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Merge pull request #81 from rapidsurveys:dev
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tidy up documentation
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@ernestguevarra
ernestguevarra authored Jan 5, 2025
2 parents 6c9c47c + 5db0022 commit ca8130a
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2 changes: 1 addition & 1 deletion NAMESPACE
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Expand Up @@ -28,7 +28,7 @@ export(create_op_screening)
export(create_op_visual)
export(create_op_wash)
export(estimate_classic)
export(estimate_op_all)
export(estimate_op)
export(estimate_probit)
export(merge_estimates)
export(probit_gam)
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273 changes: 115 additions & 158 deletions R/01-opIndicators.R
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@@ -1,14 +1,30 @@
#'
#' Create older people indicators dataset from survey data collected using the
#' standard RAM-OP questionnaire. The indicator sets covered by the standard
#' RAM-OP survey are:
#' standard RAM-OP questionnaire.
#'
#' @description
#' The indicator sets covered by the standard RAM-OP survey are:
#'
#' * Demographic indicators
#' * Dietary intake indicators
#' * Household hunger scale
#' * Katz Index of Independence in Activities of Daily Living score
#' * K6 Short form psychological distress score
#' * Brief Community Screening Instrument for Dementia (CSID)
#' * Health and health-seeking indicators
#' * Income and income sources
#' * Water, sanitation and hygiene (WASH) indicators
#' * Anthropometry and screening
#' * Visual impairment by "Tumbling E" method
#' * Miscellaneous indicators
#' * Washington Group on Disability
#'
#' @section Demographic indicators:
#'
#' **Variable** | **Description**
#' :--- | :---
#' `psu`` | Primary sampling unit
#' `resp1`` | Respondent is SUBJECT
#' `psu` | Primary sampling unit
#' `resp1` | Respondent is SUBJECT
#' `resp2` | Respondent is FAMILY CARER
#' `resp3` | Respondent is OTHER CARER
#' `resp4` | Respondent is OTHER
Expand Down Expand Up @@ -42,9 +58,9 @@
#'
#' **Variable** | **Description**
#' :--- | :---
#' `MF`` | Meal frequency
#' `DDS`` | Dietary Diversity Score (count of 11 groups)
#' `FG01`` | Cereals
#' `MF` | Meal frequency
#' `DDS` | Dietary Diversity Score (count of 11 groups)
#' `FG01` | Cereals
#' `FG02` | Roots and tubers
#' `FG03` | Fruits and vegetables
#' `FG04` | All meat
Expand Down Expand Up @@ -105,18 +121,18 @@
#'
#' **Variable** | **Description**
#' :--- | :---
#' ADL01 | Bathing
#' ADL02 | Dressing
#' ADL03 | Toileting
#' ADL04 | Transferring (mobility)
#' ADL05 | Continence
#' ADL06 | Feeding
#' scoreADL | ADL Score
#' classADL1 | Severity of dependence 1
#' classADL2 | Severity of dependence 2
#' classADL3 | Severity of dependence 3
#' hasHelp | Have someone to help with everyday activities
#' unmetNeed | Need help but has no helper
#' `ADL01` | Bathing
#' `ADL02` | Dressing
#' `ADL03` | Toileting
#' `ADL04` | Transferring (mobility)
#' `ADL05` | Continence
#' `ADL06` | Feeding
#' `scoreADL` | ADL Score
#' `classADL1` | Severity of dependence 1
#' `classADL2` | Severity of dependence 2
#' `classADL3` | Severity of dependence 3
#' `hasHelp` | Have someone to help with everyday activities
#' `unmetNeed` | Need help but has no helper
#'
#' @section K6 Short form psychological distress score:
#'
Expand All @@ -129,8 +145,8 @@
#'
#' **Variable** | **Description**
#' :--- | :---
#' K6 | K6 score
#' K6Case | K6 score > 12 (in serious psychological distress)
#' `K6` | K6 score
#' `K6Case` | K6 score > 12 (in serious psychological distress)
#'
#' @section Brief Community Screening Instrument for Dementia (CSID):
#'
Expand All @@ -144,49 +160,49 @@
#'
#' **Variable** | **Description**
#' :--- | :---
#' DS | Probable dementia by CSID screen
#' `DS` | Probable dementia by CSID screen
#'
#' @section Health and health-seeking indicators:
#'
#' **Variable** | **Description**
#' :--- | :---
#' H1 | Chronic condition
#' H2 | Takes drugs regularly for chronic condition
#' H31 | No drugs available
#' H32 | Too expensive / no money
#' H33 | Too old to look for care
#' H34 | Use traditional medicine
#' H35 | Drugs don't help
#' H36 | No-one to help me
#' H37 | No need
#' H38 | Other
#' H39 | No reason given
#' H4 | Recent disease episode
#' H5 | Accessed care for recent disease episode
#' H61 | No drugs available
#' H62 | Too expensive / no money
#' H63 | Too old to look for care
#' H64 | Use traditional medicine
#' H65 | Drugs don't help
#' H66 | No-one to help me
#' H67 | No need
#' H68 | Other
#' H69 | No reason given
#' `H1` | Chronic condition
#' `H2` | Takes drugs regularly for chronic condition
#' `H31` | No drugs available
#' `H32` | Too expensive / no money
#' `H33` | Too old to look for care
#' `H34` | Use traditional medicine
#' `H35` | Drugs don't help
#' `H36` | No-one to help me
#' `H37` | No need
#' `H38` | Other
#' `H39` | No reason given
#' `H4` | Recent disease episode
#' `H5` | Accessed care for recent disease episode
#' `H61` | No drugs available
#' `H62` | Too expensive / no money
#' `H63` | Too old to look for care
#' `H64` | Use traditional medicine
#' `H65` | Drugs don't help
#' `H66` | No-one to help me
#' `H67` | No need
#' `H68` | Other
#' `H69` | No reason given
#'
#' @section Income and income sources:
#'
#' **Variable** | **Description**
#' :--- | :---
#' M1 | Has a personal income
#' M2A | Agriculture / fishing / livestock
#' M2B | Wages / salary
#' M2C | Sale of charcoal / bricks / etc.
#' M2D | Trading (e.g. market or shop)
#' M2E | Investments
#' M2F | Spending savings / sale of assets
#' M2G | Charity
#' M2H | Cash transfer / Social security
#' M2I | Other
#' `M1` | Has a personal income
#' `M2A` | Agriculture / fishing / livestock
#' `M2B` | Wages / salary
#' `M2C` | Sale of charcoal / bricks / etc.
#' `M2D` | Trading (e.g. market or shop)
#' `M2E` | Investments
#' `M2F` | Spending savings / sale of assets
#' `M2G` | Charity
#' `M2H` | Cash transfer / Social security
#' `M2I` | Other
#'
#' @section Water, sanitation and hygiene (WASH) indicators:
#'
Expand All @@ -198,18 +214,18 @@
#'
#' **Variable** | **Description**
#' :--- | :---
#' W1 | Improved source of drinking water
#' W2 | Safe drinking water (improved source OR adequate treatment)
#' W3 | Improved sanitation facility
#' W4 | Improved non-shared sanitation facility
#' `W1` | Improved source of drinking water
#' `W2` | Safe drinking water (improved source OR adequate treatment)
#' `W3` | Improved sanitation facility
#' `W4` | Improved non-shared sanitation facility
#'
#' @section Anthropometry and screening:
#'
#' **Variable** | **Description**
#' :--- | :---
#' MUAC | Mid-upper arm circumference (mm)
#' oedema | Bilateral pitting oedema (may not be nutritional)
#' screened | Either MUAC or oedema checked previously
#' `MUAC` | Mid-upper arm circumference (mm)
#' `oedema` | Bilateral pitting oedema (may not be nutritional)
#' `screened` | Either MUAC or oedema checked previously
#'
#' @section Visual impairment by "Tumbling E" method:
#'
Expand All @@ -226,9 +242,9 @@
#'
#' **Variable** | **Description**
#' :--- | :---
#' chew | Problems chewing food
#' food | Anyone in HH receives a ration
#' NFRI | Anyone in HH received non-food relief item/s (NFRI) in previous month
#' `chew` | Problems chewing food
#' `food` | Anyone in HH receives a ration
#' `NFRI` | Anyone in HH received non-food relief item/s (NFRI) in previous month
#'
#' @section Washington Group on Disability:
#'
Expand All @@ -241,35 +257,35 @@
#'
#' **Variable** | **Description**
#' :--- | :---
#' wgVisionD0 | Vision domain 0
#' wgVisionD1 | Vision domain 1
#' wgVisionD2 | Vision domain 2
#' wgVisionD3 | Vision domain 3
#' wgHearingD0 | Hearing domain 0
#' wgHearingD1 | Hearing domain 1
#' wgHearingD2 | Hearing domain 2
#' wgHearingD3 | Hearing domain 3
#' wgMobilityD0 | Mobility domain 0
#' wgMobilityD1 | Mobility domain 1
#' wgMobilityD2 | Mobility domain 2
#' wgMobilityD3 | Mobility domain 3
#' wgRememberingD0 | Remembering domain 0
#' wgRememberingD1 | Remembering domain 1
#' wgRememberingD2 | Remembering domain 2
#' wgRememberingD3 | Remembering domain 3
#' wgSelfCareD0 | Self-care domain 0
#' wgSelfCareD1 | Self-care domain 1
#' wgSelfCareD2 | Self-care domain 2
#' wgSelfCareD3 | Self-care domain 3
#' wgCommunicatingD0 | Communication domain 0
#' wgCommunicatingD1 | Communication domain 1
#' wgCommunicatingD2 | Communication domain 2
#' wgCommunicatingD3 | Communication domain 3
#' wgP0 | Overall 0
#' wgP1 | Overall 1
#' wgP2 | Overall 2
#' wgP3 | Overall 3
#' wgPM | Any disability
#' `wgVisionD0` | Vision domain 0
#' `wgVisionD1` | Vision domain 1
#' `wgVisionD2` | Vision domain 2
#' `wgVisionD3` | Vision domain 3
#' `wgHearingD0` | Hearing domain 0
#' `wgHearingD1` | Hearing domain 1
#' `wgHearingD2` | Hearing domain 2
#' `wgHearingD3` | Hearing domain 3
#' `wgMobilityD0` | Mobility domain 0
#' `wgMobilityD1` | Mobility domain 1
#' `wgMobilityD2` | Mobility domain 2
#' `wgMobilityD3` | Mobility domain 3
#' `wgRememberingD0` | Remembering domain 0
#' `wgRememberingD1` | Remembering domain 1
#' `wgRememberingD2` | Remembering domain 2
#' `wgRememberingD3` | Remembering domain 3
#' `wgSelfCareD0` | Self-care domain 0
#' `wgSelfCareD1` | Self-care domain 1
#' `wgSelfCareD2` | Self-care domain 2
#' `wgSelfCareD3` | Self-care domain 3
#' `wgCommunicatingD0` | Communication domain 0
#' `wgCommunicatingD1` | Communication domain 1
#' `wgCommunicatingD2` | Communication domain 2
#' `wgCommunicatingD3` | Communication domain 3
#' `wgP0` | Overall 0
#' `wgP1` | Overall 1
#' `wgP2` | Overall 2
#' `wgP3` | Overall 3
#' `wgPM` | Any disability
#'
#' @param svy A data.frame collected using the standard RAM-OP questionnaire
#' @param indicators A character vector of indicator set names. The vector may
Expand All @@ -287,15 +303,18 @@
#' # Create indicators dataset from RAM-OP survey data collected from
#' # Addis Ababa, Ethiopia
#' create_op(testSVY)
#' create_op(testSVY, indicators = "demo")
#' create_op(testSVY, indicators = "hunger", sex = "m")
#'
#' @export
#' @rdname create_op
#'

create_op <- function(svy,
indicators = c("demo", "food", "hunger", "disability",
"adl", "mental", "dementia", "health",
"income", "wash", "anthro", "oedema",
indicators = c("demo", "food", "hunger",
"disability", "adl", "mental",
"dementia", "health", "income",
"wash", "anthro", "oedema",
"screening", "visual", "misc"),
sex = c("mf", "m", "f")) {
## Check specified indicators ----
Expand All @@ -311,68 +330,6 @@ create_op <- function(svy,
) |>
subset_by_sex(sex = sex)


## demographic indicators ----
#demo <- create_op_demo(svy = svy)

## Dietary intake indicators ----
#food <- create_op_food(svy = svy)

## Household Hunger Scale ----
#hunger <- create_op_hunger(svy = svy)

## Katz "Index of Independence in Activities of Daily Living" (ADL) score
#adl <- create_op_adl(svy = svy)

## K6: Short form psychological distress score ----
#mental <- create_op_mental(svy = svy)

## CISD
#dementia <- create_op_dementia(svy = svy)

## Health indicators : CHRONIC CONDITIONS
#health <- create_op_health(svy = svy)

## Income and income sources ----
#income <- create_op_income(svy = svy)

## Water, Sanitation, and Hygiene (WASH) indicators ----
#wash <- create_op_wash(svy = svy)

## Anthropometry and screening ----
#anthro <- create_op_anthro(svy = svy)
#oedema <- create_op_oedema(svy = svy)
#screening <- create_op_screening(svy = svy)

## Visual impairment by "Tumbling E" method ----
#visual <- create_op_visual(svy = svy)

## Miscellaneous indicators ----
#misc <- create_op_misc(svy = svy)

## Washington Group (WG) short set of question designed to identify ----
## people with a disability in a census or survey format.
#disability <- create_op_disability(svy = svy)

## Make summary data.frame for ALL respondents ----
# indicators <- tibble::tibble(
# demo,
# subset(food, select = c(-psu, -sex1, -sex2)),
# subset(hunger, select = c(-psu, -sex1, -sex2)),
# subset(disability, select = c(-psu, -sex1, -sex2)),
# subset(adl, select = c(-psu, -sex1, -sex2)),
# subset(mental, select = c(-psu, -sex1, -sex2)),
# subset(dementia, select = c(-psu, -sex1, -sex2)),
# subset(health, select = c(-psu, -sex1, -sex2)),
# subset(income, select = c(-psu, -sex1, -sex2)),
# subset(wash, select = c(-psu, -sex1, -sex2)),
# subset(anthro, select = c(-psu, -sex1, -sex2)),
# subset(oedema, select = c(-psu, -sex1, -sex2)),
# subset(screening, select = c(-psu, -sex1, -sex2)),
# subset(visual, select = c(-psu, -sex1, -sex2)),
# subset(misc, select = c(-psu, -sex1, -sex2))
# )

indicators <- lapply(
X = indicators, FUN = create_op_indicators, svy = svy, sex = sex
) |>
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0 R/03-classicBoot.R → R/02-classicBoot.R
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