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README.md

SUMMER

Build Status

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

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.

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Spatio-temporal Under-five Mortality Model Estimation in R

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