Added manual for custom_palette

+ some minor eolpop-package cleaning

NAMESPACE

@@ -6,6 +6,7 @@ export(M3_WithDD_noDemoStoch)
 export(M4_WithDD_WithDemoStoch)
 export(build_Leslie)
 export(calibrate_params)
+export(custom_palette_c25)
 export(elicitation)
 export(get_metrics)
 export(infer_DD)

R/custom_palette.R

@@ -23,3 +23,33 @@ custom_palette_c25 <- function(){
   )
 }
 
+
+
+
+##==============================================================================
+##                Function to control color transparency                      ==
+##==============================================================================
+#' Function to control color transparency on a plot
+#'
+#' @param someColor some color name, such as "green", "red", etc.
+#' @param percent the desired % of transparency, between 0 (no transparency) and 100 (full transparency) .
+#'
+#' @return a Hex Code including the desired transparency level, such as #RRGGBB7F
+#' @export
+#'
+#' @import RColorBrewer
+#' @import grDevices
+#'
+#' @examples
+#' make_transparent("green", percent=50)
+make_transparent <- function(someColor, percent=100)
+{
+  newColor <- col2rgb(someColor)
+  apply(newColor, 2,
+        function(curcoldata){
+          rgb(red = curcoldata[1], green = curcoldata[2], blue = curcoldata[3],
+              alpha = (100 - percent) * 255 / 100, maxColorValue = 255)
+        }
+  )
+} # End function
+################################################################################

R/plot_traj.R

@@ -55,7 +55,7 @@ plot_traj <- function(N, onset_year = NULL, xlab = "Year", ylab = "Population si
   # change color palette (we want sc0 in black)
   p <- p +
     scale_color_manual(breaks = 1:nsc,
-                       values = palette()[1:nsc],
+                       values = palette.colors(n = 9*10, recycle = TRUE)[1:nsc],
                        labels = Legend, aesthetics = c("colour", "fill"))
 
 
@@ -92,33 +92,3 @@ plot_traj <- function(N, onset_year = NULL, xlab = "Year", ylab = "Population si
 } # End function
 ################################################################################
 
-
-
-
-##==============================================================================
-##                Function to control color transparency                      ==
-##==============================================================================
-#' Function to control color transparency on a plot
-#'
-#' @param someColor some color name, such as "green", "red", etc.
-#' @param percent the desired % of transparency, between 0 (no transparency) and 100 (full transparency) .
-#'
-#' @return a Hex Code including the desired transparency level, such as #RRGGBB7F
-#' @export
-#'
-#' @import RColorBrewer
-#' @import grDevices
-#'
-#' @examples
-#' make_transparent("green", percent=50)
-make_transparent <- function(someColor, percent=100)
-{
-  newColor <- col2rgb(someColor)
-  apply(newColor, 2,
-        function(curcoldata){
-          rgb(red = curcoldata[1], green = curcoldata[2], blue = curcoldata[3],
-              alpha = (100 - percent) * 255 / 100, maxColorValue = 255)
-        }
-  )
-} # End function
-################################################################################

R/rMAX_spp.R

@@ -53,8 +53,7 @@ rMAX_spp <- function(surv, afr){
 #' Johnson, F. A., M. A. H. Walters, and G. S. Boomer. 2012. Allowable levels of take for the trade in
 #' Nearctic songbirds. Ecological Applications 22:1114-1130.
 #'
-#' @param surv Adult survival. Single value between 0 and 1.
-#' @param afr Age at first reproduction. Single integer value.
+#' @param rMAX_species Species rMAX value (Between 0 and +Inf)
 #'
 #' @return the theoretical Rmax of the species
 #' @export

man/custom_palette_c25.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/custom_palette.R
+\name{custom_palette_c25}
+\alias{custom_palette_c25}
+\title{Custom color palette: 25 distinct colors}
+\usage{
+custom_palette_c25()
+}
+\value{
+a vector of 25 color names
+}
+\description{
+Custom color palette: 25 distinct colors
+}
+\examples{
+custom_palette_c25()
+}

man/theta_spp.Rd

@@ -7,9 +7,7 @@
 theta_spp(rMAX_species)
 }
 \arguments{
-\item{surv}{Adult survival. Single value between 0 and 1.}
-
-\item{afr}{Age at first reproduction. Single integer value.}
+\item{rMAX_species}{Species rMAX value (Between 0 and +Inf)}
 }
 \value{
 the theoretical Rmax of the species