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

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

## Documentation for package ‘surveyPrev’ version 2.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A C D E F G H I M P R S W Z

## -- A --

addNewIndicator | Create new row to add in indicatorList.
addUpper | Attach upper-level admin names to lower-level polygons
adminInfo | Get admin information
aggPopulation | Get population information
aggSurveyWeight | Get survey weight by admin levels
AH_TOBC_W_OTH | AH_TOBC_W_OTH
AH_TOBU_M_ASM | AH_TOBU_M_ASM
AH_TOBU_M_SNN | AH_TOBU_M_SNN
AH_TOBU_W_SNM | AH_TOBU_W_SNM
AH_TOBU_W_SNN | AH_TOBU_W_SNN
AN_ANEM_W_ANY | AN_ANEM_W_ANY IRdata Percentage of women aged 15-49 classified as having any anemia
AN_NUTS_W_OVW | AN_NUTS_W_OVW Women who are overweight according to BMI (25.0-29.9) nt_wm_ovwt in github IR
AN_NUTS_W_THN | AN_NUTS_W_THN IRdata Women who are thin according to BMI (<18.5)

## -- C --

CH_ARIS_C_ADV | CH_ARIS_C_ADV Children with ARI for whom advice or treatment was sought; ch_ari_care in github KR
CH_DIAT_C_ABI | CH_DIAT_C_ABI
CH_DIAT_C_ADV | CH_DIAT_C_ADV Treatment of diarrhea: Advice or treatment was sought; ch_diar_care in github KR
CH_DIAT_C_AMO | CH_DIAT_C_AMO
CH_DIAT_C_NOT | CH_DIAT_C_NOT
CH_DIAT_C_ORS | CH_DIAT_C_ORS
CH_DIAT_C_ORT | CH_DIAT_C_ORT
CH_DIAT_C_OSI | CH_DIAT_C_OSI
CH_DIAT_C_RHF | CH_DIAT_C_RHF
CH_DIFP_C_FAL | CH_DIFP_C_FAL
CH_FEVR_C_FEV | CH_FEVR_C_FEV
CH_FEVT_C_ADV | CH_FEVT_C_ADV Children with fever for whom advice or treatment was sought ch_fev_care in github ml_fev_care should produce the same data KR
CH_SZWT_C_L25 | CH_SZWT_C_L25
CH_VACC_C_BAS | CH_VACC_C_BAS KRdata Children with all 8 basic vaccinations (age 12-23)
CH_VACC_C_BCG | CH_VACC_C_BCG Percentage of children 12-23 months who had received BCG vaccination ms_afm_15 in github KR
CH_VACC_C_DP1 | CH_VACC_C_DP1 KRdata Pentavalent 1st dose vaccination Percentage of children (age 12-23) with 1st dose of Pentavalent vaccine
CH_VACC_C_DP3 | CH_VACC_C_DP3 KRdata Pentavalent 3rd dose vaccination Percentage of children (age 12-23) with 3rd dose of Pentavalent vaccine
CH_VACC_C_MSL | CH_VACC_C_MSL KRdata Measles vaccination received Percentage of children (age 12-23)
CH_VACC_C_NON | CH_VACC_C_NON KRdata Children with no vaccinations (age 12-23)
CH_VACC_C_PN3 | CH_VACC_C_PN3 KRdata Pneumococcal 3rd dose vaccination Percentage of children (age 12-23)
CH_VACC_C_RT1 | CH_VACC_C_RT1 KRdata Rotavirus 1 vaccination received
CH_VACS_C_PN3 | CH_VACS_C_PN3 KRdata Pneumococcal 3 vaccination received
clusterInfo | Get cluster information
clusterModel | Calculate cluster model estimates using beta binomial model
clusterModel_u5mr | Calculate cluster model estimates using beta binomial model for U5MR
CM_ECMR_C_IMF | CM_ECMR_C_IMF imr 5 years prior to survey.
CM_ECMR_C_IMR | CM_ECMR_C_IMR imr 10 years prior to survey.
CM_ECMR_C_NNF | CM_ECMR_C_NNF NMR five years prior to survey.
CM_ECMR_C_NNR | CM_ECMR_C_NNR BRdata Neonatal mortality rate
CM_ECMR_C_U5F | CM_ECMR_C_U5F u5mr 5 years prior to survey.
CM_ECMR_C_U5M | CM_ECMR_C_U5M u5mr 10 years prior to survey.
CN_ANMC_C_ANY | CN_ANMC_C_ANY PRdata Children with any anemia Children under five with any anemia
CN_BRFI_C_EVR | CN_BRFI_C_EVR
CN_BRFS_C_EXB | CN_BRFS_C_EXB KRdata Children exclusively breastfed Prevalence of exclusive breastfeeding of children under six months of age
CN_IYCF_C_4FA | CN_IYCF_C_4FA Percentage of children age 6-23 months fed five or more food groups. The food groups are a. breastmilk b. infant formula, milk other than breast milk, cheese or yogurt or other milk products; c. foods made from grains, roots, and tubers, including porridge and fortified baby food from grains; d. vitamin A-rich fruits and vegetables (and red palm oil); e. other fruits and vegetables; f. eggs; g. meat, poultry, fish, and shellfish (and organ meats); h. legumes and nuts. nt_mdd in github KR
CN_NUTS_C_HA2 | CN_NUTS_C_HA2
CN_NUTS_C_HA3 | CN_NUTS_C_HA3
CN_NUTS_C_WA2 | CN_NUTS_C_WA2
CN_NUTS_C_WA3 | CN_NUTS_C_WA3
CN_NUTS_C_WAP | CN_NUTS_C_WAP
CN_NUTS_C_WH2 | CN_NUTS_C_WH2
CN_NUTS_C_WH3 | CN_NUTS_C_WH3
CN_NUTS_C_WHP | CN_NUTS_C_WHP
CO_INUS_W_EVU | CO_INUS_W_EVU
CO_INUS_W_U12 | CO_INUS_W_U12
CO_MOBB_W_BNK | CO_MOBB_W_BNK
CO_MOBB_W_MBF | CO_MOBB_W_MBF
CO_MOBB_W_MOB | CO_MOBB_W_MOB
CP_BREG_C_CRT | CP_BREG_C_CRT
CP_BREG_C_NCT | CP_BREG_C_NCT
CP_BREG_C_REG | CP_BREG_C_REG

## -- D --

datainfo | Summarize Sample and Event Information by Administrative Level
directEST | Calculate direct estimates
directEST_u5mr | Helper function for the U5MR direct estimation
directEST_varfix | Calculate direct estimates
DV_AFSV_W_A10 | DV_AFSV_W_A10
DV_AFSV_W_A12 | DV_AFSV_W_A12
DV_EXPV_W_12M | DV_EXPV_W_12M Percentage of women who have experienced physical violence in the past 12 months often or sometimes dv_phy_12m in github IR
DV_EXSV_W_12M | DV_EXSV_W_12M Percentage of women who ever experienced sexual violence dv_sex_12m in github IR
DV_EXSV_W_EVR | DV_EXSV_W_EVR Percentage of women who ever experienced sexual violence dv_sex in github IR
DV_PCPV_W_CBF | DV_PCPV_W_CBF
DV_PCPV_W_CHD | DV_PCPV_W_CHD
DV_PCPV_W_EMP | DV_PCPV_W_EMP
DV_PCPV_W_FLW | DV_PCPV_W_FLW
DV_PCPV_W_OLW | DV_PCPV_W_OLW
DV_STPS_W_BFR | DV_STPS_W_BFR
DV_VPRG_W_VPG | DV_VPRG_W_VPG

## -- E --

ED_EDUC_W_SEH | ED_EDUC_W_SEH IRdata Percentage of women with secondary or higher education
ED_LITR_W_LIT | ED_LITR_W_LIT
ED_MDIA_W_3MD | ED_MDIA_W_3MD
ED_MDIA_W_N3M | ED_MDIA_W_N3M
ED_MDIA_W_NWS | ED_MDIA_W_NWS
ED_MDIA_W_RDO | ED_MDIA_W_RDO
ED_MDIA_W_TLV | ED_MDIA_W_TLV
EM_EMPM_W_EMP | EM_EMPM_W_EMP
exceedPlot | Plot exceedance probability of model results

## -- F --

FG_KFCC_W_HFC | FG_KFCC_W_HFC IRdata Percentage of women who have ever heard of female circumcision
FG_PFCC_W_WCC | FG_PFCC_W_WCC IRdata Percentage of women circumcised (women who experienced female genital cutting (FGM))
fhModel | Calculate smoothed direct estimates
FP_CUSA_W_ANY | FP_CUSA_W_ANY
FP_CUSA_W_EMC | FP_CUSA_W_EMC
FP_CUSA_W_FCN | FP_CUSA_W_FCN
FP_CUSA_W_FST | FP_CUSA_W_FST
FP_CUSA_W_IMP | FP_CUSA_W_IMP
FP_CUSA_W_INJ | FP_CUSA_W_INJ
FP_CUSA_W_IUD | FP_CUSA_W_IUD
FP_CUSA_W_MCN | FP_CUSA_W_MCN
FP_CUSA_W_MOD | FP_CUSA_W_MOD IRdata Modern contraceptive prevalence rate (women currently using any modern method of contraception)
FP_CUSA_W_MST | FP_CUSA_W_MST
FP_CUSA_W_PIL | FP_CUSA_W_PIL
FP_CUSA_W_STD | FP_CUSA_W_STD
FP_CUSA_W_TRA | FP_CUSA_W_TRA
FP_CUSA_W_WTH | FP_CUSA_W_WTH
FP_CUSM_W_MOD | FP_CUSM_W_MOD IRdata Modern contraceptive prevalence rate (Married women currently using any modern method of contraception)
FP_EFPM_M_NWS | FP_EFPM_M_NWS
FP_EFPM_M_TLV | FP_EFPM_M_TLV
FP_EFPM_W_NWS | FP_EFPM_W_NWS
FP_EFPM_W_RDO | FP_EFPM_W_RDO
FP_EFPM_W_TLV | FP_EFPM_W_TLV
FP_EVUM_W_MOD | FP_EVUM_W_MOD
FP_KMTA_W_ANY | FP_KMTA_W_ANY
FP_KMTA_W_EMC | FP_KMTA_W_EMC
FP_KMTA_W_FCN | FP_KMTA_W_FCN
FP_KMTA_W_FST | FP_KMTA_W_FST
FP_KMTA_W_IMP | FP_KMTA_W_IMP
FP_KMTA_W_INJ | FP_KMTA_W_INJ
FP_KMTA_W_IUD | FP_KMTA_W_IUD
FP_KMTA_W_MST | FP_KMTA_W_MST
FP_KMTA_W_OMD | FP_KMTA_W_OMD
FP_KMTA_W_PIL | FP_KMTA_W_PIL
FP_KMTA_W_STD | FP_KMTA_W_STD
FP_KMTA_W_TRA | FP_KMTA_W_TRA
FP_KMTA_W_WTH | FP_KMTA_W_WTH
FP_NADA_W_UNT | FP_NADA_W_UNT IRdata Women with an unmet need for family planning for spacing and limiting
FP_NADM_W_PDM | FP_NADA_W_UNT IRdata Women with an unmet need for family planning for spacing and limiting
FP_NADM_W_UNT | FP_NADM_W_UNT #unmet_family IRdata Married women with an unmet need for family planning for spacing and limiting, line 17 manually added by Qianyu
FP_NDYA_W_PDM | FP_NADA_W_UNT IRdata Women with an unmet need for family planning for spacing and limiting

## -- G --

getCovariate | Extract Covariate Data from A list of Rasters
getDHSdata | Download DHS survey data
getDHSgeo | Download DHS geo data
getDHSindicator | Process DHS data
getUR | Function to threshold population raster to obtain urban/rural fractions by Admin1 and Admin2 areas
get_api_table | Function to obtain subnational estimates from DHS API
get_geoBoundaries | Download geoBoundaries Shapefile as sf Object

## -- H --

HA_AFSY_M_A15 | HA_AFSY_M_A15
HA_AFSY_M_A18 | HA_AFSY_M_A18
HA_AFSY_W_A18 | HA_AFSY_W_A18
HA_ANSS_M_CND | HA_ANSS_M_CND
HA_ANSS_W_CND | HA_ANSS_W_CND
HA_ANSS_W_RSX | HA_ANSS_W_RSX
HA_CATH_W_ATN | HA_CATH_W_ATN
HA_CATH_W_NRS | HA_CATH_W_NRS
HA_HIVP_B_HIV | HA_HIVP_B_HIV hv_hiv_pos "HIV prevalence among general population"
HA_HRSX_W_CND | HA_HRSX_W_CND
HA_HVST_M_HRD | HA_HVST_M_HRD
HA_HVST_M_USD | HA_HVST_M_USD
HA_HVTY_M_TRR | HA_HVTY_M_TRR
HA_HVTY_W_TRR | HA_HVTY_W_TRR
HA_KAID_W_HRD | HA_KAID_W_HRD Percentage of women who have heard of HIV or AIDS hk_ever_heard in github IR
HA_STIS_M_DIS | HA_STIS_M_DIS
HA_STIS_M_SOR | HA_STIS_M_SOR
HA_STIS_W_STI | HA_STIS_W_STI Percentage of women reporting a sexually transmitted infection in the 12 months preceding the survey among women who ever had sexual intercourse hk_sti in github IR
HC_AGEG_P_ADL | HC_AGEG_P_ADL
HC_ELEC_H_ELC | HC_ELEC_H_ELC Percentage of households with electricity ph_electric in github HR
HC_FLRM_H_CER | HC_FLRM_H_CER Percentage of households with ceramic tile floors ph_floor in github HR
HC_HEFF_H_RDO | HC_HEFF_H_RDO Percentage of households possessing a radio ph_radio in github HR
HC_WIXQ_P_12Q | HC_WIXQ_P_12Q PRdata Population in the lowest and second wealth quintile
HC_WIXQ_P_2ND | HC_WIXQ_P_2ND PRdata Population in the second wealth quintile
HC_WIXQ_P_LOW | HC_WIXQ_P_LOW PRdata Population in the lowest wealth quintile

## -- I --

indicatorList | Table of supported DHS indicators.
intervalPlot | Get scatter plot for any two model results

## -- M --

match_all_result | Indicator matching table.
MA_CWIV_W_CWV | MA_CWIV_W_CWV
MA_MBAG_W_B15 | MA_MBAG_W_B15 Women first married by exact age 15 ms_afm_15 in github IR
MA_MBAG_W_B18 | ##' MA_MBAG_W_B18 Percentage of women first married by exact age 18 ms_afm_18 in github IR
MA_MBAY_W_B15 | MA_MBAY_W_B15 Young women age 20-24 first married by exact age 15 ms_afm_15 in github IR
MA_MBAY_W_B18 | MA_MBAY_W_B18 Percentage of Young women age 20-24 first married by exact age 18 ms_afm_18 in github IR
MA_MSTA_W_NMA | MA_MSTA_W_NMA
ML_NETC_C_ITN | ML_NETC_C_ITN PRdata Percentage of children under age five who slept under an insecticide treated net (ITN) the night before the survey
ML_NETP_H_IT2 | ML_NETP_H_IT2 HRdata Households with access to an insecticide-treated mosquito net (ITN)
ML_NETU_P_ITN | ML_NETU_P_ITN PRdata Percentage of the de facto household population who slept under an insecticide treated net the night before the survey
ML_PMAL_C_RDT | ML_PMAL_C_RDT PRdata Malaria prevalence according to RDT

## -- P --

prevMap | static prevalence map for any subnational level
prevMap.web | leaflet (interactive) prevalence map for any subnational level
PR_DESL_W_WNM | PR_DESL_W_WNM

## -- R --

rankPlot | Get ranking plot of model results
RH_ANCN_W_N01 | AH_TOBC_W_OTH
RH_ANCN_W_N4F | RH_ANCN_W_N4F IRdata Antenatal visits for pregnancy: 4+ visits FIVE year
RH_ANCN_W_N4P | RH_ANCN_W_N4P IRdata Antenatal visits for pregnancy: 4+ visits TWO year
RH_ANCN_W_NON | RH_ANCN_W_N4P IRdata Antenatal visits for pregnancy: no visits TWO year
RH_DELA_C_SKF | RH_DELA_C_SKF BRdata Assistance during delivery from a skilled provider
RH_DELA_C_SKP | RH_DELA_C_SKP BRdata Assistance during delivery from a skilled provider
RH_DELP_C_DHF | RH_DELP_C_DHF
RH_DELP_C_DHT | RH_DELP_C_DHT
RH_DELP_C_HOM | RH_DELP_C_HOM
RH_DELP_C_HOT | RH_DELP_C_HOT
RH_DELP_C_PRT | RH_DELP_C_PRT
RH_DELP_C_PRV | RH_DELP_C_PRV
RH_DELP_C_PUB | RH_DELP_C_PUB
RH_DELP_C_PUT | RH_DELP_C_PUT
RH_PAHC_W_DIS | RH_PAHC_W_DIS IRdata Problems in accessing health care: Distance to health facility
RH_PAHC_W_MON | RH_PAHC_W_MON IRdata Problems in accessing health care: Getting money for treatment
RH_PAHC_W_PRM | RH_PAHC_W_PRM IRdata Problems in accessing health care: Getting permission to go for treatment
RH_PCCT_C_DY2 | RH_PCCT_C_DY2 Newborn's first postnatal checkup: 1-2 days RH_PCCT_C_DY2 in github IR
RH_PCMT_W_DY2 | RH_PCMT_W_DY2 Mother's first postnatal checkup: 1-2 days IR
RH_PCMT_W_NON | RH_PCMT_W_NON No Mother's postnatal checkup in 42 days IR
ridgeprevPlot | ridge plot for prevalence

## -- S --

scatterPlot | Get scatter plot for any two model results
scatterPlot.web | web-based scatter plot

## -- W --

WE_AWBT_M_ARG | WE_AWBT_M_ARG
WE_AWBT_M_BFD | WE_AWBT_M_BFD
WE_AWBT_M_OUT | WE_AWBT_M_OUT
WE_AWBT_M_REF | WE_AWBT_M_REF
WE_AWBT_W_ARG | WE_AWBT_W_ARG
WE_AWBT_W_BFD | WE_AWBT_W_BFD
WE_AWBT_W_NEG | WE_AWBT_W_NEG
WE_AWBT_W_OUT | WE_AWBT_W_OUT
WE_AWBT_W_REF | WE_AWBT_W_REF
WS_SRCE_H_USG | WS_SRCE_H_USG Percentage of households whose main source of drinking water is an unprotected spring ph_wtr_source in github "unprotected spring" = 42, HR
WS_SRCE_P_BAS | WS_SRCE_P_BAS PRdata Population using a basic water source
WS_TLET_H_IMP | WS_TLET_H_IMP PRdata Percentage of households using an improved sanitation facility
WS_TLET_P_BAS | WS_TLET_P_BAS PRdata Population with access to a basic sanitation service
WS_WTRT_P_BLC | WS_WTRT_P_BLC
WS_WTRT_P_BOL | WS_WTRT_P_BOL
WS_WTRT_P_SOL | WS_WTRT_P_SOL
WS_WTRT_P_STN | WS_WTRT_P_STN

## -- Z --

ZambiaAdm1 | Admin 1 Polygon Map for Zambia.
ZambiaAdm2 | Admin 2 Polygon Map for Zambia.
ZambiaPopWomen | Population estimates for Women of age 15 to 49 in Zambia in 2018.