prerelease push: no errors or warnings or notes

DESCRIPTION

@@ -15,7 +15,8 @@ Imports:
     viridis,
     tidyr,
     dplyr,
-    ggplot2
+    ggplot2,
+    magrittr
 Suggests:
     knitr
 Author: Andrew Jackson and Andrew Parnell

NAMESPACE

@@ -29,3 +29,4 @@ export(siberEllipses)
 export(siberMVN)
 export(sigmaSEA)
 export(specificCentroidVectors)
+importFrom(magrittr,"%>%")

R/allCentroidVectors.R

@@ -17,10 +17,16 @@
 #'   the plots if you ask for it nicely: thedata <- 
 #'   plotCentroidVectors(centroids)
 #'   
+#' @importFrom magrittr %>%
+#' 
 #' @export
+# magrittr::`%>%`
 
 allCentroidVectors <- function (centroids, upper = TRUE, do.plot = TRUE, ...) {
 
+  # appease CRAN checks
+  comparison <- NULL
+
   dd <- dim(centroids$r)
 
   # number of pairwise comparisons
@@ -60,9 +66,16 @@ allCentroidVectors <- function (centroids, upper = TRUE, do.plot = TRUE, ...) {
   colnames(distances) <- new.names
   colnames(angles)    <- new.names
 
+  if(do.plot){
+    siberDensityPlot(distances)
+    siberDensityPlot(angles)
+  }
+
+  # browser()
+
   # convert from wide to long format
   long_data_angles <- tidyr::gather(data.frame(angles),
-                             key = comparison, value = angle)
+                             key = comparison, value = angles)
 
   long_data_distances <- tidyr::gather(data.frame(distances),
                                 key = comparison, value = distances)

R/specificCentroidVectors.R

@@ -5,7 +5,7 @@
 #' 
 #' @param centroids the list containing distance and angle matrices as returned 
 #'   by \code{\link{siberCentroids}}.
-#' @param txt a character vector of the pattern used to find paired matches in
+#' @param do.these a character vector of the pattern used to find paired matches in
 #'   the matrix of all comparisons. Usually the group names within any of the 
 #'   communities.
 #' @param upper a logical determining whether to plot the upper or lower 
@@ -19,15 +19,16 @@
 #' @return A nice plot. You can get the corresponding matrices used to generate 
 #'   the plots if you ask for it nicely: thedata <- 
 #'   plotCentroidVectors(centroids)
-#'   
+#' @importFrom magrittr %>%
+#' 
 #' @export
+# magrittr::`%>%`
 
 specificCentroidVectors <- function (centroids, do.these, upper = TRUE, 
                                    do.plot = TRUE, ...) {
 
-  # first i need to find all the indices for which the same group name appears 
-  # in the centroid$labels so I can extract them only.
-  # ** ACTUALLY THIS IS GOING TO BE DONE OUTSIDE**
+  # appease CRAN checks
+  comparison <- NULL
 
   # how big is the data array
   dd <- dim(centroids$r)
@@ -86,7 +87,7 @@ specificCentroidVectors <- function (centroids, do.these, upper = TRUE,
 
   # convert from wide to long format
   long_data_angles <- tidyr::gather(data.frame(angles),
-                             key = comparison, value = angle)
+                             key = comparison, value = angles)
 
   long_data_distances <- tidyr::gather(data.frame(distances),
                                 key = comparison, value = distances)

cran-comments.md

@@ -1,4 +1,4 @@
-An update to the package `spatstat` on which `SIBER` depends has precipiated a minor version update. My package now uses `spatsat.utils` as per the advice of the package maintainers.
+An update to the package `spatstat` on which `SIBER` depends has precipiated a minor version update. My package now uses `spatsat.utils` as per the advice of the dependent package maintainers. There were also some warnings thrown by inappropriate vignette builder options in the yaml headers which have now all been fixed. All issues in the package reports https://cran.r-project.org/web/checks/check_results_SIBER.html have been addressed.
 
 ## Resubmission
 N/A
@@ -7,24 +7,15 @@ N/A
 N/A
 
 ## Test environments
-* local OS X 10.10.5 install, R 3.3.3
+* local OS X 10.12.4 install, R 3.4.0
 * win-builder (R-release) via devtools::build_win()
 * win-builder (R-devel) via devtools::build_win()
 
 ## R CMD check results
 There were no ERRORs, WARNINGs or NOTES on my local build.
 
-There were no ERRORS and 1 WARNING from win-builder on either release or devel. 
-* checking top-level files ... WARNING
-Conversion of 'NEWS.md' failed:
-pandoc.exe: Could not fetch https://CRAN.R-project.org/web/CRAN_web.css
-TlsExceptionHostPort (HandshakeFailed (Error_Protocol ("certificate rejected: [NameMismatch \"CRAN.R-project.org\"]",True,CertificateUnknown))) "CRAN.R-project.org" 443
-
-This warning appears to be on the CRAN side and is not under my control.
-
 ## CRAN Package Check Results for Package SIBER
-There was one error thrown by CRAN's remote checks: https://cran.rstudio.com/web/checks/check_results_SIBER.html. I am not concerned about this error as it occurred on the r-oldrel-windows-ix86+x86_64 build and appears to result from an incorrect, inappropriate or missing installation of JAGS on which SIBER depends via the package rjags which also fails on this release with the same error.
-+ error: The environment variable JAGS_HOME is set to "c:/Program Files/JAGS/JAGS-4.0.0" but no JAGS installation can be found there.
+No ERRORS or WARNINGS.
 
 ## Downstream dependencies
 There are no downstream dependencies.

vignettes/Centroid-Vectors.R

@@ -86,7 +86,7 @@ angles_distances <- allCentroidVectors(centroids, do.plot = FALSE)
 # = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 
 # function to do the histograms on each group
 my.hist <- function(df){
-  test <- hist(df$angle, 
+  test <- hist(df$angles, 
              breaks = seq(from = -pi, to = pi, length = 60), 
              plot = FALSE)
 
@@ -116,7 +116,7 @@ print(all.roses)
 ## ----polar-density, fig.width = 10, fig.height = 7-----------------------
 
 median_vectors <- dplyr::summarise(group_by(angles_distances, comparison),
-          medAngle = median(angle), medDist = median(distances))
+          medAngle = median(angles), medDist = median(distances))
 
 origins <- data.frame(comparison = median_vectors$comparison, 
                       x = 0, y = 0)
@@ -137,8 +137,8 @@ for_arrows <- dplyr::bind_rows(origins, ends)
 
 # = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 
 # create the cartesian points for the estimated tips of the arrows
-cart_positions <- with(angles_distances, data.frame(x = distances * cos(angle),
-                             y = distances * sin(angle),
+cart_positions <- with(angles_distances, data.frame(x = distances * cos(angles),
+                             y = distances * sin(angles),
                              comparison = comparison ))
 
 # rename as above

vignettes/Centroid-Vectors.Rmd

@@ -133,7 +133,7 @@ The posterior distributions of the angles can then be visualise as a polar histo
 # = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 
 # function to do the histograms on each group
 my.hist <- function(df){
-  test <- hist(df$angle, 
+  test <- hist(df$angles, 
              breaks = seq(from = -pi, to = pi, length = 60), 
              plot = FALSE)
 
@@ -172,7 +172,7 @@ The names for each comparison are not the prettiest or most informative. Here th
 ```{r polar-density, fig.width = 10, fig.height = 7 }
 
 median_vectors <- dplyr::summarise(group_by(angles_distances, comparison),
-          medAngle = median(angle), medDist = median(distances))
+          medAngle = median(angles), medDist = median(distances))
 
 origins <- data.frame(comparison = median_vectors$comparison, 
                       x = 0, y = 0)
@@ -193,8 +193,8 @@ for_arrows <- dplyr::bind_rows(origins, ends)
 
 # = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 
 # create the cartesian points for the estimated tips of the arrows
-cart_positions <- with(angles_distances, data.frame(x = distances * cos(angle),
-                             y = distances * sin(angle),
+cart_positions <- with(angles_distances, data.frame(x = distances * cos(angles),
+                             y = distances * sin(angles),
                              comparison = comparison ))
 
 # rename as above