Package: SUMMER 1.4.1

SUMMER: Small-Area-Estimation Unit/Area Models and Methods for Estimation in R

Provides methods for spatial and spatio-temporal smoothing of demographic and health indicators using survey data, with particular focus on estimating and projecting under-five mortality rates, described in Mercer et al. (2015) <doi:10.1214/15-AOAS872>, Li et al. (2019) <doi:10.1371/journal.pone.0210645>, Wu et al. (DHS Spatial Analysis Reports No. 21, 2021), and Li et al. (2023) <arxiv:2007.05117>.

Authors:Zehang R Li [cre, aut], Bryan D Martin [aut], Yuan Hsiao [aut], Jessica Godwin [aut], John Paige [aut], Peter Gao [aut], Jon Wakefield [aut], Samuel J Clark [aut], Geir-Arne Fuglstad [aut], Andrea Riebler [aut]

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SUMMER.pdf |SUMMER.html✨
SUMMER/json (API)
NEWS

# Install 'SUMMER' in R:
install.packages('SUMMER', repos = c('https://richardli.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/richardli/summer/issues

Datasets:
  • BRFSS - The BRFSS dataset
  • DemoData - Simulated child mortality person-month dataset.
  • DemoData2 - Simulated dataset for prevalence mapping.
  • DemoMap - Uganda Admin-1 region map for illustration purpose
  • DemoMap2 - Kenya Admin-1 region map for illustration purpose
  • KenData - Auxiliary data for Kenya 2014 DHS.
  • KingCounty - Map of King County
  • MalawiData - Auxiliary data for Malawi 2000, 2004, 2010, and 2015 DHS.
  • MalawiMap - Malawi Admin-2 map
  • easpaKenya - Kenya 2009 Census Frame and Related Datasets
  • easpaKenyaNeonatal - Kenya 2009 Census Frame and Related Datasets
  • poppaKenya - Kenya 2009 Census Frame and Related Datasets
  • poppsubKenya - Kenya 2009 Census Frame and Related Datasets

On CRAN:

bayesian-inferencesmall-area-estimationspace-time

9.23 score 23 stars 2 packages 125 scripts 1.2k downloads 45 exports 78 dependencies

Last updated 2 months agofrom:8df192aedd. Checks:OK: 6 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winOKOct 29 2024
R-4.5-linuxOKOct 29 2024
R-4.4-winOKOct 29 2024
R-4.4-macOKOct 29 2024
R-4.3-winNOTEOct 29 2024
R-4.3-macOKOct 29 2024

Exports:adjustPopMataggregateSurveyareaPopToAreaBenchmarkcalibrateByRegionChangeRegioncompareEstimatesexpitfitGenericfitINLAfitINLA2getAdjustedgetAmatgetAreaNamegetBirthsgetCountsgetDiaggetDirectgetDirectListgetPoppsubgetSmoothedgetSmoothedDensityhatchPlotlogitlogitNormMeanmakePopIntegrationTabmapEstimatesmapPlotmapPointspixelPopToAreapoppRegionFromPopMatprojKenyaridgePlotrstsetThresholdsByRegionsimhypersimPopCustomsimPopSPDEsimSPDEsmoothAreasmoothClustersmoothDirectsmoothSurveysmoothUnittcpPlot

Dependencies:bitbit64bootclassclassIntclicliprcolorspacecpp11crayondata.tableDBIdeldirdotCall64e1071fansifarverfieldsforcatsggplot2ggridgesgluegridExtragtablehavenhmsisobandKernSmoothlabelinglatticelifecyclemagrittrmapsMASSMatrixmgcvminqamitoolsmunsellnlmenumDerivpillarpkgconfigplyrprettyunitsprogressproxyR6RColorBrewerRcppRcppArmadilloreadrreshape2rlangs2scalessfshadowtextspspamspDataspdepstringistringrsurveysurvivalterratibbletidyselecttzdbunitsutf8vctrsviridisviridisLitevroomwithrwk

Case Study: Estimating Subnational U5MR using DHS data

Rendered fromu5mr-dhs-vignette.html.asisusingR.rsp::asison Oct 29 2024.

Last update: 2022-07-25
Started: 2022-07-25

Estimating Subnational U5MR using Simulated Data

Rendered fromu5mr-vignette.html.asisusingR.rsp::asison Oct 29 2024.

Last update: 2022-07-25
Started: 2019-10-16

Generic small area estimation

Rendered fromsmall-area-estimation.html.asisusingR.rsp::asison Oct 29 2024.

Last update: 2022-06-24
Started: 2022-06-24

Readme and manuals

Help Manual

Help pageTopics
SUMMER package documentation.SUMMER-package SUMMER
Helper function of 'pixelPopToArea'aggPixelPreds
Aggregate populations to the specified areal levelaggPop areaPopToArea pixelPopToArea
Aggregate estimators from different surveys.aggregateSurvey
Benchmark posterior draws to national estimatesBenchmark
The BRFSS datasetBRFSS
Calibrate the point level totals so their sum matches the regional totalscalibrateByRegion
Map region names to a common set.ChangeRegion
Plot heatmap comparing pairwise posterior exceedence probabilities for svysae objectcompareEstimates
Simulated child mortality person-month dataset.DemoData
Simulated dataset for prevalence mapping.DemoData2
Uganda Admin-1 region map for illustration purposeDemoMap
Kenya Admin-1 region map for illustration purposeDemoMap2
Expit transformationexpit
Adjust direct estimates and their associated variancesgetAdjusted
Extract adjacency matrix from the mapgetAmat
Determines which administrative areas contain the given pointsgetAreaName
Reformat full birth records into person-month formatgetBirths
Aggregate person-month data into counts and totals by groups.getCounts
Extract posterior summaries of random effectsgetDiag
Obtain the Horvitz-Thompson direct estimates and standard errors using delta method for a single survey.getDirect
Obtain the Horvitz-Thompson direct estimates and standard errors using delta method for multiple surveys.getDirectList
Extract smoothed estimates.getSmoothed
Plot maps with uncertainty hatching.hatchPlot
New random IID models for m-year to period random effectsiid.new
New random IID models for m-year to period random effectsiid.new.pc
Auxiliary data for Kenya 2014 DHS.KenData
Kenya 2009 Census Frame and Related DatasetseaspaKenya easpaKenyaNeonatal kenyaPopulationData poppaKenya poppsubKenya
Map of King CountyKingCounty
Logit transformationlogit
Calculate the mean of a distribution whose logit is GaussianlogitNormMean
Generating pixellated populations, and population framesadjustPopMat getPoppsub makePopIntegrationTab
Auxiliary data for Malawi 2000, 2004, 2010, and 2015 DHS.MalawiData
Malawi Admin-2 mapMalawiMap
Mapping estimates for svysae objectmapEstimates
Plot region-level variables on a mapmapPlot
Map GPS points to polygon regionsmapPoints
Plot projection output.plot.SUMMERproj
Generate a population frame of a similar format to poppa argument of 'simPopCustom' with a custom set of regionspoppRegionFromPopMat
Print method for the smoothing models.print.SUMMERmodel
Print method for the smoothing models from 'smoothSurvey'.print.SUMMERmodel.svy
Print method for the combined projection output.print.SUMMERprojlist
Map projection for KenyaprojKenya
Calculate and plot posterior densities of the projected estimatesgetSmoothedDensity ridgePlot
Simulate spatial and temporal random effectsrst
New random walk 1 and 2 models for m-year to period random effectsrw.new
New random walk 1 and 2 models for m-year to period random effectsrw.new.pc
Set thresholds of population density for urbanicity classifications within each region of the given typesetThresholdsByRegion
Simulate hyperpriors from an GMRFsimhyper
Simulate populations and areal prevalencessimPop simPopCustom simPopSPDE
Internal functions for population simulationgetExpectedNperEA getSortIndices rmultinom1 rMyMultinomial rMyMultinomialSubarea rStratifiedMultnomial rStratifiedMultnomialBySubarea sampleNMultilevelMultinomial sampleNMultilevelMultinomialFixed simPopInternal
Simulate from the SPDE spatial modelsimSPDE
Small area estimation via basic area level modelsmoothArea
Cluster-level space-time smoothing models for mortality ratesfitINLA2 smoothCluster
Smoothed direct estimates for mortality ratesfitINLA smoothDirect
Fit space-time smoothing models for a generic outcome from complex surveys.fitGeneric smoothSurvey
Smooth via basic unit level modelsmoothUnit
New Type I to IV space time interaction models for m-year to period random effectsst.new
New Type I to IV space time interaction models for m-year to period random effectsst.new.pc
Summary method for the smoothing models.summary.SUMMERmodel
Summary method for the smoothing model and output from 'smoothSurvey'.summary.SUMMERmodel.svy
Summary method for the combined projection output. This function is the print method for class 'SUMMERprojlist'.summary.SUMMERprojlist
Discrete-color maps based on the True Classification ProbabilitiestcpPlot