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fix(RR dataelements): wrong indicator names + ref to NER file #89

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fix(RR dataelements): wrong indicator names + ref to NER file #89

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128 changes: 70 additions & 58 deletions ...ines/snt_dhis2_reporting_rate_dataelement/code/snt_dhis2_reporting_rate_dataelement.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
"tags": []
},
"source": [
"# Calcualate Reporting Rate (method: \"Data Element\")\n",
"# Calculate Reporting Rate (method: \"Data Element\")\n",
"Based on facilities reporting data for malaria-related indicators"
]
},
Expand Down Expand Up @@ -78,33 +78,31 @@
},
{
"cell_type": "markdown",
"id": "a7a15634-4623-40f2-8e2d-3fa47203aa6e",
"id": "7dedcc32-c531-498d-90b9-89b0ee9fb9be",
"metadata": {
"papermill": {
"duration": 0.00011,
"end_time": "2026-01-16T10:23:56.165873",
"duration": 9.5e-05,
"end_time": "2026-01-16T10:23:56.200231",
"exception": false,
"start_time": "2026-01-16T10:23:56.165763",
"start_time": "2026-01-16T10:23:56.200136",
"status": "completed"
},
"tags": []
},
"source": [
"### 1.1. Fallback parameters values\n",
"This parameters are injected by papermill when running in OH via pipeline run interface. <br>\n",
"The code cell below here provides fallback paramater values needed when running this notebook locally."
"### 1.2. Load and check `snt config` file"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "b17f7685-5291-4e5d-9eec-2d1f9435fccb",
"id": "5b6d29ea-91f3-4c53-b95e-4b485f88383f",
"metadata": {
"papermill": {
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"duration": 0.521572,
"end_time": "2026-01-16T10:23:56.721932",
"exception": false,
"start_time": "2026-01-16T10:23:56.165983",
"start_time": "2026-01-16T10:23:56.200360",
"status": "completed"
},
"tags": [],
Expand All @@ -114,41 +112,51 @@
},
"outputs": [],
"source": [
"if (!exists(\"ROUTINE_FILE\")) {ROUTINE_FILE <- \"NER_routine_outliers-mean_imputed.parquet\"}\n",
"# Load SNT config\n",
"config_json <- tryCatch({ jsonlite::fromJSON(file.path(CONFIG_PATH, \"SNT_config.json\")) },\n",
" error = function(e) {\n",
" msg <- paste0(\"[ERROR] Error while loading configuration\", conditionMessage(e)) \n",
" cat(msg) \n",
" stop(msg) \n",
" })\n",
"\n",
"if (!exists(\"DATAELEMENT_METHOD_DENOMINATOR\")) {DATAELEMENT_METHOD_DENOMINATOR <- \"ROUTINE_ACTIVE_FACILITIES\"} # or \"PYRAMID_OPEN_FACILITIES\"\n",
"if (!exists(\"ACTIVITY_INDICATORS\")) {ACTIVITY_INDICATORS <- c(\"CONF\", \"PRES\", \"SUSP\")} \n",
"if (!exists(\"VOLUME_ACTIVITY_INDICATORS\")) {VOLUME_ACTIVITY_INDICATORS <- c(\"CONF\", \"PRES\")}\n",
"if (!exists(\"USE_WEIGHTED_REPORTING_RATES\")) {USE_WEIGHTED_REPORTING_RATES <- FALSE}"
"log_msg(paste0(\"SNT configuration loaded from : \", file.path(CONFIG_PATH, \"SNT_config.json\")))\n",
"\n",
"# Configuration settings\n",
"COUNTRY_CODE <- config_json$SNT_CONFIG$COUNTRY_CODE\n",
"ADMIN_1 <- toupper(config_json$SNT_CONFIG$DHIS2_ADMINISTRATION_1)\n",
"ADMIN_2 <- toupper(config_json$SNT_CONFIG$DHIS2_ADMINISTRATION_2)"
]
},
{
"cell_type": "markdown",
"id": "7dedcc32-c531-498d-90b9-89b0ee9fb9be",
"id": "a7a15634-4623-40f2-8e2d-3fa47203aa6e",
"metadata": {
"papermill": {
"duration": 0.000095,
"end_time": "2026-01-16T10:23:56.200231",
"duration": 0.00011,
"end_time": "2026-01-16T10:23:56.165873",
"exception": false,
"start_time": "2026-01-16T10:23:56.200136",
"start_time": "2026-01-16T10:23:56.165763",
"status": "completed"
},
"tags": []
},
"source": [
"### 1.2. Load and check `snt config` file"
"### 1.3. Fallback parameters values\n",
"This parameters are injected by papermill when running in OH via pipeline run interface. <br>\n",
"The code cell below here provides fallback paramater values needed when running this notebook locally."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "5b6d29ea-91f3-4c53-b95e-4b485f88383f",
"id": "b17f7685-5291-4e5d-9eec-2d1f9435fccb",
"metadata": {
"papermill": {
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"end_time": "2026-01-16T10:23:56.721932",
"duration": 0.033954,
"end_time": "2026-01-16T10:23:56.199937",
"exception": false,
"start_time": "2026-01-16T10:23:56.200360",
"start_time": "2026-01-16T10:23:56.165983",
"status": "completed"
},
"tags": [],
Expand All @@ -158,46 +166,42 @@
},
"outputs": [],
"source": [
"# Load SNT config\n",
"config_json <- tryCatch({ jsonlite::fromJSON(file.path(CONFIG_PATH, \"SNT_config.json\")) },\n",
" error = function(e) {\n",
" msg <- paste0(\"[ERROR] Error while loading configuration\", conditionMessage(e)) \n",
" cat(msg) \n",
" stop(msg) \n",
" })\n",
"\n",
"log_msg(paste0(\"SNT configuration loaded from : \", file.path(CONFIG_PATH, \"SNT_config.json\")))"
"if (!exists(\"ROUTINE_FILE\")) {ROUTINE_FILE <- glue(\"{COUNTRY_CODE}_routine_outliers_imputed.parquet\")}\n",
"if (!exists(\"DATAELEMENT_METHOD_DENOMINATOR\")) {DATAELEMENT_METHOD_DENOMINATOR <- \"ROUTINE_ACTIVE_FACILITIES\"} # or \"PYRAMID_OPEN_FACILITIES\"\n",
"if (!exists(\"ACTIVITY_INDICATORS\")) {ACTIVITY_INDICATORS <- c(\"CONF\", \"PRES\", \"SUSP\")} \n",
"if (!exists(\"VOLUME_ACTIVITY_INDICATORS\")) {VOLUME_ACTIVITY_INDICATORS <- c(\"CONF\", \"PRES\")}\n",
"if (!exists(\"USE_WEIGHTED_REPORTING_RATES\")) {USE_WEIGHTED_REPORTING_RATES <- FALSE}"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "c26c981c-dadd-48ac-ae35-613b8ba61a82",
"cell_type": "markdown",
"id": "2285e5ea-72da-415c-adf7-49ce49a3ab63",
"metadata": {
"papermill": {
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"end_time": "2026-01-16T10:23:56.755117",
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"exception": false,
"start_time": "2026-01-16T10:23:56.722114",
"start_time": "2026-01-16T10:23:56.165763",
"status": "completed"
},
"tags": [],
"vscode": {
"languageId": "r"
}
"tags": []
},
"source": [
"### 1.4. Set parameters\n",
"Set paramater values needed to run this notebook."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "c340cdb0-1b68-4255-9095-27006d0f9b0b",
"metadata": {},
"outputs": [],
"source": [
"# Configuration settings\n",
"COUNTRY_CODE <- config_json$SNT_CONFIG$COUNTRY_CODE\n",
"ADMIN_1 <- toupper(config_json$SNT_CONFIG$DHIS2_ADMINISTRATION_1)\n",
"ADMIN_2 <- toupper(config_json$SNT_CONFIG$DHIS2_ADMINISTRATION_2)\n",
"\n",
"# DHIS2_INDICATORS <- names(config_json$DHIS2_DATA_DEFINITIONS$DHIS2_INDICATOR_DEFINITIONS) \n",
"# Only consider the core 4 indicators \n",
"# (Referring to SNT_config.json might be problematic if the indicators are set but empty. i.e., with no valid de id!)\n",
"DHIS2_INDICATORS <- c(\"CONF\", \"PRES\", \"SUSP\", \"TESTS\") \n",
"\n",
"DHIS2_INDICATORS <- c(\"CONF\", \"PRES\", \"SUSP\", \"TEST\")\n",
"ACTIVITY_INDICATORS <- unlist(ACTIVITY_INDICATORS)\n",
"VOLUME_ACTIVITY_INDICATORS <- unlist(VOLUME_ACTIVITY_INDICATORS)\n",
"fixed_cols <- c('PERIOD', 'YEAR', 'MONTH', 'ADM1_ID', 'ADM2_ID', 'OU_ID')\n",
Expand All @@ -209,7 +213,7 @@
"id": "e44ae2ab-4af7-475a-8cbe-6d669895a18b",
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Expand All @@ -226,7 +230,7 @@
"id": "39e2add7-bbc7-4312-9a6f-9886d675f532",
"metadata": {
"papermill": {
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Expand Down Expand Up @@ -388,7 +392,7 @@
"id": "bcbd3a9f-5e45-4ae5-8671-e23155236295",
"metadata": {
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Expand Down Expand Up @@ -657,7 +661,7 @@
"id": "160c08ec-cc9a-4e1a-99ec-f703db83a71d",
"metadata": {
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Expand Down Expand Up @@ -869,7 +873,7 @@
"id": "c75f2249",
"metadata": {
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Expand Down Expand Up @@ -1079,7 +1083,7 @@
"id": "2866816a-7015-4c5c-b904-f553f3b4790d",
"metadata": {
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Expand Down Expand Up @@ -1122,6 +1126,14 @@
"write.csv(reporting_rate_dataelement, file_path, row.names = FALSE)\n",
"log_msg(glue(\"Exported : {file_path}\"))"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "8ebed94f-2a13-4f90-b7da-5a4b14352bd9",
"metadata": {},
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"source": []
}
],
"metadata": {
Expand Down