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differences for PR #231 
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‎fig/mpox_data_cleaning_pipeline-rendered-unnamed-chunk-2-1.png‎

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‎install.R‎

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pak::pak("knitr")
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pak::pak("xml2")
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pak::pak("lintr")
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library(knitr)
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opts_chunk$set(comment = "")
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library(xml2)
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x <- read_xml("<foo> <bar> text <baz/> </bar> </foo>")
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x
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xml_name(x)
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library(lintr)
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available_tags(packages = "lintr")

‎md5sum.txt‎

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"file" "checksum" "built" "date"
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"CODE_OF_CONDUCT.md" "549f00b0992a7743c2bc16ea6ce3db57" "site/built/CODE_OF_CONDUCT.md" "2026-05-12"
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"LICENSE.md" "14377518ee654005a18cf28549eb30e3" "site/built/LICENSE.md" "2026-05-12"
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"config.yaml" "0f7deb99a9178d8470bd18343974bd37" "site/built/config.yaml" "2026-05-12"
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"index.md" "32bc80d6f4816435cc0e01540cb2a513" "site/built/index.md" "2026-05-12"
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"links.md" "fe82d0a436c46f4b07b82684ed2cceaf" "site/built/links.md" "2026-05-12"
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"pull_request_template.md" "6ae1abf4b06b0425eebca43b6db281ae" "site/built/pull_request_template.md" "2026-05-12"
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"renv.lock" "a89eb6fbc7b7b00ccc16820c2ba6395c" "site/built/renv.lock" "2026-05-12"
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"episodes/read-cases.Rmd" "7333844e42fcf127fbdf0b63785a744c" "site/built/read-cases.md" "2026-05-12"
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"episodes/clean-data.Rmd" "5d7d9f89d85d4cf8bcfb9b0d78b182fd" "site/built/clean-data.md" "2026-05-12"
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"episodes/validate.Rmd" "2d01a5ad5453b11791fbc5f33b97dca3" "site/built/validate.md" "2026-05-12"
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"episodes/describe-cases.Rmd" "bde8c21decb3810f1351894b0997c5fe" "site/built/describe-cases.md" "2026-05-12"
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"instructors/instructor-notes.md" "ca3834a1b0f9e70c4702aa7a367a6bb5" "site/built/instructor-notes.md" "2026-05-12"
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"learners/epikinetics-descriptive.md" "50400941620956b3366fd99d51ed465b" "site/built/epikinetics-descriptive.md" "2026-05-12"
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"learners/epikinetics-statistics.md" "26868caf5a6b4a948ecb8f95c40694ab" "site/built/epikinetics-statistics.md" "2026-05-12"
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"learners/mpox_data_cleaning_pipeline.Rmd" "10ea9694190cfd20fb286cdc71b0c707" "site/built/mpox_data_cleaning_pipeline.md" "2026-05-12"
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"learners/mpox_data_cleaning_pipeline.md" "5ca83e5cc976420771e2b4ee0f713cb1" "site/built/mpox_data_cleaning_pipeline.md" "2026-05-12"
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"learners/reference.md" "f081702f1c557d1ce455b7d38306737b" "site/built/reference.md" "2026-05-12"
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"learners/setup.md" "65457a0cdd39d17bd46c96e356c74261" "site/built/setup.md" "2026-05-12"
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"profiles/learner-profiles.md" "31b503c4b5bd1f0960ada730eca4a25e" "site/built/learner-profiles.md" "2026-05-12"
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"renv/profiles/lesson-requirements/renv.lock" "a89eb6fbc7b7b00ccc16820c2ba6395c" "site/built/renv.lock" "2026-05-12"
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"CODE_OF_CONDUCT.md" "549f00b0992a7743c2bc16ea6ce3db57" "site/built/CODE_OF_CONDUCT.md" "2026-06-10"
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"LICENSE.md" "14377518ee654005a18cf28549eb30e3" "site/built/LICENSE.md" "2026-06-10"
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"config.yaml" "0f7deb99a9178d8470bd18343974bd37" "site/built/config.yaml" "2026-06-10"
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"index.md" "32bc80d6f4816435cc0e01540cb2a513" "site/built/index.md" "2026-06-10"
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"links.md" "fe82d0a436c46f4b07b82684ed2cceaf" "site/built/links.md" "2026-06-10"
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"pull_request_template.md" "6ae1abf4b06b0425eebca43b6db281ae" "site/built/pull_request_template.md" "2026-06-10"
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"episodes/read-cases.Rmd" "7333844e42fcf127fbdf0b63785a744c" "site/built/read-cases.md" "2026-06-10"
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"episodes/clean-data.Rmd" "5d7d9f89d85d4cf8bcfb9b0d78b182fd" "site/built/clean-data.md" "2026-06-10"
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"episodes/validate.Rmd" "2d01a5ad5453b11791fbc5f33b97dca3" "site/built/validate.md" "2026-06-10"
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"episodes/describe-cases.Rmd" "bde8c21decb3810f1351894b0997c5fe" "site/built/describe-cases.md" "2026-06-10"
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"instructors/instructor-notes.md" "ca3834a1b0f9e70c4702aa7a367a6bb5" "site/built/instructor-notes.md" "2026-06-10"
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"learners/epikinetics-descriptive.md" "50400941620956b3366fd99d51ed465b" "site/built/epikinetics-descriptive.md" "2026-06-10"
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"learners/epikinetics-statistics.md" "26868caf5a6b4a948ecb8f95c40694ab" "site/built/epikinetics-statistics.md" "2026-06-10"
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"learners/mpox_data_cleaning_pipeline.Rmd" "abfb0e1abf80706943dd13bd47adf94a" "site/built/mpox_data_cleaning_pipeline.md" "2026-06-10"
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"learners/mpox_data_cleaning_pipeline.md" "5ca83e5cc976420771e2b4ee0f713cb1" "site/built/mpox_data_cleaning_pipeline.md" "2026-06-10"
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"learners/reference.md" "f081702f1c557d1ce455b7d38306737b" "site/built/reference.md" "2026-06-10"
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"learners/setup.md" "65457a0cdd39d17bd46c96e356c74261" "site/built/setup.md" "2026-06-10"
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"profiles/learner-profiles.md" "31b503c4b5bd1f0960ada730eca4a25e" "site/built/learner-profiles.md" "2026-06-10"
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"renv/profiles/lesson-requirements/renv.lock" "e83c63a9f76c5b9d15cbb3ae0f70e833" "site/built/renv.lock" "2026-06-10"

‎read-cases.md‎

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``` error
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Error in `httr2::req_perform()` at readepi/R/read_dhis2-helpers.R:57:3:
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! HTTP 500 Internal Server Error.
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! Failed to perform HTTP request.
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Caused by error in `curl::curl_fetch_memory()` at httr2/R/req-perform.R:220:5:
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! Timeout was reached [smc.moh.gm]:
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Connection timeout after 10000 ms
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```
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``` r
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# A tibble: 3 × 16
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case_id person_id date_onset case_origin case_status outcome sex
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<chr> <chr> <date> <chr> <chr> <chr> <chr>
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1 VPMCMM-YUZENC-P3JN… U2BJQK-M… 2025-11-01 IN_COUNTRY CONFIRMED DECEAS… <NA>
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2 T4Y6UI-DXJMR3-MBVF… X7U4QL-Z… NA IN_COUNTRY NOT_CLASSI… NO_OUT… <NA>
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3 U2QLP2-4DXBFG-6QRA… WINV7F-C… 2026-03-27 POINT_OF_E… NOT_CLASSI… NO_OUT… <NA>
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1 U2QLP2-4DXBFG-6QRA… WINV7F-C… 2026-03-27 POINT_OF_E… NOT_CLASSI… NO_OUT… <NA>
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2 UZWZTD-BFNG4C-VXMD… QYLUZS-S… NA IN_COUNTRY NOT_CLASSI… NO_OUT… <NA>
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3 ULMPMT-PBQOQ2-ETGY… WVP6NB-J… 2026-05-31 IN_COUNTRY NOT_CLASSI… NO_OUT… <NA>
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# ℹ 9 more variables: date_of_birth <chr>, country <chr>, city <chr>,
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# latitude <chr>, longitude <chr>, contact_id <chr>,
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# date_last_contact <date>, date_first_contact <date>, Ct_values <chr>

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