From 5463cb82e551275cee858a6f4577358495c7bcc8 Mon Sep 17 00:00:00 2001
From: Ed Ionides <ionides@umich.edu>
Date: Tue, 20 Aug 2024 10:57:49 -0400
Subject: [PATCH] 0.36.0 submitted to CRAN

---
 DESCRIPTION             |  4 +--
 R/package.R             |  4 +--
 cran-comments.md        | 70 ++++++++++-------------------------------
 man/spatPomp-package.Rd |  4 +--
 4 files changed, 22 insertions(+), 60 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 919e8c3..f343695 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: spatPomp
 Type: Package
 Title: Inference for Spatiotemporal Partially Observed Markov Processes
-Version: 0.35.2
-Date: 2024-08-05
+Version: 0.36.0
+Date: 2024-08-20
 Authors@R: c(
   person("Kidus", "Asfaw", email = "kidusasfaw1990@gmail.com", role = c("aut")),
   person("Edward", "Ionides", email = "ionides@umich.edu",role = c("cre","aut")),
diff --git a/R/package.R b/R/package.R
index 21debe7..a36d41a 100644
--- a/R/package.R
+++ b/R/package.R
@@ -16,7 +16,7 @@
 #' @section Data analysis using \pkg{spatPomp}:
 #' The first step in using \pkg{spatPomp} is to encode one's model(s) and data
 #'  in objects of class \code{spatPomp}.
-#' This can be done via a call to the \link[=spatPomp]{spatPomp} constructor
+#' This can be done via a call to the \code{\link[=spatPomp]{spatPomp}} constructor
 #' function.
 #'
 #' @section Extending the \pkg{pomp} platform for developing inference tools:
@@ -35,7 +35,7 @@
 #' @references \asfaw2020
 #' @author Kidus Asfaw, Joonha Park, Allister Ho, Edward Ionides, Aaron A. King
 #'
-#' @seealso \link[=pomp-package]{pomp package}
+#' @seealso \code{\link[=pomp::pomp]{pomp}}
 #'
 #' @keywords models datasets ts
 #'
diff --git a/cran-comments.md b/cran-comments.md
index 005da7e..ede920c 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,63 +1,25 @@
 
-#### spatPomp 0.35.0
+#### spatPomp 0.36.0
 
-spatPomp 0.35.0 has various technical updates without significant changes for the user. Test coverage has increased to 100%.
+spatPomp 0.36.0 updates 0.35.0 with some bug fixes and the inclusion of vignettes.
 
-#### Test environments:
+#### Test environments
 
-## devtools::check_win_devel()
-Status: OK
+Experimenting with test validation based on GitHub actions in
+.github/workflows/r-cmd-check.yml
+and 
+.github/workflows/test-coverage.yml
 
-## devtools::check_win_release()
-Status: OK
+R-CMD-check / ubuntu-latest (devel) (push) Successful in 3m
+test-coverage / test-coverage (push) Successful in 5m
+R-CMD-check / ubuntu-latest (release) (push) Successful in 3m
+R-CMD-check / ubuntu-20.04 (4.1.0) (push) Successful in 3m
+R-CMD-check / macOS-latest (release) (push) Successful in 2m
+R-CMD-check / windows-latest (release) (push) Successful in 5m
+codecov/patch - Coverage not affected when comparing bc34025...bb41d65
+codecov/project - 100.00% (+0.08%) compared to bc34025
 
-## devtools::check_mac_release()
-This gave an error message:
-  Internal Server Error (HTTP 500). Failed to Uploading package.
-Instead, spatPomp was checked with the current version of R on
-an M1 and x86 Mac
-
-Mac Sonoma 14.5 on Apple M1 Max with R4.4.0
-R CMD check --as-cran spatPomp_0.35.0.tar.gz
-Status: OK
-
-Mac Sonoma 14.4.1 on x86 with R4.4.0
-R CMD check --as-cran spatPomp_0.35.0.tar.gz
-Status: OK
-
-## R4.4.0 on Ubuntu 22.04.4
-Status: OK
-
-## Reverse dependencies
+#### Reverse dependencies
 
 none found by devtools::revdep("spatPomp")
 
-#### Quality control
-
-## Memory leak
-R4.4.0 on Ubuntu 22.04.4
-
-R --vanilla -d "valgrind --tool=memcheck --track-origins=yes --leak-check=full" < tests/bm.R 2>&1 | tee valgrind-bm.Rout
-
-This identifies a memory leak. As identified in previous CRAN uploads of spatPomp, the problem seems to be in png.
-
-R -d "valgrind --tool=memcheck --track-origins=yes --leak-check=full" --vanilla -e "png(filename='p.png'); plot(1:10); dev.off()"
-## HAS LEAK
-==4041830== LEAK SUMMARY:
-==4041830==    definitely lost: 9,984 bytes in 31 blocks
-==4041830==    indirectly lost: 20,273 bytes in 864 blocks
-==4041830==      possibly lost: 4,813 bytes in 51 blocks
-
-R -d "valgrind --tool=memcheck --track-origins=yes --leak-check=full" --vanilla -e "pdf(file='p.pdf'); plot(1:10); dev.off()"
-
-## NO LEAK
-==4041953== LEAK SUMMARY:
-==4041953==    definitely lost: 0 bytes in 0 blocks
-==4041953==    indirectly lost: 0 bytes in 0 blocks
-==4041953==      possibly lost: 0 bytes in 0 blocks
-
-## Unit tests
-
-Unit test code coverage is fairly constant in recent releases, at about 90%
-covr::package_coverage(type="tests") was run in R4.4.0 on intel Mac (Sonoma 14.4.1)
-coverage: 100%
diff --git a/man/spatPomp-package.Rd b/man/spatPomp-package.Rd
index f2431ab..33c47fc 100644
--- a/man/spatPomp-package.Rd
+++ b/man/spatPomp-package.Rd
@@ -19,7 +19,7 @@ whether or not these units correspond to spatial locations.
 
 The first step in using \pkg{spatPomp} is to encode one's model(s) and data
  in objects of class \code{spatPomp}.
-This can be done via a call to the \link[=spatPomp]{spatPomp} constructor
+This can be done via a call to the \code{\link[=spatPomp]{spatPomp}} constructor
 function.
 }
 
@@ -46,7 +46,7 @@ and compared on a growing body of models and datasets.
 \asfaw2020
 }
 \seealso{
-\link[=pomp-package]{pomp package}
+\code{\link[=pomp::pomp]{pomp}}
 }
 \author{
 Kidus Asfaw, Joonha Park, Allister Ho, Edward Ionides, Aaron A. King