SUMMER

Spatio-temporal Under-five Mortality Models of Estimation in R

Major update (version 0.3.0)

Version 0.3.0 contains some major updates from the previous versions. Some of the substantial change to existing functions are listed here. For a complete log of changes, see the News section.

Function name changes

The following functions have been renamed. Most of the function arguments remain the same:

• countrySummary is now getDirect
• cuontrySummary_mult is now getDirectList
• fitspace is now fitGeneric
• projINLA is now getSmooth

New functions

The following new functions are added:

• getDiag: produce diagnostic plots for the fitted model.
• getAdjusted: produce adjusted estimates for a fitted model
• getAmat: automatic extract spatial adjacency matrix from the polygon file.
• hatchPlot: plot variables on a map with hatching indicating the width of the credible interval.

New methods

fitINLA2: implements new smoothing methods based on binomial models at cluster level.

Installation - CRAN

The package is now available on CRAN. The easiest way to download is to install directly using the code below.

install.packages("SUMMER")

Installation - Development Version

To download the development version of the SUMMER package, use the code below.

# install.packages("devtools")
devtools::install_github("bryandmartin/SUMMER")

Usage

To see example usage of all main functions, build the package vignette. Note that the vignette will take a few minutes to compile.

# install.packages("devtools")
devtools::install_github("bryandmartin/SUMMER", build_vignettes = TRUE)
# Use this to view the vignette in the SUMMER HTML help
help(package = "SUMMER", help_type = "html")
# Use this to view the vignette as an isolated HTML file
utils::browseVignettes(package = "SUMMER")

Bug Reports / Change Requests

If you encounter a bug or would like make a change request, please file it as an issue here.

Random notes for package authors:

• In order to use devtools::check to check the package with static vignettes, use the hidden option devtools::check(clean_doc = FALSE) to avoid deleting the inst/doc folder.
• Also for large PDF vignette, run tools::compactPDF(gs_quality = "ebook", paths = "inst/doc/") to please CRAN.