# Spatio-Temporal Under-Five Mortality Methods for Estimation

## Documentation for package ‘SUMMER’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

SUMMER-package | SUMMER package documentation.
aggregateSurvey | Aggregate estimators from different surveys.
BRFSS | The BRFSS dataset
ChangeRegion | Map region names to a common set.
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
expit | Expit transformation
fitGeneric | Fit space-time smoothing models for a generic outcome from complex surveys.
fitINLA | Smoothed direct estimates for mortality rates
fitINLA2 | Cluster-level space-time smoothing models for mortality rates
getAdjusted | Adjust direct estimates and their associated variances
getAmat | Extract adjacency matrix from the map
getBirths | Reformat full birth records into person-month format
getCounts | Aggregate person-month data into counts and totals by groups.
getDiag | Extract posterior summaries of random effects
getDirect | Obtain the Horvitz-Thompson direct estimates and standard errors using delta method for a single survey.
getDirectList | Obtain the Horvitz-Thompson direct estimates and standard errors using delta method for multiple surveys.
getSmoothed | Extract smoothed estimates.
getSmoothedDensity | Calculate and plot posterior densities of the projected estimates
hatchPlot | Plot maps with uncertainty hatching.
iid.new | New random IID models for m-year to period random effects
iid.new.pc | New random IID models for m-year to period random effects
KenData | Auxiliary data for Kenya 2014 DHS.
KingCounty | Map of King County
logit | Logit transformation
MalawiData | Auxiliary data for Malawi 2000, 2004, 2010, and 2015 DHS.
MalawiMap | Malawi Admin-2 map
mapPlot | Plot region-level variables on a map
mapPoints | Map GPS points to polygon regions
plot.SUMMERproj | Plot projection output.
ridgePlot | Calculate and plot posterior densities of the projected estimates
rst | Simulate spatial and temporal random effects
rw.new | New random walk 1 and 2 models for m-year to period random effects
rw.new.pc | New random walk 1 and 2 models for m-year to period random effects
simhyper | Simulate hyperpriors from an GMRF
smoothCluster | Cluster-level space-time smoothing models for mortality rates
smoothDirect | Smoothed direct estimates for mortality rates
smoothSurvey | Fit space-time smoothing models for a generic outcome from complex surveys.
st.new | New Type I to IV space time interaction models for m-year to period random effects
st.new.pc | New Type I to IV space time interaction models for m-year to period random effects
SUMMER | SUMMER package documentation.
tcpPlot | Discrete-color maps based on the True Classification Probabilities