CRAN version 0.1.11 (exported methods)

mfasiolo · Nov 15, 2023 · 9098d6f · 9098d6f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: mgcViz
 Title: Visualisations for Generalized Additive Models
-Date: 2022-11-28
-Version: 0.1.10
+Date: 2023-10-05
+Version: 0.1.11
 Authors@R: c(person("Matteo", "Fasiolo", email = "matteo.fasiolo@gmail.com", role = c("aut", "cre")),
   person("Raphael", "Nedellec", email = "raphael.nedellec@edf.fr", role = c("aut")), 
   person("Yannig", "Goude", role = c("ctb")), 
@@ -30,11 +30,10 @@ Suggests:
     testthat,
     MASS, 
     webshot2
-Additional_repositories: https://dmurdoch.github.io/drat
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
 URL: https://github.com/mfasiolo/mgcViz

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,6 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method("+",gg)
+S3method(.prepare,ALE)
+S3method(.prepare,fs.interaction)
+S3method(.prepare,mgcv.smooth)
+S3method(.prepare,mrf.smooth)
+S3method(.prepare,random.effect)
+S3method(.prepare,sos.smooth)
 S3method(ALE,gam)
 S3method(check,gamViz)
 S3method(plot,ALE1D)

diff --git a/R/I_prepare.mgcv.smooth.R b/R/I_prepare.mgcv.smooth.R
@@ -38,6 +38,7 @@
 #' @param ... Other graphics parameters to pass on to plotting commands. 
 #' See details for smooth plot specific options.
 #' @noRd
+#' @export
 .prepare.mgcv.smooth <- function(x, data = NULL, label = "", se1.mult = 1, se2.mult = 2,
                                  n = 100, n2 = 40,  xlab = NULL, ylab = NULL, 
                                  main = NULL, ylim = NULL, xlim = NULL, 

diff --git a/R/I_prepare_ALE.R b/R/I_prepare_ALE.R
@@ -2,6 +2,8 @@
 # Prepare ALE effects
 # This function will be called by ALE.gam
 #############
+#' @noRd
+#' @export
 .prepare.ALE <- function(o, xnam, data, type, K, bins, predFun, jacFun, varFun, center, ...) {
 
   .x <- data[[xnam]]

diff --git a/R/I_prepare_fs_interaction.R b/R/I_prepare_fs_interaction.R
@@ -1,4 +1,5 @@
 #' @noRd
+#' @export
 .prepare.fs.interaction <- function(x, data = NULL, label = "",
                                     n = 100, xlab = NULL, ylab = NULL, main = NULL,
                                     ylim = NULL, xlim = NULL, ...) {

diff --git a/R/I_prepare_mrf_smooth.R b/R/I_prepare_mrf_smooth.R
@@ -1,8 +1,10 @@
+#' @noRd
+#' @export
 .prepare.mrf.smooth <- function(x, data, label, se1.mult, se2.mult,
                                 partial.resids, se, n, n2,
                                 xlab, ylab, main,
                                 ylim, xlim, too.far,
-                                trans, phi, theta, scheme) {
+                                trans, phi, theta, scheme, ...) {
 
   raw <- data[x$term][[1]]
   dat <- data.frame(x=factor(names(x$xt$polys),levels=levels(x$knots)))
@@ -13,4 +15,4 @@
   return(list(X=X, scale=FALSE, se=FALSE, raw=raw, xlab=xlabel, ylab=ylabel,
               main=label))
 
-} ## end prepare.sos.smooth
+}
diff --git a/R/I_prepare_random_effect.R b/R/I_prepare_random_effect.R
@@ -1,4 +1,5 @@
 #' @noRd
+#' @export
 .prepare.random.effect <- function(x, data = NULL, label = "",
                                    n = 100, xlab = NULL, ylab = NULL, main = NULL,
                                    ylim = NULL, xlim = NULL, ...) {

diff --git a/R/I_prepare_sos_smooth.R b/R/I_prepare_sos_smooth.R
@@ -1,8 +1,10 @@
+#' @noRd
+#' @export
 .prepare.sos.smooth <- function(x, data, label, se1.mult = 1, se2.mult = 1,
                                 partial.resids = NULL, se, n, n2,
                                 xlab = NULL, ylab = NULL, main = NULL,
                                 ylim = NULL, xlim = NULL, too.far,
-                                trans, phi, theta, scheme) {
+                                trans, phi, theta, scheme, ...) {
 
   ## plot method function for sos.smooth terms
   if (scheme == 1){ 

diff --git a/R/generic_functions.R b/R/generic_functions.R
@@ -71,5 +71,3 @@ ALE <- function(o, ...) UseMethod("ALE")
 
 ###### Internal generics
 .prepare <- function(...) UseMethod(".prepare")
-
-.plot <- function(...) UseMethod(".plot")
diff --git a/inst/CITATION b/inst/CITATION
@@ -1,16 +1,15 @@
 citHeader("To cite the mgcViz package in publications use:")
 
-citEntry(entry = "Article", 
-         author = personList(as.person("Matteo Fasiolo"), as.person("Raphael Nedellec"), 
-                           as.person("Yannig Goude"), as.person("Simon N. Wood") ),
-         title = "Scalable visualisation methods for modern Generalized Additive Models.", 
-         journal = "Arxiv preprint", 
-         year = 2018, 
-         url = "https://arxiv.org/abs/1809.10632", 
-         textVersion=paste(
-			       "Fasiolo M., Nedellec R., Goude Y. and Wood S. N. (2018)",
-			       "Scalable visualisation methods for modern Generalized Additive Models.", 
-			       "ArXiv preprint arXiv:1809.10632."
-			       ))
+bibentry(
+ bibtype="Article",
+ title="Scalable visualisation methods for modern Generalized Additive Models.",
+ journal="Journal of the Royal Statistical Society (B)",
+ volume= "29",
+ number="1",
+ pages="78-86",
+ year="2020",
+ author="Fasiolo, Matteo and Nedellec, Rapha{\"e}l and Goude, Yannig and Wood, Simon N",
+ textVersion="Fasiolo, M., Nedellec, R., Goude, Y. and Wood, S.N., 2020. Scalable visualization methods for modern generalized additive models. Journal of computational and Graphical Statistics, 29(1), pp.78-86." )
+
 
 citFooter("As mgcViz is often updated, you may want to cite its version number. Find it with 'help(package=mgcViz)'.")