MARSS: Multivariate Autoregressive State-Space Modeling

MARSS-User-Guide

This is the MARSS User Guide for the MARSS R package: https://cran.r-project.org/package=MARSS. This is part of the Applied Time Series Analysis for Environmental Science suite of software and educational material. See the GitHub repository for the MARSS source code.

To rebuild the User Guide

Open terminal
cd to the inst/userguide folder
make will build the User Guide
When preparing for a new MARSS release, copy doc folder into inst before running R CMD build. Note running devtools::check will delete the inst/doc folder so do the copy right before making a release or submitting to CRAN.

Make sure build and check pass
Remake the User Guide and make sure nothing is broken
Run the code in inst/testing-releases
Run the tests in tests
[ ] Run checks without building the vignettes

devtools::check(document = FALSE, vignettes=FALSE)

[ ] Run examples only

devtools::run_examples(pkg="~/Documents/GitHub/MARSS", document=FALSE, fresh=TRUE)

[ ] spellcheck the whole package

#devtools::install_github("ropensci/spelling")
spelling::spell_check_package()
fils <- dir("vignettes/manual_files", full.names = TRUE)
fils <- fils[stringr::str_detect(fils, "Rnw")]
spelling::spell_check_files(fils, ignore = spelling::get_wordlist(pkg = "."), lang = "en_US")

[ ] Check Manual

setwd("~/Documents/GitHub")
devtools::build_manual(pkg="MARSS")

[ ] Build the package into tar.gz. Note do not use devtools::build() it destroys the inst/doc folder. Note, the Mac LaTeX installation doesn't install packages on the fly. You may need to install the needed packages. From terminal: tlmgr install imakeindex, tlmgr install collection-fontsrecommended, tlmgr install footmisc, tlmgr install appendix`, plus a few more in header.tex.

Open terminal

cd ~/Documents/GitHub
rm MARSS_3.11.4.tar.gz
R CMD build MARSS
rm -r ~/Dropbox/MARSS
rm ~/Dropbox/MARSS_3.11.4.tar.gz
cp MARSS_3.11.4.tar.gz ~/Dropbox/MARSS_3.11.4.tar.gz
cd ~/Dropbox
tar -xvzf MARSS_3.11.4.tar.gz
rm ~/Dropbox/MARSS/vignettes/Makefile
R CMD build --no-build-vignettes MARSS

Run version tests

[ ] Run this vignettes/versiontest.R
[ ] Run checks on the built package

rm -r ~/Dropbox/MARSS.Rcheck
R CMD check --timings --as-cran MARSS_3.11.7.tar.gz

Run internal tests

[ ] Run tests/model.R to set up models for tests
[ ] Then run devtools::test() but I find running the tests one by one in RStudio is easier to make sense of. Some tests will through errors, but all test should pass. Errors are correct if the test passes and result should be try-error.
- [ ] test.coef
- [ ] test-forecast
- [ ] test-GDF
- [ ] test-KFAS
- [ ] test-MARSSkfss
- [ ] test-plotting
- [ ] test-print
- [ ] test-residualsHarvey
- [ ] test-structTS
- [ ] test-tt

Check the documentation pdfs

[ ] EMDerivation
[ ] Quick Start
[ ] Residuals
[ ] User Guide

Compress documentation pdfs

[ ] Manually compress the pdfs in the doc folder Dropbox/MARSS/inst/doc
[ ] Rebuild package with smaller docs, and then re-Run checks on the built package to see that it passes size checks

R CMD build --no-build-vignettes MARSS
rm -r ~/Dropbox/MARSS.Rcheck
R CMD check --timings --as-cran MARSS_3.11.4.tar.gz

Update the doc folder for GitHub. This has to be done manually by copying from

[ ] Dropbox/MARSS/inst/doc into GitHub/MARSS/inst/doc

Prepare for release:

Update the doc folder on GitHub. This has to be done manually

[ ] Copy Dropbox/MARSS/inst/doc into GitHub/MARSS/inst/doc

Re-read the submission guidelines to see if anything changed: https://cran.r-project.org/submit.html

Check that package builds on Windows

[ ] Upload the Dropbox/MARSS_X.X.X.tar.gz file to https://win-builder.r-project.org

Upload package to CRAN

[ ] https://cran.r-project.org/submit.html

The items below are for cases where you are submitting the package files without any extra processing. I process my vignette PDFs separately, so the below won't work. But when submitting there is a link to check the tar.gz file on Windows.