Package: surveyPrev 1.0.0

Qianyu Dong

surveyPrev: Mapping the Prevalence of Binary Indicators using Survey Data in Small Areas

Provides a pipeline to perform small area estimation and prevalence mapping of binary indicators using health and demographic survey data, described in Fuglstad et al. (2022) <doi:10.48550/arXiv.2110.09576> and Wakefield et al. (2020) <doi:10.1111/insr.12400>.

Authors:Qianyu Dong [cre, aut], Zehang R Li [aut], Yunhan Wu [aut], Andrea Boskovic [aut], Jon Wakefield [aut]

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

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

Peer review:

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

Datasets:

On CRAN:

5.75 score 1 stars 9 scripts 224 downloads 38 exports 156 dependencies

Last updated 8 days agofrom:dcce028d2b. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 15 2024
R-4.5-winWARNINGNov 15 2024
R-4.5-linuxWARNINGNov 15 2024
R-4.4-winWARNINGNov 15 2024
R-4.4-macWARNINGNov 15 2024
R-4.3-winWARNINGNov 15 2024
R-4.3-macWARNINGNov 15 2024

Exports:adminInfoaggPopulationaggSurveyWeightch_allvac_eitherch_diar_ors_rhfch_meas_eitherch_novac_eitherch_pent1_eitherch_pent3_eitherclusterInfoclusterModeldirectESTexceedPlotfhModelfp_cruse_modfp_unmet_totget_api_tablegetDHSdatagetDHSgeogetDHSindicatorgetURhv_hiv_posintervalPlotml_hhaccessNMRnt_ch_any_anemnt_ch_stuntnt_ch_wastnt_ebfnt_wm_any_anemnt_wm_thinph_sani_basicph_sani_improverankPlotrh_anc_4vsrh_del_pvskillscatterPlotwatersource_adj

Dependencies:askpassbackportsbase64encbitbit64blobbootbriobroombslibcachemcallrcellrangerclassclassIntclicliprcolorspaceconflictedcpp11crayoncurldata.tabledatawizardDBIdbplyrdeldirdigestdotCall64dplyrdtplyre1071evaluatefansifarverfastmapfieldsfontawesomeforcatsforeignfsgarglegenericsgetPassggplot2ggridgesgluegoogledrivegooglesheets4gridExtragtablehavenhighrhmshtmltoolshttridsinsightiotoolsisobandjquerylibjsonliteKernSmoothknitrlabelinglabelledlatticelifecyclelubridatemagrittrmapsMASSMatrixmatrixStatsmemoisemgcvmimeminqamitoolsmodelrmunsellnaniarnlmenormnumDerivopensslpillarpkgconfigplyrprettyunitsprocessxprogressproxypspurrrqdapRegexR6raggrappdirsrasterRColorBrewerRcppRcppArmadillordhsreadrreadxlrematchrematch2reprexreshape2rlangrmarkdownrstudioapirvests2sassscalesselectrsfshadowtextsjlabelledspspamspDataspdepstorrstringistringrSUMMERsurveysurvivalsyssystemfontsterratextshapingtibbletidyrtidyselecttidyversetimechangetinytextzdbunitsUpSetRutf8uuidvctrsviridisviridisLitevisdatvroomwithrwkxfunxml2yaml

Create customized indicators

Rendered fromvignette-data-preparation.html.asisusingR.rsp::asison Nov 15 2024.

Last update: 2024-03-20
Started: 2024-03-05

Prevalence mapping using DHS data

Rendered fromvignette-main.html.asisusingR.rsp::asison Nov 15 2024.

Last update: 2024-03-20
Started: 2024-03-20

Readme and manuals

Help Manual

Help pageTopics
Get admin informationadminInfo
Get population informationaggPopulation
Get survey weight by admin levelsaggSurveyWeight
CH_VACS_C_BAS Children with all 8 basic vaccinations (age 12-23) "All basic vaccinations according to either source"ch_allvac_either
CH_DIAT_C_ORT KR Diarrhea treatment (Children under five with diarrhea treated with either ORS or RHF)ch_diar_ors_rhf
CH_VACC_C_MSL MCV: Measles Measles vaccination received Percentage of children (age 12-23) ch_meas_either CH_VAC.do KR "Measles vaccination according to either source"ch_meas_either
CH_VACS_C_NON KR Children with no vaccinations (age 12-23)ch_novac_either
CH_VACC_C_DP1 KR Percentage of children (age 12-23) Pentavalent 1rd dose vaccination according to either source"ch_pent1_either
CH_VACC_C_DP3 DPT3 KR Percentage of children (age 12-23) Pentavalent 3rd dose vaccination according to either source"ch_pent3_either
Get cluster informationclusterInfo
Calculate cluster model estimates using beta binomial modelclusterModel
Calculate direct estimatesdirectEST
Plot exceedance probability of model resultsexceedPlot
Calculate smoothed direct estimatesfhModel
FP_CUSM_W_MOD IRdata Modern contraceptive prevalence rate (Married women currently using any modern method of contraception)fp_cruse_mod
FP_NADA_W_UNT #unmet_family IRdata women with an unmet need for family planning for spacing and limitingfp_unmet_tot
Function to obtain subnational estimates from DHS APIget_api_table
Download DHS survey datagetDHSdata
Download DHS geo datagetDHSgeo
Process DHS datagetDHSindicator
Function to threshold population raster to obtain urban/rural fractions by Admin1 and Admin2 areasgetUR
HA_HIVP_W_HIV hv_hiv_pos "HIV positive test result"hv_hiv_pos
Get scatter plot for any two model resultsintervalPlot
ML_ITNA_P_ACC Households with at least one insecticide-treated mosquito net (ITN) for every two persons who stayed in the household the previous night Persons with access to an insecticide-treated mosquito net (ITN) ML_NETS_HH.do HR Households with >1 ITN per 2 household members Percentage of households with at least one ITN for every 2 persons who stayed in the household last nightml_hhaccess
CM_ECMR_C_NNR nmr CM_ECMR_C_NNR BR (not from dhs github) Neonatal mortality rate !!!!!!NMR
CN_ANMC_C_ANY Children with any anemia "Any anemia - child 6-59 months" PR NT_CH_NUT.do Children under five with any anemiant_ch_any_anem
CN_NUTS_C_HA2 stunting Children stunted NT_CH_NUT.do PR "Stunted child under 5 years" Stunting rate (Prevalence of stunted (HAZ < -2) children under five (0-59 months)) Percentage of children under age five stunted (below -2 standard deviations of height-for-age according to the WHO standard).nt_ch_stunt
CN_NUTS_C_WH2 wasting Children wasted NT_CH_NUT.do PR "Wasted child under 5 years" Wasting rate (Prevalence of wasted (HAZ < -2) children under five (0-59 months)) Percentage of children under age five with a weight-for-height z-score (WHZ) more than two standard deviations below the median WHO growth standards.nt_ch_wast
CN_BRFS_C_EXB Children exclusively breastfed NT_IYCF.do KR "Exclusively breastfed - last-born under 6 months" Children exclusively breastfed (Prevalence of exclusive breastfeeding of children under six months of age)nt_ebf
AN_ANEM_W_ANY womananemia nt_wm_any_anem "Any anemia - women" NT_WM_NUT.do Percentage of women aged 15-49 classified as having any anemiant_wm_any_anem
AN_NUTS_W_THN Women who are thin according to BMI (<18.5) NT_WM_NUT.do "Thin BMI - women" IR !!!!!!!! Underweight (Prevalence of underweight (BMI < 18.5) women of reproductive age)nt_wm_thin
WS_TLET_P_BAS Population with access to a basic sanitation service WS_TLET_P_BAS in DHS API PH_SANI.do PR ph_sani_basic "Basic sanitation facility"ph_sani_basic
WS_TLET_H_IMP Percentage of households using an improved sanitation facility PH_SANI.do PR ph_sani_improve "Access to improved sanitation" country-specificph_sani_improve
Get ranking plot of model resultsrankPlot
RH_ANCN_W_N4P ancvisit4+ RH_ANCN_W_N4P IR Antenatal visits for pregnancy: 4+ visitsrh_anc_4vs
RH_DELA_C_SKP IR or BR Assistance during delivery from a skilled providerrh_del_pvskill
Get scatter plot for any two model resultsscatterPlot
Table of built-in indicators.surveyPrevIndicators
WS_SRCE_P_BAS Population using a basic water source PH_WATER.do ph_wtr_basic "Basic water service" PRwatersource_adj
Admin 1 Polygon Map for Zambia.ZambiaAdm1
Admin 2 Polygon Map for Zambia.ZambiaAdm2
Population estimates for Women of age 15 to 49 in Zambia in 2018.ZambiaPopWomen