par tweaks in vignette and example added for getNCBI

R/getNCBI.R

@@ -7,14 +7,16 @@
 #'
 #' @return a data.frame with nrow == length(species) 
 #' @name getNCBI
+#' @examples
+#'   mouse <- getNCBI("Peromyscus leucopus")
+#'   worm  <- getNCBI("Ascaris lumbricoides", host=FALSE)
 #' @importFrom taxize classification get_uid
 #' @importFrom stats na.omit 
 #' @importFrom utils tail
 #' @importFrom plyr mutate
 #' @export
 
 
-
 getNCBI <- function(species, host=TRUE){ 
 
   mutate_cond <- function(.data, condition, ..., envir = parent.frame()) {

README.md

@@ -4,6 +4,7 @@
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5821896.svg)](https://doi.org/10.5281/zenodo.5821896)
 
+
 ### insectDisease: Programmatically access insect disease data from the Ecological Database of the World's Insect Pathogens (EDWIP)
 
 See preprint ([available here](https://ecoevorxiv.org/yd3x5/))

cran-comments.md

@@ -2,6 +2,29 @@
 
 This package is a new submission.
 
+During CRAN checks, some issues were found.
+
+```
+
+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/dataManip.R
+e.g.:
+oldpar <- par(mar=c(4,4,0.5,0.5))
+...
+par(oldpar)
+-> You need to set oldpar <- par(mar=c(4,4,0.5,0.5)) before you use par() the first time. So, now you have par(mar=c(4,4,0.5,0.5)) the firest time in line 45, this should already be oldpar <- par(mar=c(4,4,0.5,0.5))
+
+Please add small executable examples in your Rd-files to illustrate the use of the exported function but also enable automatic testing.
+
+Please fix and resubmit.
+
+Best,
+Victoria Wimmer 
+```
+
+All of these issues have been addressed, and we thank Benjamin Altmann and Victoria Wimmer for helpful comments.
+
+
+
 
 ```
 Status: OK

vignettes/dataManip.Rmd

@@ -25,6 +25,7 @@ library(plyr)
 library(dplyr)
 library(corrplot)
 knitr::opts_chunk$set(fig.width=6, fig.height=6) 
+oldpar <- par(mar=c(4,4,0.5,0.5))
 
 ```
 
@@ -215,7 +216,7 @@ We can then make the bubble plot, which describes the number of unique hosts, pa
 
 ```{r}
 
-oldpar <- par(mar=c(4,4,0.5,0.5))
+
 
 bubble <- edwip4 %>%
   dplyr::group_by(Group) %>%