prepare for CRAN submission

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: spatPomp
 Type: Package
 Title: Inference for Spatiotemporal Partially Observed Markov Processes
-Version: 0.33.1
-Date: 2023-11-30
+Version: 0.34.0
+Date: 2023-12-03
 Authors@R: c(
   person("Kidus", "Asfaw", email = "[email protected]", role = c("aut")),
   person("Edward", "Ionides", email = "[email protected]",role = c("cre","aut")),
@@ -11,9 +11,10 @@ Authors@R: c(
   person("Joonha", "Park", email = "[email protected]", role = c("ctb")),
   person("Jesse", "Wheeler", email = "[email protected]", role = c("ctb")),
   person("Jifan", "Li", email = "[email protected]", role = c("ctb")),
-  person("Ning", "Ning", email = "[email protected]", role = c("ctb")))
+  person("Ning", "Ning", email = "[email protected]", role = c("ctb")),
+  person("Haogao", "Gu", email = "[email protected]", role = c("ctb")))
 URL: https://github.com/kidusasfaw/spatPomp
-Description: Inference on panel data using spatiotemporal partially-observed Markov process (SpatPOMP) models. To do so, it relies on and extends a number of facilities that the 'pomp' package provides for inference on time series data using partially-observed Markov process (POMP) models. Implemented methods include filtering and inference methods in Park and Ionides (2020) <doi:10.1007/s11222-020-09957-3>, Rebeschini and van Handel (2015) <doi:10.1214/14-AAP1061>, Evensen and van Leeuwen (1996) <doi:10.1029/94JC00572>, Ionides et al. (2021) <doi:10.1080/01621459.2021.1974867>, Ionides, Ning and Wheeler (2022) <doi:10.5705/ss.202022.0188>, Ning and Ionides (2023) <arXiv:2110.10745>. Pre-print statistical software article: Asfaw et al. (2021) <arXiv:2101.01157>.
+Description: Inference on panel data using spatiotemporal partially-observed Markov process (SpatPOMP) models. The 'spatPomp' package extends 'pomp' to include algorithms taking advantage of the spatial structure in order to assist with handling high dimensional processes. See Asfaw et al. (2023) <arXiv:2101.01157> for further description of the package.
 SystemRequirements: For Windows users, Rtools (see https://cran.r-project.org/bin/windows/Rtools/).
 License: GPL-3
 Encoding: UTF-8

cran-comments.md

@@ -1,77 +1,77 @@
 
-#### spatPomp 0.33.0
+#### spatPomp 0.34.0
 
-spatPomp 0.33.0 is an update of 0.33.0 with some minor
-updates and bug fixes, and some new methods for ibpf and bpfilter objects.
-
-This release also fixes an issue with M1 mac which led to spatPomp being
-temporarily pulled from CRAN. The issue involved inconsistent results from
-stats::arima on M1 compared to other platforms. Specifically, running
-arima on the same data on other platforms gave a log-likelihood of
-206.2569593745 compared to 196.3173327754. This issue has been avoided
-in 0.33.0 by omitting a unit test for spatPomp::arima_benchmark.
+spatPomp 0.34.0 is an update of 0.33.0 with some minor updates and
+bug fixes. It also has updates essential for compatibility with
+pomp 5.5.0.0.
 
 #### Test environments:
 
 ## devtools::check_win_devel()
-
-One note:
-Maintainer: 'Edward Ionides <[email protected]>'
-New submission
-Package was archived on CRAN
+Status: OK
 
 ## devtools::check_win_release()
-
-One note:
-Maintainer: 'Edward Ionides <[email protected]>'
-New submission
-Package was archived on CRAN
+Status: OK
 
 ## devtools::check_mac_release()
 
+The following NOTEs and the corresponding WARNING did not seem to require any action. The
+spatPomp package is not supporsed to include the source for the packages that it
+requires, and installing them from CRAN is the intended action.
+
+Building package dependency tree..
+(from /Volumes/PkgBuild/work/1701616455-16fc4133d5f711ca/packages/CRAN/src/contrib)
+./dtree --desc /Volumes/PkgBuild/work/1701616455-16fc4133d5f711ca/packages/CRAN/meta/src/contrib /Volumes/PkgBuild/work/1701616455-16fc4133d5f711ca/packages/CRAN/src/contrib > /Volumes/PkgBuild/work/1701616455-16fc4133d5f711ca/packages/CRAN/dep.list
+NOTE: there is no source for package pomp [pomp], installed CRAN version will be used.
+NOTE: there is no source for package testthat [testthat], installed CRAN version will be used.
+NOTE: there is no source for package doParallel [doParallel], installed CRAN version will be used.
+NOTE: there is no source for package parallel [parallel], installed CRAN version will be used.
+NOTE: there is no source for package doRNG [doRNG], installed CRAN version will be used.
+NOTE: there is no source for package foreach [foreach], installed CRAN version will be used.
+NOTE: there is no source for package dplyr [dplyr], installed CRAN version will be used.
+NOTE: there is no source for package tidyr [tidyr], installed CRAN version will be used.
+NOTE: there is no source for package stringr [stringr], installed CRAN version will be used.
+NOTE: there is no source for package abind [abind], installed CRAN version will be used.
+NOTE: there is no source for package rlang [rlang], installed CRAN version will be used.
+NOTE: there is no source for package magrittr [magrittr], installed CRAN version will be used.
+NOTE: there is no source for package ggplot2 [ggplot2], installed CRAN version will be used.
+NOTE: there is no source for package pomp [pomp], installed CRAN version will be used.
+
+Status: 1 WARNING
+  - installing from sources
+
+## Rhub builder Debian Linux, R-release, GCC
 Status: OK
 
-Various warnings were produced, which did not result in NOTES.
-The reason for these warnings is diagnosed as an issue with the
-pomp package, resolved by the pomp development version,
-commit c42cef25b2013ecfddfaf6838bee78a00dcc5ccc at
-https://github.com/kingaa/pomp, which concerns an M1 mac
-treatment of null objects returned by .Call. 
-
-## R CMD check --as-cran in R4.3.1 on Ubuntu 22.04.2
-
-One note:
-Maintainer: ‘Edward Ionides <[email protected]>’
-New submission
-Package was archived on CRAN
-CRAN repository db overrides:
-  X-CRAN-Comment: Archived on 2023-06-09 as issues were not corrected
-    in time.
-
 ## Reverse dependencies
 
 none found by devtools::revdep("spatPomp")
 
 #### Quality control
 
-rhub::check_with_valgrind() found a small memory leak which turned out to be due to png() rather than any spatPomp functionality. This was reported to [email protected], and still remains an issue in R4.3.1. The problem can be reproduced on Ubuntu 22.04.2 by
+## Memory leak
+
+rhub::check_with_valgrind() found a small memory leak which turned out to be due to png() rather than any spatPomp functionality. This was reported to [email protected], and still remains an issue in R4.3.2. The problem can be reproduced on Ubuntu 22.04.3 by
 
 R -d "valgrind --tool=memcheck --track-origins=yes --leak-check=full" --vanilla -e "png(filename='p.png'); plot(1:10); dev.off()"
 ## HAS LEAK
-==1021711== LEAK SUMMARY:
-==1021711==    definitely lost: 9,216 bytes in 30 blocks
-==1021711==    indirectly lost: 19,370 bytes in 838 blocks
-==1021711==      possibly lost: 3,868 bytes in 8 blocks
+==540949== LEAK SUMMARY:
+==540949==    definitely lost: 8,448 bytes in 28 blocks
+==540949==    indirectly lost: 12,424 bytes in 532 blocks
+==540949==      possibly lost: 11,866 bytes in 328 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
-==1031300== LEAK SUMMARY:
-==1031300==    definitely lost: 0 bytes in 0 blocks
-==1031300==    indirectly lost: 0 bytes in 0 blocks
-==1031300==      possibly lost: 0 bytes in 0 blocks
+==541137== LEAK SUMMARY:
+==541137==    definitely lost: 0 bytes in 0 blocks
+==541137==    indirectly lost: 0 bytes in 0 blocks
+==541137==      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 R4.3.1 on Ubuntu 22.04.2
+covr::package_coverage(type="tests") was run in R4.3.2 on Ubuntu 22.04.3
+0.34.0   coverage: 89.76%
 0.33.0   coverage: 89.64%
 0.32.0   coverage: 89.43%
 0.31.0.0 coverage: 88.9%