excursions is an R package that contains functions that compute probabilistic excursion sets, contour credibility regions, and simultaneous confidence bands for latent Gaussian random processes and fields.
The theory of the methods used in the package are described in the papers Bolin and Lindgren (2015), Bolin and Lindgren (2016) , and Bolin et al (2015).
A manual for the package (version 2.2.2) can be found here and the code used in the manual can be downloaded here.
The development version of the package contains new features and fixes that are not on CRAN, see NEWS.md. To install this version, see the instructions below.
The latest CRAN release of the package can be installed directly from CRAN with install.packages("excursions").
The latest stable version (which is sometimes slightly more recent than the CRAN version), can be installed by using the command
remotes::install_bitbucket("davidbolin/excursions", ref = "master")in R. The development version can be installed using the command
remotes::install_bitbucket("davidbolin/excursions", ref = "devel")If you want to install the package using the remotes::install_bitbucket-method on Windows, you first need to install Rtools and add the paths to Rtools and gcc to the Windows PATH environment variable. This can be done for the current R session only using the commands
rtools = "C:\\Rtools\\bin"
gcc = "C:\\Rtools\\gcc-4.6.3\\bin"
Sys.setenv(PATH = paste(c(gcc, rtools, Sys.getenv("PATH")), collapse = ";"))where the variables rtools and gcc need to be changed if Rtools is not installed directly on C:.
The package version format for released versions is major.minor.bugfix. All regular development should be performed on the devel branch or in a feature branch, managed with git flow feature. On the devel branch, the vestion number is major.minor.bugfix.9000, where the first three components reflect the latest released version with changes present in the default branch. Bugfixes should be applied via the git flow bugfix and git flow hotfix methods, as indicated below. For git flow configuration, use master as the stable master branch, devel as the develop branch, and v as the version tag prefix. See the git flow tutorial for more information.
For non master and devel branches that collaborators need access to (e.g. release branches, feature branches, etc, use the git flow publish mechanism).
- Prepare a new stable release with CRAN submission:
git flow release start major.(minor+1).0
## Update the DESCRIPTION version number as major.(minor+1).0
## Update the version in NEWS.md
## Commit the changes
## At this point, see the CRAN submission section below.
git flow release finish 'VERSION'
## Resolve/update the DESCRIPTION and NEWS.md version number conflict
## in favour of the released version, with extra .9000, e.g. with
## the help of git mergetool
## Add a new version section in NEWS.md
## Commit the merge
- Do a hotfix (branch from stable master; use bugfix for release branch bugfixes):
git flow hotfix start hotfix_branch_name
## Do the bugfix, update the verison number major.minor.(bugfix+1), and commit
## Optionally, do CRAN submission
git flow hotfix finish hotfix_branch_name
## Resolve merge conflicts (hopefully mostly due to version numbers)
- CRAN submission
## Perform CRAN checks (usually on the release branch version)
## If unsuccessful then do bugfixes with increasing bugfix version, until ok
## Submit to CRAN
## If not accepted then do more bugfixes and repeat