The goal of {tidyndr} is to provide a specialized, simple and easy to use functions that wrap around existing functions in R for manipulation of the NDR patient line-list file allowing the user to focus on the tasks to be completed rather than the code/formula details.
The functions presented are similar to the PEPFAR MER indicators and are currently grouped into four categories:
The read_ndr function for reading the patient-level line-list downloaded from the front-end of the NDR in ‘csv’ format.
The PEPFAR treatment group of indicators that can be performed on the NDR line-list.
The ‘Viral Load’ indicators (tx_vl_eligible(), tx_pvls_den() tx_pvls_num() and tx_vl_unsuppressed()).
The summary functions (summarise_ndr() and disaggregrate()) provides a tabular summary for the tasks that have been completed using any of the functions above.
You can install the released version of tidyndr from CRAN with:
Or the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("stephenbalogun/tidyndr",
build_vignette = TRUE)library(tidyndr)
#> Attaching package: 'tidyndr'
#> A package for analysis of the front-end patient-level data from the Nigeria National Data Repository.read_ndr() reads the downloaded “.csv” file into R using vroom::vroom() behind the scene and passing appropriate column types to the col_types argument. It also formats the variable names using the snakecase style.
## read from a local file path (not run)
# file_path <- system.file("extdata", "ndr_example.csv", package = "tidyndr")
# read_ndr(file_path, time_stamp = "2021-02-15")
### read line-list available on the internet
path <- "https://raw.githubusercontent.com/stephenbalogun/example_files/main/ndr_example.csv"
ndr_example <- read_ndr(path, time_stamp = "2021-02-20")
#>
#> Three new variables created:
#> [1] `date_lost`
#> [2] `appointment_date
#> [2] `current_statusThe functions included in this group are:
tx_new()
tx_curr()
tx_ml() and tx_ml_outcomes()
tx_rtt()
Other supporting functions are: tx_mmd(), tx_regimen() and tx_appointment()
## Subset "TX_NEW"
tx_new(ndr_example, from = "2021-07-01", to = "2021-09-30")
#> Warning: One or more parsing issues, see `problems()` for details
#> # A tibble: 0 x 52
#> # ... with 52 variables: ip <fct>, state <fct>, lga <fct>, facility <fct>,
#> # datim_code <fct>, sex <fct>, patient_identifier <chr>,
#> # hospital_number <chr>, date_of_birth <date>, age_at_art_initiation <dbl>,
#> # current_age <dbl>, art_start_date <date>, art_start_date_source <fct>,
#> # last_drug_pickup_date <date>, last_drug_pickup_date_q1 <date>,
#> # last_drug_pickup_date_q2 <date>, last_drug_pickup_date_q3 <date>,
#> # last_drug_pickup_date_q4 <date>, last_regimen <fct>, ...
## Generate line-list of clients with medication refill in October 2021
ndr_example %>%
tx_appointment(from = "2021-10-01",
to = "2021-10-31"
)
#> # A tibble: 0 x 52
#> # ... with 52 variables: ip <fct>, state <fct>, lga <fct>, facility <fct>,
#> # datim_code <fct>, sex <fct>, patient_identifier <chr>,
#> # hospital_number <chr>, date_of_birth <date>, age_at_art_initiation <dbl>,
#> # current_age <dbl>, art_start_date <date>, art_start_date_source <fct>,
#> # last_drug_pickup_date <date>, last_drug_pickup_date_q1 <date>,
#> # last_drug_pickup_date_q2 <date>, last_drug_pickup_date_q3 <date>,
#> # last_drug_pickup_date_q4 <date>, last_regimen <fct>, ...
## Generate list of clients who were active at the beginning of October 2021 but became inactive at the end of December 2021.
tx_ml(new_data = ndr_example,
from = "2021-10-01",
to = "2021-12-31")
#> # A tibble: 0 x 52
#> # ... with 52 variables: ip <fct>, state <fct>, lga <fct>, facility <fct>,
#> # datim_code <fct>, sex <fct>, patient_identifier <chr>,
#> # hospital_number <chr>, date_of_birth <date>, age_at_art_initiation <dbl>,
#> # current_age <dbl>, art_start_date <date>, art_start_date_source <fct>,
#> # last_drug_pickup_date <date>, last_drug_pickup_date_q1 <date>,
#> # last_drug_pickup_date_q2 <date>, last_drug_pickup_date_q3 <date>,
#> # last_drug_pickup_date_q4 <date>, last_regimen <fct>, ...The tx_vl_eligible(), tx_pvls_den() and the tx_pvls_num() functions come in handy when you need to generate the line-list of clients who are eligible for viral load test at a given point for a given facility/state, those who have a valid viral load result (not more than 1 year for people aged 20 years and above and not more than 6 months for paediatrics and adolescents less or equal to 19 years), and those who are virally suppressed (out of those with valid viral load results). When the sample = TRUE attribute is supplied to the tx_vl_eligible() function, it generates the line-list of only those who are due for a viral load test out of all those who are eligible.
## Generate list of clients who are eligible for VL (i.e. expected to have a documented VL result)
ndr_example %>%
tx_vl_eligible(ref = "2021-12-31")
#> # A tibble: 27,020 x 52
#> ip state lga facility datim_code sex patient_identif~ hospital_number
#> <fct> <fct> <fct> <fct> <fct> <fct> <chr> <chr>
#> 1 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ M State 3001 0001
#> 2 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ F State 1002 0001
#> 3 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ F State 3003 0001
#> 4 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ M State 1003 0002
#> 5 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ F State 2004 0002
#> 6 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ F State 3005 0001
#> 7 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ F State 2005 0001
#> 8 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ M State 1004 0003
#> 9 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ F State 3007 0002
#> 10 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ F State 1005 0004
#> # ... with 27,010 more rows, and 44 more variables: date_of_birth <date>,
#> # age_at_art_initiation <dbl>, current_age <dbl>, art_start_date <date>,
#> # art_start_date_source <fct>, last_drug_pickup_date <date>,
#> # last_drug_pickup_date_q1 <date>, last_drug_pickup_date_q2 <date>,
#> # last_drug_pickup_date_q3 <date>, last_drug_pickup_date_q4 <date>,
#> # last_regimen <fct>, last_clinic_visit_date <date>,
#> # days_of_arv_refill <dbl>, pregnancy_status <fct>, ...
## Generate list of clients that will be expected to have a viral load test done by March 2022
ndr_example %>%
tx_vl_eligible("2022-03-31",
sample = TRUE)
#> # A tibble: 27,020 x 52
#> ip state lga facility datim_code sex patient_identif~ hospital_number
#> <fct> <fct> <fct> <fct> <fct> <fct> <chr> <chr>
#> 1 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ M State 3001 0001
#> 2 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ F State 1002 0001
#> 3 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ F State 3003 0001
#> 4 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ M State 1003 0002
#> 5 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ F State 2004 0002
#> 6 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ F State 3005 0001
#> 7 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ F State 2005 0001
#> 8 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ M State 1004 0003
#> 9 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ F State 3007 0002
#> 10 IP_na~ Stat~ LGA0~ Facilit~ datim_cod~ F State 1005 0004
#> # ... with 27,010 more rows, and 44 more variables: date_of_birth <date>,
#> # age_at_art_initiation <dbl>, current_age <dbl>, art_start_date <date>,
#> # art_start_date_source <fct>, last_drug_pickup_date <date>,
#> # last_drug_pickup_date_q1 <date>, last_drug_pickup_date_q2 <date>,
#> # last_drug_pickup_date_q3 <date>, last_drug_pickup_date_q4 <date>,
#> # last_regimen <fct>, last_clinic_visit_date <date>,
#> # days_of_arv_refill <dbl>, pregnancy_status <fct>, ...
### Calculate the Viral Load Coverage as of December 2021
no_of_vl_results <- tx_pvls_den(ndr_example,
ref = "2021-12-31") %>%
nrow()
no_of_vl_eligible <- tx_vl_eligible(ndr_example,
ref = "2021-12-31") %>%
nrow()
vl_coverage <- scales::percent(no_of_vl_results / no_of_vl_eligible)
print(vl_coverage)
#> [1] "2%"For all the ‘Treatment’ and ‘Viral Suppression’ indicators (except tx_ml_outcomes(), which should be use with tx_ml()), you have control over the level of action (state or facility) by supplying to the states and/or facilities arguments the values of interest . For more than one state or facility, combine the values with the c() e.g.
## subset clients that have medication appointment in between January and March of 2021 in
## and are also due for viral load
ndr_example %>%
tx_appointment(from = "2022-01-01",
to = "2022-03-31",
) %>%
tx_vl_eligible(sample = TRUE)
#> # A tibble: 0 x 52
#> # ... with 52 variables: ip <fct>, state <fct>, lga <fct>, facility <fct>,
#> # datim_code <fct>, sex <fct>, patient_identifier <chr>,
#> # hospital_number <chr>, date_of_birth <date>, age_at_art_initiation <dbl>,
#> # current_age <dbl>, art_start_date <date>, art_start_date_source <fct>,
#> # last_drug_pickup_date <date>, last_drug_pickup_date_q1 <date>,
#> # last_drug_pickup_date_q2 <date>, last_drug_pickup_date_q3 <date>,
#> # last_drug_pickup_date_q4 <date>, last_regimen <fct>, ...You might want to generate a summary table of all the indicators you have pulled out. The summarise_ndr() (or summarize_ndr()) allows you to do this with ease. It accepts all the line-lists you are interested in creating a summary table for, the level at which you want the summary to be created (country/ip, state or facility), and the names you want to give to each of your summary column.
## generates line-list of TX_NEW between July and December 2021
new <- tx_new(ndr_example, from = "2021-07-01", to = "202112-31")
## generates line-list of currently active clients
curr <- tx_curr(ndr_example)
## generates line-list of clients who were active at the beginning of the October but inactive at end of December 2021
ml <- tx_ml(new_data = ndr_example, from = "2021-10-01", to = "2021-12-31")
summarise_ndr(new, curr, ml,
level = "state",
names = c("tx_new", "tx_curr", "tx_ml"))
#> # A tibble: 4 x 5
#> ip state tx_new tx_curr tx_ml
#> <chr> <chr> <int> <int> <int>
#> 1 Total - 0 27020 0
#> 2 IP_name State 1 0 5645 0
#> 3 IP_name State 2 0 7929 0
#> 4 IP_name State 3 0 13446 0The disaggregate() allows you to summarise an indicator of interest into finer details based on “current_age”, “sex” “pregnancy_status”, “art_duration”, “months_dispensed (of ARV)” or “age_sex”. These are supplied to the by parameter of the function. The default disaggregates the variable of interest at the level of “states” but can also do this at “country/ip”, “lga” or “facility” level when any of this is supplied to the level parameter.
## generates line-list of TX_NEW between July and September 2021
new_clients <- tx_new(ndr_example, from = "2021-07-01", to = "2021-09-30")
disaggregate(new_clients,
by = "current_age", pivot_wide = FALSE)
#> # A tibble: 65 x 4
#> ip state current_age number
#> <chr> <chr> <chr> <int>
#> 1 IP_name State 1 <1 0
#> 2 IP_name State 1 1-4 0
#> 3 IP_name State 1 5-9 0
#> 4 IP_name State 1 10-14 0
#> 5 IP_name State 1 15-19 0
#> 6 IP_name State 1 20-24 0
#> 7 IP_name State 1 25-29 0
#> 8 IP_name State 1 30-34 0
#> 9 IP_name State 1 35-39 0
#> 10 IP_name State 1 40-44 0
#> # ... with 55 more rows
## disaggregate 'TX_CURR' by sex
ndr_example %>%
tx_curr() %>%
disaggregate(by = "sex")
#> # A tibble: 5 x 5
#> ip state Male Female unknown
#> <chr> <chr> <int> <int> <int>
#> 1 IP_name "State 1" 1661 3984 0
#> 2 IP_name "State 2" 2335 5594 0
#> 3 IP_name "State 3" 5894 7552 0
#> 4 IP_name "" 0 0 0
#> 5 Total "-" 9890 17130 0Please note that the tidyndr project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.