data_clean: Clean ANC-RT Data

In brittanyblouin/ANCRTAdjust: Adjusting HIV prevalence from ANC-RT data for common biases

Description

Cleans ANC-RT data so that it can be used with other functions in the ANCRTAdjust package.

Usage

data_clean(data, total_age_cat = NULL)

Arguments

data

A country-specific ANC-RT database. The function check_data should have been run on the data to properly prepare the data for use here. The following variables (with these variable names) must be included in data: time: The time period that the data was collected. faciluid: The unique facility identifier. n_clients: The number of women from the specified facility, during the specified time period, that attended their first ANC visit. n_status: The number of women from the specified facility, during the specified time period, that had their HIV status ascertained at their first ANC visit, either by testing or through previous knowledge. testpos: The number of women from the specified facility, during the specified time period, that tested positive for HIV at their first ANC visit. knownpos: The number of women from the specified facility, during the specified time period, that already knew that they were HIV-positive at their first ANC visit. testneg: The number of women from the specified facility, during the specified time period, that tested negative for HIV at their first ANC visit. totpos: The number of women from the specific facility, during the specified time period, that were HIV-positive at their first ANC visit. age: Age category of pregnant women (optional).

total_age_cat

The value of the age variable indicating all age categories combined (only necessary if age disaggregated data is included).

Details

This function has been developed to clean common issues associated with ANC-RT data. The following tasks are accomplished:

• Age disaggregated data is removed (if applicable).

• testneg_c is set to n_status - knownpos - testpos or n_status - totpos if testneg is missing. testneg_c is set to 0 if negative.

• knownpos_c is set to n_status - testneg_c - testpos or totpos - testpos if knownpos is missing. knownpos_c is set to 0 if negative.

• testpos_c is set to n_status - testneg_c - knownpos_c or totpos - knownpos if testpos is missing. testpos_c is set to 0 if negative.

• n_status_c is set to testpos_c + testneg_c + knownpos_c when all of these variables are available. If either of the three variables is missing, n_status_c = n_status.

• totpos_c is set to knownpos_c + testpos_c if both of these variables are available. If either testpos_c or knownpos_c are missing but totpos is available, totpos_c is set to totpos. If totpos_c is missing but n_status_c and testneg_c are available, totpos_c = n_status_c - testneg_c.

• The three suggested n_status_c adjustments are created in the case that n_status_c > n_clients:

  • n_status_c_impute uses the impute adjustment option

  • n_status_c_remove uses the remove adjustment option

  • n_status_c_setmax uses the set to maximum adjustment option

• totpos_c is adjusted if totpos_c > n_status_c:

  • totpos_c: totpos_c is set to missing when totpos_c > n_status_c

  • totpos_c_impute: totpos_c is set to missing when totpos_c > n_status_c_impute

  • totpos_c_remove: totpos_c is set to missing when totpos_c > n_status_c_remove

  • totpos_c_setmax: totpos_c is set to missing when totpos_c > n_status_c_setmax

• The data is checked for duplicates (i.e. more than one observation exists with the same faciluid and time).

Value

A cleaned ANC-RT database with additional variables:

• testneg_c: Cleaned testneg (according to description)

• testpos_c: Cleaned testpos (according to description)

• knownpos_c: Cleaned knownpos (according to description)

• n_status_c: Cleaned n_status (according to description)

• n_status_c_impute: Adjusted n_status_c using the impute adjustment option for multiple testing

• n_status_c_remove: Adjusted n_status_c using the remove adjustment option for multiple testing

• n_status_c_setmax: Adjusted n_status_c using the set to maximum adjustment option for multiple testing

• totpos_c: Cleaned totpos (according to description)

• totpos_c_impute: Adjusted totpos_c if the impute adjustment option for multiple testing is used

• totpos_c_remove: Adjusted totpos_c if the remove adjustment option for multiple testing is used

• totpos_c_setmax: Adjusted totpos_c if the set to maximum adjustment option for multiple testing is used

Author(s)

Mathieu Maheu-Giroux

Brittany Blouin

brittanyblouin/ANCRTAdjust documentation built on Oct. 28, 2019, 4:53 a.m.