Fixed Suggests failures, moved to Depends or added requireNamespace

Author: CollinErickson

.Rbuildignore

@@ -10,3 +10,4 @@ Scratch
 ^\.github$
 ^doc$
 ^Meta$
+^CRAN-SUBMISSION$

DESCRIPTION

@@ -12,18 +12,19 @@ Description: Provides functions for making contour plots.
 License: GPL-3
 RoxygenNote: 7.3.1
 Imports:
-    rlang
-Suggests: 
-    knitr,
-    rmarkdown,
-    lhs,
-    mlegp,
-    ggplot2,
-    laGP,
-    locfit,
-    mgcv,
-    covr,
-    testthat
+  rlang
+Depends:
+  ggplot2,
+  lhs,
+  rmarkdown
+Suggests:
+  covr, 
+  knitr,
+  laGP,
+  locfit,
+  mgcv,
+  mlegp,
+  testthat
 VignetteBuilder: knitr
 URL: https://github.com/CollinErickson/ContourFunctions
 Encoding: UTF-8

NAMESPACE

@@ -15,6 +15,7 @@ export(gcf_func)
 export(gcf_grid)
 export(multicolor.title)
 export(text_plot)
+importFrom(ggplot2,ggplot)
 importFrom(grDevices,cm.colors)
 importFrom(graphics,.filled.contour)
 importFrom(graphics,Axis)
@@ -35,6 +36,9 @@ importFrom(graphics,screen)
 importFrom(graphics,split.screen)
 importFrom(graphics,text)
 importFrom(graphics,title)
+importFrom(lhs,randomLHS)
 importFrom(rlang,.data)
+importFrom(rmarkdown,html_vignette)
+importFrom(stats,lm)
 importFrom(stats,predict)
 importFrom(utils,capture.output)

R/cf_data.R

@@ -10,8 +10,8 @@
 #' @param xlim  x limits for the contour plot, will be set to data limits +- 5\% if not specified
 #' @param ylim  y limits for the contour plot, will be set to data limits +- 5\% if not specified
 #' @param xylim x and y limits for the contour plot
-#' @param fit Method to fit a model with. Current options are laGP (default)
-#' and mlegp. laGP is faster but might cause trouble.
+#' @param fit Method to fit a model with. Current options are laGP (default),
+#' mlegp, gam (uses mgcv), and locfit. laGP is faster but might cause trouble.
 #' @param gg If TRUE, will use ggplot2 by calling gcf_func
 #' @param show_points Whether the input data points should be shown on the plot.
 #' If missing, is TRUE when there are more than 300 points.
@@ -20,6 +20,8 @@
 #' @param ...  passed to cf_func
 #' @importFrom utils capture.output
 #' @importFrom stats predict
+#' @importFrom rmarkdown html_vignette 
+#' @importFrom stats lm
 #' @examples 
 #' x <- runif(20)
 #' y <- runif(20)
@@ -58,19 +60,19 @@ cf_data <- function(x, y=NULL, z=NULL,
   }
   # Check fit name given
   if (fit == "") {
-    if (length(x) > 200) {
+    if (length(x) > 200 && requireNamespace("locfit", quietly = TRUE)) {
       fit <- "locfit"
       message("Fitting with locfit since n > 200")
     } else {
       fit <- "lagp"
-      message("Fitting with laGP since n <= 200")
+      message("Fitting with laGP since n <= 200 (or locfit not available)")
     }
   }
   # Fits a Gaussian process model that interpolates perfectly, i.e., no smoothing
-  if (fit == "mlegp") {
+  if (fit == "mlegp" && requireNamespace("mlegp", quietly = TRUE)) {
     co <- capture.output(mod <- mlegp::mlegp(X=data.frame(x,y),Z=z,verbose=0))
     pred.func <- function(xx) {mlegp::predict.gp(mod,xx)}
-  } else if (fit %in% c("lagp")) {
+  } else if (fit %in% c("lagp") && requireNamespace("laGP", quietly = TRUE)) {
     X <- data.frame(x, y)
     da <- laGP::darg(list(mle=TRUE), X=X)
     ga <- laGP::garg(list(mle=TRUE), y=z)
@@ -80,15 +82,15 @@ cf_data <- function(x, y=NULL, z=NULL,
                     dab=da$ab, gab=ga$ab, verb=0, maxit=1000)
 
     pred.func <- function(xx) {laGP::predGPsep(mod1, xx, lite=TRUE)$mean}
-  } else if (fit == "locfit") {
+  } else if (fit == "locfit" && requireNamespace("locfit", quietly = TRUE)) {
     # browser()
     X <- data.frame(x, y, z)
     lfmod <- locfit::locfit(z ~ x + y, data=X, family=family)
     pred.func <- function(xx) {
       # browser()
       predict(lfmod, data.frame(x=xx[,1], y=xx[,2]))
     }
-  } else if (fit == "gam") {
+  } else if (fit == "gam" && requireNamespace("mgcv", quietly = TRUE)) {
     # browser()
     X <- data.frame(x=x, y=y, z=z)
     gammod <- mgcv::gam(z ~ te(x, y), data=X, family=family)
@@ -98,7 +100,15 @@ cf_data <- function(x, y=NULL, z=NULL,
       predict(gammod, data.frame(x=xx[,1], y=xx[,2]), type='response')
     }
   } else {
-    stop(paste0("fit is unknown"))
+    warning(paste0("Defaulting to use LM for fit. This is bad. Choose a better",
+                   " option for fit and ensure the package is installed."))
+    X <- data.frame(x=x, y=y, z=z)
+    lmmod <- lm(z ~ x + y + x*y, data=X)
+    pred.func <- function(xx) {
+      # browser()
+      predict(lmmod, data.frame(x=xx[,1], y=xx[,2]), type='response')
+    }
+    # stop(paste0("fit is unknown, or the requested package is not installed"))
   }
 
   minx <- min(x);maxx <- max(x);miny <- min(y);maxy <- max(y)

R/cf_highdim.R

@@ -39,6 +39,7 @@
 #' @param ... Arguments passed to cf_func, and then probably through to cf_grid
 #'
 #' @importFrom graphics contour mtext
+#' @importFrom lhs randomLHS
 #' @return NULL
 #' @export
 #' @references Hwang, Yongmoon, Sang-Lyul Cha, Sehoon Kim, Seung-Seop Jin,

R/gcf_grid.R

@@ -49,6 +49,7 @@
 #' @return ggplot2 object
 #' @export
 #' @importFrom rlang .data
+#' @importFrom ggplot2 ggplot
 #'
 #' @examples
 #' x <- y <- seq(-4*pi, 4*pi, len = 27)

cran-comments.md

@@ -1,6 +1,10 @@
 I received an email that I need to fix the note on CRAN by 8/27/24.
 Apologies for missing that deadline.
 
+I tried to submit on 9/8 but was rejected for failing when Suggests packages
+aren't available. I have either moved packages to Depends, or added
+requireNamespace around functions from the packages in Suggests.
+
 ## Test environments
 * local Windows 10 install, R 4.4.1
 * win-builder (devel)