SUMMER

SAE Unit/area Models and Methods for Estimation in R

Next major update (version 1.3.0)

Version 1.3.0 will add population and prevalence simulation functionality based on population frame and population density information, along with methods for aggregating pixel level prevalences and populations to the areal level. These functions are currently available in the dev branch.

Updates will include:

• New major functions.
  • simSPDE: Simulates from the SPDE spatial model.
  • simPopSPDE: Simulates population in a country based on SPDE spatial model and population frame information.
  • simPopPixel: Simulates population in a country based on custom spatial model and population frame information.
• New minor functions.
  • aggPixelPreds and areaPopToArea: Functions for aggregating populations and prevalences to the areal level.
  • Functions for setting pixellated grid and population density grid.
  • Functions for adjusting population density grid based on population frame information.
  • Functions for projections to use with Kenya maps and for getting Admin areas given spatial locations.
• New internal functions for helping with population simulation.
• New datasets
  • kenyaMaps: Kenya administrative area map shapefiles, and a triangular mesh for the SPDE model for Kenya.
  • kenyaPopulationData: General and neonatal population frames for Kenya, and general and neonatal population density information for Kenya.
  • popMatKenya and popMatKenyaNeonatal: General and neonatal population density grids at 5km resolution.

Major update (version 1.1.0)

• Major expansion for smoothSurvey to implement popular SAE methods. Syntax change to the function.
• Allows smoothDirect and smoothCluster to fit space-only models.
• smoothSurvey, smoothDirect, and smoothCluster now returns S3 classed objects.

Major update (version 1.0.0)

Version 1.0.0 contains many major updates from the previous versions:

• Major updates to functions.
  • fitGeneric is now smoothSurvey
  • fitINLA is now smoothDirect
  • fitINLA2 is now smoothCluster
  • More extensions in both smoothed direct and cluster level models.
  • Major changes to how temporal models are specified with time.model and st.time.model.
  • More interpretable parameterization of slope and random slopes.
  • More visualization options.
  • Note: Previous function name and argument syntax remain to work as before, but may not receive high priority in maintenance in the future.
• Many minor improvements in functions.
  • Better model summary message.
  • Removed unnecessary function arguments, e.g., geo in various functions.
  • Removed the requirement to repeated specifying Amat, year_label and year_range. Now they are only required in the model fitting stage.
• New vignettes.

Major update (version 0.3.0)

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

• Function name changes
  • countrySummary is now getDirect
  • cuontrySummary_mult is now getDirectList
  • fitspace is now fitGeneric
  • projINLA is now getSmooth
• New functions
  • 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.

Citation

To cite the SUMMER package in publications use

  @Manual{li2020space,
    title = {Space-Time Smoothing of Demographic and Health Indicators using the R Package SUMMER},
    author = {Zehang R Li and Bryan D Martin and Tracy Q Dong and Geir-Arne Fuglstad and Jessica Godwin and John Paige and Andrea Riebler and Samuel Clark and Jon Wakefield},
    year = {2020},
    journal = {arXiv preprint}
  }

To cite specific version of the SUMMER package use

• v1.0.0

  @Manual{summer2020,
    title = {SUMMER: Spatio-Temporal Under-Five Mortality Methods for Estimation},
    author = {Zehang R Li and Bryan D Martin and Yuan Hsiao and Jessica Godwin and Jon Wakefield and Samuel J Clark and Geir-Arne Fuglstad and Andrea Riebler},
    year = {2020},
    note = {R package version 1.0.0},
  }

• earlier versions (e.g., v0.3.0)

  @Manual{summer2019,
    title = {SUMMER: Spatio-Temporal Under-Five Mortality Methods for Estimation},
    author = {Bryan D Martin and Zehang R Li and Yuan Hsiao and Jessica Godwin and Jon Wakefield and Samuel J Clark and Geir-Arne Fuglstad and Andrea Riebler},
    year = {2019},
    note = {R package version 0.3.0},
  }

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("richardli/SUMMER")

Examples of most of the main functions are described in the several vignettes listed on https://cran.r-project.org/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.