Roll up 0.1.3

10 files changed, 11 insertions, 43 deletions

diff --git a/.local_checks/@making_IPMbook_package.R b/.local_checks/@making_IPMbook_package.R
index 48bdcf9..7b4a08c 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_0.1.2.9007.tar.gz"  # <-- fix version number here
+pkg <- "IPMbook_0.1.3.tar.gz"  # <-- fix version number here
 
 # Pick one to check:
 ## on desktop
diff --git a/DESCRIPTION b/DESCRIPTION
index 8ea9e91..aa014cd 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: IPMbook
 Type: Package
 Title: Functions and Data for the Book 'Integrated Population Models'
-Version: 0.1.2.9007
-Date: 2021-10-11
+Version: 0.1.3
+Date: 2021-12-10
 Depends: R (>= 2.10)
 Imports: stats, abind
 Suggests:
diff --git a/NEWS b/NEWS
index 1effce7..1bfed07 100644
--- a/NEWS
+++ b/NEWS
@@ -1,34 +1,10 @@
-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`.
-
-CHANGES in version 0.1.2.9005 (2021-10-03)
+CHANGES in version 0.1.3 (2021-12-10)
 
   * Added `ch2matrix` utility to convert capture histories in text format to matrices.
 
-CHANGES in version 0.1.2.9004 (2021-10-01)
-
-  * `marray*` functions now deal correctly with trap losses if only 1 capture.
-
-  * `marray*` functions deal with with groups specified as columns in the `freq` argument.
-
-CHANGES in version 0.1.2.9003 (2021-09-29)
-
-  * `marray*` functions now accept data frames for capture histories.
-
-CHANGES in version 0.1.2.9002 (2021-09-28)
-
   * Modified `marray` and `marrayAge` to deal with trap losses. (Not applicable to `marrayDead`.)
 
-CHANGES in version 0.1.2.9001 (2021-09-27)
-
-  * Modified `marray*` functions to accept a matrix of unique capture histories accompanied by a vector of frequencies.
-
-CHANGES in version 0.1.2.9000 (2021-09-25)
+  * Modified `marray*` functions to accept a wider range of input formats.
 
   * Modified `zInit` and `zKnown` to handle all-zero capture histories.
 
diff --git a/R/onAttach.R b/R/onAttach.R
deleted file mode 100644
index a13c21e..0000000
--- a/R/onAttach.R
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-.onAttach <- function(libname, pkgname) {
-  version <- try(packageVersion('IPMbook'), silent=TRUE)
-  if(!inherits(version, "try-error"))
-    packageStartupMessage("This is IPMbook ", version,
-      ". For overview type ?IPMbook; for changes do news(p='IPMbook').")
-}
diff --git a/man/data_woodchat10.Rd b/man/data_woodchat10.Rd
index 6523069..0b844f0 100644
--- a/man/data_woodchat10.Rd
+++ b/man/data_woodchat10.Rd
@@ -28,7 +28,7 @@ Demographic parameters based on the woodchat shrike are introduced in Schaub & K
 Simulated data
 }
 \references{
-Schaub, M., Kéry, M. (2022) \emph{Integrated Population Models}, Academic Press, chapter 10.
+Schaub, M., Kéry, M. (2022) \emph{Integrated Population Models}, Academic Press, section 10.5.1.
 }
 
 \examples{
diff --git a/man/data_woodchat11.Rd b/man/data_woodchat11.Rd
index 5c28042..09a72de 100644
--- a/man/data_woodchat11.Rd
+++ b/man/data_woodchat11.Rd
@@ -33,7 +33,7 @@ Bruno Ullrich
 \references{
 Ullrich, B. (2017) Entdeckung und Aussterben einer Population des Rotkopfwürgers \emph{Lanius senator} in den Streuobstwiesen des Mittleren Albvorlandes, Landkreise Göppingen und Esslingen am Neckar. \emph{Ökologie der Vögel} 35, 273-335.
 
-Schaub, M., Kéry, M. (2022) \emph{Integrated Population Models}, Academic Press, chapter 11.
+Schaub, M., Kéry, M. (2022) \emph{Integrated Population Models}, Academic Press, section 11.4.
 
 Schaub, M., B. Ullrich (2021) A drop in immigration results in the extinction of a local woodchat shrike population. \emph{Animal Conservation} 24, accepted <https://doi.org/10.1111/acv.12639>
 }
diff --git a/man/data_woodchat66.Rd b/man/data_woodchat66.Rd
index 0dc49f9..bc8f3a7 100644
--- a/man/data_woodchat66.Rd
+++ b/man/data_woodchat66.Rd
@@ -28,7 +28,7 @@ Demographic parameters based on the woodchat shrike are introduced in Schaub & K
 Simulated data
 }
 \references{
-Schaub, M., Kéry, M. (2022) \emph{Integrated Population Models}, Academic Press, section 6.6.
+Schaub, M., Kéry, M. (2022) \emph{Integrated Population Models}, Academic Press, section 6.6.2.
 }
 \examples{
 data(woodchat66)
diff --git a/man/data_woodchat7.Rd b/man/data_woodchat7.Rd
index 9e9e76d..5a81aec 100644
--- a/man/data_woodchat7.Rd
+++ b/man/data_woodchat7.Rd
@@ -27,7 +27,7 @@ Simulation of data with demographic parameters based on the woodchat shrike are
 Simulated data
 }
 \references{
-Schaub, M., Kéry, M. (2022) \emph{Integrated Population Models}, Academic Press,  chapter 7.
+Schaub, M., Kéry, M. (2022) \emph{Integrated Population Models}, Academic Press,  section 7.2.1.
 }
 \examples{
 data(woodchat7)
diff --git a/man/demoMCMC.Rd b/man/demoMCMC.Rd
index 829d5ea..637d985 100644
--- a/man/demoMCMC.Rd
+++ b/man/demoMCMC.Rd
@@ -52,7 +52,7 @@ Adapted from code in Ntzoufras (2009), p. 48.
 \references{
 Ntzoufras, I. (2009) \emph{Bayesian Modeling Using WinBUGS}, Wiley, Hoboken NJ.
 
-Schaub, M., Kéry, M. (2021), \emph{Integrated Population Models}, Academic Press, chapter 13.
+Schaub, M., Kéry, M. (2022), \emph{Integrated Population Models}, Academic Press, section 2.5.
 }
 \examples{
 require(graphics)
diff --git a/man/marrayDead.Rd b/man/marrayDead.Rd
index 9b516f3..3ea7dd4 100644
--- a/man/marrayDead.Rd
+++ b/man/marrayDead.Rd
@@ -34,7 +34,7 @@ An m-array, a (years-1) x years x groups array, where element [i, j, g] contains
 Michael Schaub
 }
 \references{
-Schaub, M., Kéry, M. (2022) \emph{Integrated Population Models}, Academic Press, chapter 12.4.2.
+Schaub, M., Kéry, M. (2022) \emph{Integrated Population Models}, Academic Press, chapter 12.4.3.
 }
 
 \examples{