changes for resubmission to CRAN

DESCRIPTION

@@ -75,5 +75,5 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Language: en-US

R/misc-manipulation.R

@@ -5,11 +5,9 @@
 #' @param condition Logical condition to be evaluated
 #' @examples
 #' d <- tibble::as_tibble(mtcars)
-#' d %>%
-#'   only_if(TRUE)(dplyr::filter)(mpg > 25)
+#' d %>% only_if(TRUE)(dplyr::filter)(mpg > 25)
 #'
-#' d %>%
-#'   only_if(FALSE)(dplyr::filter)(mpg > 25)
+#' d %>% only_if(FALSE)(dplyr::filter)(mpg > 25)
 #' @author David Robinson, https://twitter.com/drob/status/785880369073500161
 #' @export
 #' @return None. Called for side effects.

R/save-plot.R

@@ -17,11 +17,11 @@
 #' @param embed_fonts Logical. Use Ghostscript to embed fonts in a PDF graphic?
 #' @param ... Additional arguments passed to [ggplot2::ggsave()]
 #' @examplesIf interactive()
-#' ggplot(mtcars, aes(mpg, wt)) +
+#' p <- ggplot(mtcars, aes(mpg, wt)) +
 #'  geom_point()
 #'
-#' ggsave("mtcars.pdf")
-#' ggsave("mtcars.png")
+#' ggsave2(p, "/mtcars.pdf", path = tempdir())
+#' ggsave2(p, "/mtcars.png", path = tempdir())
 #' @return None. Called for side effects.
 #' @export
 ggsave2 <- function(plot = ggplot2::last_plot(), filename, device = NULL,

README.md

@@ -5,7 +5,7 @@
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/atlas-aai/ratlas/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/atlas-aai/ratlas/actions/workflows/check-standard.yaml)
+[![R-CMD-check](https://github.com/atlas-aai/ratlas/workflows/R-CMD-check/badge.svg)](https://github.com/atlas-aai/ratlas/actions)
 [![Codecov test
 coverage](https://codecov.io/gh/atlas-aai/ratlas/branch/main/graph/badge.svg)](https://app.codecov.io/gh/atlas-aai/ratlas?branch=main)
 

cran-comments.md

@@ -1,5 +1,23 @@
 ## Resubmission
 
+This is a resubmission. The previous submission raised-- 
+
+- Unexecutable code in man/only_if.Rd:
+   d %>%:
+
+- Please ensure that your functions do not write by default or in your 
+examples/vignettes/tests in the user's home filespace (including the 
+package directory and getwd()) -> man/ggsave2.Rd
+
+- Please always make sure to reset to user's options(), working directory 
+or par() after you changed it in examples and vignettes and demos.
+-> inst/doc/plotting.R
+
+These issues have now been fixed.
+
+
+## Resubmission
+
 This is a resubmission. The previous submission raised-- 
    Check: Rd cross-references, Result: NOTE
    Found the following Rd file(s) with Rd \link{} targets missing package

inst/rmarkdown/templates/atlas-presentation/skeleton/skeleton.Rmd

@@ -96,10 +96,10 @@ class: final-slide
 
 # Connect With Us!
 
-<i class="fas fa-globe" style="color:#165C7D;"></i> [ATLAS4Learning.org](https://atlas4learning.org)
+<i class="fas fa-globe" style="color:#165C7D;"></i> [atlas.ku.edu](https://atlas.ku.edu)
 
 <i class="fas fa-envelope" style="color:#165C7D;"></i> [[email protected]](mailto:[email protected])
 
-<i class="fab fa-twitter" style="color:#165C7D;"></i> [@ATLAS4Learning](https://twitter.com/atlas4learning)
+<i class="fab fa-twitter" style="color:#165C7D;"></i> [@ATLAS4Learning](https://x.com/atlas4learning)
 
 <i class="fab fa-github" style="color:#165C7D;"></i> [@ATLAS-AAI](https://github.com/atlas-aai)

vignettes/plotting.Rmd

@@ -187,17 +187,18 @@ img <- function(obj, nam) {
 ```
 
 ```{r cont-ex, echo = FALSE, fig.asp = 0.15, fig.cap = "(ref:cont-ex-cap)"}
-par(mfrow=c(1, 1), mar=rep(1, 4))
+oldpar <- par(mfrow=c(1, 1), mar=rep(1, 4))
 img(rev(seq_gradient_pal(low = "#132B43", high = "#56B1F7",
                          space = "Lab")(seq(0, 1, length=n_col))), "")
+par(oldpar)
 ```
 
 The simulated color blindness for this scale is shown in Figure \@ref(fig:cont-cvd). Here, several types of color blindness result in large sections of the palette where it is difficult to differentiate values.
 
 (ref:cont-cvd-cap) The default {ggplot2} color palette for continuous scales with different types of color blindness.
 
 ```{r cont-cvd, echo = FALSE, fig.asp = 0.5, fig.cap = "(ref:cont-cvd-cap)"}
-par(mfrow=c(4, 1), mar=rep(1, 4))
+oldpar <- par(mfrow=c(4, 1), mar=rep(1, 4))
 img(dichromat(rev(seq_gradient_pal(low = "#132B43", high = "#56B1F7",
                                    space = "Lab")(seq(0, 1, length=n_col))),
               "deutan"), "Deutanomaly")
@@ -210,6 +211,7 @@ img(dichromat(rev(seq_gradient_pal(low = "#132B43", high = "#56B1F7",
 img(desaturate(rev(seq_gradient_pal(low = "#132B43", high = "#56B1F7",
                                     space = "Lab")(seq(0, 1, length=n_col)))),
     "Desaturated")
+par(oldpar)
 ```
 
 ### Using color blind safe palettes
@@ -230,12 +232,13 @@ ggplot(mtcars, aes(x = mpg, y = disp)) +
 For continuous color scales, the viridis family of color palettes should be used. These palettes were created by [Stéfan van der Walt](https://github.com/stefanv) and [Nathaniel Smith](https://github.com/njsmith) and are shown in Figure \@ref(fig:show-viridis).
 
 ```{r show-viridis, echo = FALSE, fig.asp = 0.6, fig.cap = "The viridis color scales."}
-par(mfrow=c(5, 1), mar=rep(1, 4))
+oldpar <- par(mfrow=c(5, 1), mar=rep(1, 4))
 img(rev(viridis(n_col)), "Viridis")
 img(rev(magma(n_col)), "Magma")
 img(rev(plasma(n_col)), "Plasma")
 img(rev(inferno(n_col)), "Inferno")
 img(rev(cividis(n_col)), "Cividis")
+par(oldpar)
 ```
 
 These color scales are perceptually uniform, perform well for a variety of colorblindness, and maintain the ability to discriminate across the perceptual spectrum when rendered or printed in gray scale. These color scales can be applied using `ggplot2::scale_color_viridis_c()`. Figure \@ref(fig:viridis-compare) shows and example of using the the viridis color palette. There is also a discrete option for the viridis color palette (`ggplot2::scale_color_viridis_d()`); however, the Okabe Ito palette is preferred for discrete scales.