Kokoda95/maproutine

An R package for standardizing, harmonizing, validating, and preparing routine malaria surveillance data from DHIS2 systems for geospatial risk modelling and epidemiological analysis across sub-Saharan Africa. # maproutine `maproutine` provides tools for standardizing, harmonizing, validating, and preparing routine malaria surveillance data from DHIS2 systems for geospatial risk modelling and epidemiological analysis across sub-Saharan Africa. ## Installation You can install the development version of maproutine from GitHub with: ``` r # Using devtools # install.packages("devtools") devtools::install_github("Kokoda95/maproutine") ``` ## The problem Routine malaria data from DHIS2 varies widely in column naming across countries and even across districts within the same country. `maproutine` solves this by mapping raw DHIS2 column names — in English or French — to a consistent naming convention: [_method][_severity][_level]_ [_sex] For example: | Raw DHIS2 column | Standardized name | |----|----| | `Confirmed malaria cases Age under five yrs` | `conf_u5` | | `Malaria mRDT +ve Age five yrs and above` | `pos_rdt_ov5` | | `Cas testé TDR positif - Paludisme simple Moins de 5 ans, Feminin` | `conf_rdt_simp_u5_f` | | `conf_palu_grve_mic_fosa_m5` | `conf_mic_sev_hf_u5` | ## Example ``` r library(maproutine) # Standardize a Tanzania data frame using the built-in dictionary df_std Warning in standardize_indicators(example.dhis2$TZA): 1 column(s) could not be mapped and were kept as-is: #> HF_Name #> #> Tip: add them to `custom_map` or a country profile. #> #> ── Indicator mapping report ─────────────────────────────────── #> #> ✓ Dictionary (6): #> Number of OPD attendance Age under five yrs -> opd_u5 #> Number of OPD attendance Age five yrs and above -> opd_ov5 #> Malaria suspected under 5 -> susp_u5 #> Malaria suspected above 5 -> susp_ov5 #> Confirmed malaria cases Age under five yrs -> conf_u5 #> Confirmed malaria cases Age five yrs and above -> conf_ov5 #> #> Admin / metadata (kept) (2): #> Region #> Council #> #> ✗ Unmatched (not renamed) (1): #> …