Modify marrayAge

6 files changed, 17 insertions, 37 deletions

diff --git a/.local_checks/@making_IPMbook_package.R b/.local_checks/@making_IPMbook_package.R
index 62578d1..48bdcf9 100644
--- a/.local_checks/@making_IPMbook_package.R
+++ b/.local_checks/@making_IPMbook_package.R
@@ -20,7 +20,7 @@ devtools::load_all("D:/Github/IPMbook_package/IPMbook")
 # ==========================
 unlink(list.files(pattern="Rplots.pdf", recursive=TRUE))
 system("R CMD build IPMbook")  # Produces the .tar.gz
-pkg <- "IPMbook_0.1.2.9006.tar.gz"  # <-- fix version number here
+pkg <- "IPMbook_0.1.2.9007.tar.gz"  # <-- fix version number here
 
 # Pick one to check:
 ## on desktop
diff --git a/DESCRIPTION b/DESCRIPTION
index a472a79..8ea9e91 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: IPMbook
 Type: Package
 Title: Functions and Data for the Book 'Integrated Population Models'
-Version: 0.1.2.9006
-Date: 2021-10-04
+Version: 0.1.2.9007
+Date: 2021-10-11
 Depends: R (>= 2.10)
 Imports: stats, abind
 Suggests:
diff --git a/NEWS b/NEWS
index 7bfb296..1effce7 100644
--- a/NEWS
+++ b/NEWS
@@ -1,4 +1,8 @@
-CHANGES in version 0.1.2.9005 (2021-10-04)
+CHANGES in version 0.1.2.9007 (2021-10-11)
+
+  * `marrayAge` now accepts a scalar value for `age`.
+
+CHANGES in version 0.1.2.9006 (2021-10-04)
 
   * `marray*` functions gain a `groups` argument, as an alternative to columns in `freq`.
 
diff --git a/R/groupfreq.R b/R/groupfreq.R
index 26752ad..7eae54d 100644
--- a/R/groupfreq.R
+++ b/R/groupfreq.R
@@ -1,5 +1,5 @@
 
-# Function to combine a vector of frequncies and a vector of group IDs
+# Function to combine a vector of frequencies and a vector of group IDs
 #  into a matrix with frequencies for each group
 
 # Input:
@@ -18,29 +18,3 @@ groupfreq <- function(freq, groups) {
   out[cbind(1:nind, as.numeric(groups))] <- freq
   return(out)
 }
-
-
-# For testing:
-if(FALSE) {
-library(wiqid)
-data(dippers)
-CH <- dippers[, 1:7]
-groups <- dippers$sex
-CHf <- CH[groups=="F", ]
-CHm <- CH[groups=="M", ]
-
-freq <- rep(1, length(groups))
-
-library(IPMbook)
-
-mf <- marray(CHf)
-mm <- marray(CHm)
-
-f2 <- groupfreq(freq, groups)
-mg <- marray(CH, freq=f2)
-mg
-all(mg[,,1] == mf)
-all(mg[,,2] == mm)
-
-
-}
diff --git a/R/marrayAge.R b/R/marrayAge.R
index c397a73..250065a 100644
--- a/R/marrayAge.R
+++ b/R/marrayAge.R
@@ -20,7 +20,7 @@
 ################################################
 
 
-marrayAge <- function(ch, age, mAge = 1, freq = 1, groups = NULL){
+marrayAge <- function(ch, age = 1, mAge = 1, freq = 1, groups = NULL){
   if(is.data.frame(ch))
     ch <- as.matrix(ch)
   if (!is.matrix(ch))
@@ -29,6 +29,8 @@ marrayAge <- function(ch, age, mAge = 1, freq = 1, groups = NULL){
   stopifNegative(ch, allowNA=TRUE, allowZero=TRUE)
   age <- round(age)
   stopifNegative(age, allowNA=FALSE, allowZero=FALSE)
+  if(length(age) == 1)
+    age <- rep(age, nrow(ch))
   mAge <- round(mAge[1])
   stopifNegative(mAge, allowNA=FALSE, allowZero=FALSE)
   if(is.data.frame(freq))
@@ -49,7 +51,7 @@ marrayAge <- function(ch, age, mAge = 1, freq = 1, groups = NULL){
   # stopifnotLength(freq, nind, allow1=FALSE)  ## FIXME
   n.occasions <- ncol(ch)
   ng <- ncol(freq)   # number of groups, can be 1
-  
+
   # Remove capture histories of individuals that are marked at last occasion
   first <- getFirst(ch)
   # last <- which(first == n.occasions)
@@ -75,7 +77,7 @@ marrayAge <- function(ch, age, mAge = 1, freq = 1, groups = NULL){
 
   # Create empty m-array, add dimnames
   marr <- array(0, dim = c(n.occasions-1, n.occasions, maxAge, ng))
-  
+
   gNames <- colnames(freq)
   if(is.null(gNames))
     gNames <- paste0("G", 1:ng)
@@ -92,7 +94,7 @@ marrayAge <- function(ch, age, mAge = 1, freq = 1, groups = NULL){
     cap.occ <- which(ch[i,]!=0)
     capID <- paste0("Y", cap.occ)
     cap.age <- age.matrix[i, cap.occ]
-    
+
     for(g in 1:ng) {
       if (length(capID) == 1 && !traploss[i,g]) {  # no recaptures
          marr[capID[1], 'never', cap.age[1], g] <- marr[capID[1], 'never', cap.age[1],g] + absfreq[i,g]
diff --git a/man/marrayAge.Rd b/man/marrayAge.Rd
index 4ee33c1..0d65341 100644
--- a/man/marrayAge.Rd
+++ b/man/marrayAge.Rd
@@ -9,14 +9,14 @@ Creates age-dependent m-arrays
 Converts single-state capture-recapture data to age-dependent m-arrays.
 }
 \usage{
-marrayAge(ch, age, mAge = 1, freq = 1, groups = NULL)
+marrayAge(ch, age = 1, mAge = 1, freq = 1, groups = NULL)
 }
 \arguments{
   \item{ch}{
 an individuals x time matrix with capture histories (0: not captured; 1: captured). See Details.
 }
   \item{age}{
-vector with the age class at first capture for each individual.
+vector with the age class at first capture for each individual, or a scalar that will be used for all individuals.
 }
   \item{mAge}{
 maximum number of age classes for which m-arrays are constructed; ignored if \code{max(age) > mAge}. Only required if the \code{age} vector has fewer age classes than we want to separate (e.g. capture histories \code{ch} contains only individuals marked as juveniles, and we want 2 age classes).