by examples, doesn't exist permanently.
 
 ***