Skip to content

Snt25 659 outliers (IQR) #119

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
EstebanMontandon merged 6 commits into from
Sep 16, 2026
Merged

Snt25 659 outliers (IQR) #119

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
9f2215b
chores(outliers iqr): irq fixes
EstebanMontandon Sep 10, 2026
1dee0a5
fix(iqr): warnings imputation fixes + reporting script
EstebanMontandon Sep 11, 2026
620a4b1
fix(iqr): fixes snt_utils and iqr report
EstebanMontandon Sep 11, 2026
6582926
Merge branch 'main' into SNT25-659-outliers
EstebanMontandon Sep 11, 2026
1aa32ad
fix(snt_utils): OUTPUT_PLOTS_PATH fix
EstebanMontandon Sep 15, 2026
4a700a3
Merge branch 'main' into SNT25-659-outliers
EstebanMontandon Sep 16, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 6 additions & 5 deletions code/snt_utils.r
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
# Description: This script contains utility functions used for SNT computation workflow.
# Author: Esteban Montandon
# Created: [2024-10-01]
# Last updated: [2026-09-09]
# Last updated: [2026-09-11]
# Dependencies: stringi, httr, arrow, tools, jsonlite, data.table, dplyr, tidyr, sf, terra, glue,
# tsibble, fable, DHS.rates, readr, rlang, utils, reticulate
# Notes:
Expand All @@ -23,7 +23,7 @@
#' @export
format_names <- function(x) {
# add any other matching logic here
x <- stri_trans_general(str = x, id = "Latin-ASCII") # remove weird characters
x <- stringi::stri_trans_general(str = x, id = "Latin-ASCII") # remove weird characters
x <- gsub("[^a-zA-Z0-9]", " ", toupper(x)) # replace non-alphanum with space
# x <- gsub("(?i)PROVINCE|ZONE DE SANTE|AIRE DE SANTE|CENTRE DE SANTE", "", x) # TEMPORARY SKIP
x <- gsub(" +", " ", x) # collapse multiple spaces
Expand Down Expand Up @@ -130,8 +130,9 @@ init_snt_workspace <- function(
paths_to_check = list(
CONFIG_PATH = file.path(snt_root_path, "configuration"),
UPLOADS_PATH = file.path(snt_root_path, "uploads"),
DATA_PATH = file.path(snt_root_path, "data"),
INTERMEDIATE_RESULTS = file.path(snt_root_path, "pipelines", snt_pipeline_name, "intermediate_results")
DATA_PATH = file.path(snt_root_path, "data"),
INTERMEDIATE_RESULTS_PATH = file.path(snt_root_path, "pipelines", snt_pipeline_name, "intermediate_results"),
OUTPUT_PLOTS_PATH = file.path(snt_root_path, "pipelines", snt_pipeline_name, "reporting", "outputs", "figures") # reporting
)
lapply(paths_to_check, dir.create, recursive = TRUE, showWarnings = FALSE) # create if they do not exist
return(paths_to_check)
Expand All @@ -150,7 +151,7 @@ init_snt_workspace <- function(
#' @export
load_snt_config <- function(snt_config_path) {
# config file path
config_json <- tryCatch({ fromJSON(snt_config_path) },
config_json <- tryCatch({ jsonlite::fromJSON(snt_config_path) },
error = function(e) {
stop(glue::glue("[ERROR] Error while loading configuration: {snt_config_path}"))
})
Expand Down
Loading