From d1e9bc6da77b3dd78832189b9086097ba6f396ce Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Fri, 15 Nov 2024 12:22:23 +0000 Subject: [PATCH 1/5] Update with 2025 options --- inst/default_options.csv | 77 ++++++++++++++++++++-------------------- 1 file changed, 38 insertions(+), 39 deletions(-) diff --git a/inst/default_options.csv b/inst/default_options.csv index 8444a45..b8e5ac1 100644 --- a/inst/default_options.csv +++ b/inst/default_options.csv @@ -1,40 +1,39 @@ 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file From 3fb558d79402deedb86083a04cb4a2814fff7ad2 Mon Sep 17 00:00:00 2001 From: rtesra <70330391+rtesra@users.noreply.github.com> Date: Fri, 15 Nov 2024 12:52:15 +0000 Subject: [PATCH 2/5] Update default_options.csv Update model options for countries with no 2023 results --- inst/default_options.csv | 79 +++++++++++++++++++++------------------- 1 file changed, 41 insertions(+), 38 deletions(-) diff --git a/inst/default_options.csv b/inst/default_options.csv index b8e5ac1..4ed5afa 100644 --- a/inst/default_options.csv +++ b/inst/default_options.csv @@ -1,39 +1,42 @@ 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file From 18ca4ebdd32b670403173a400756a97f5c27f778 Mon Sep 17 00:00:00 2001 From: Rob Ashton Date: Fri, 15 Nov 2024 12:58:35 +0000 Subject: [PATCH 3/5] Remove duplicate MOZ entry, update tests --- inst/default_options.csv | 83 +++++++++++++++++------------------ tests/testthat/test-options.R | 2 +- 2 files changed, 42 insertions(+), 43 deletions(-) diff --git a/inst/default_options.csv b/inst/default_options.csv index 4ed5afa..558394b 100644 --- a/inst/default_options.csv +++ b/inst/default_options.csv @@ -1,42 +1,41 @@ 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+XXX,XXX,2,CY2024Q4,CY2025Q3,CY2017Q4,CMR2018DHS; CMR2017PHIA,CIV2017PHIA,,invalid,,TRUE,TRUE,TRUE,2024,12,2017,2024,2017,2024,national,TRUE,250,1000,1000,TRUE,-4,TRUE,1,TRUE,1,TRUE,1,national,sex_age_group,national,sex_age_group,national,sex_age_group,national,sex_age_group,logistic,1,TRUE,TRUE,TRUE,FALSE,invalid,TRUE,CY2026Q3,CY2027Q3, +ZAF,ZAF,2,CY2024Q4,CY2025Q3,CY2017Q2,ZAF2017HSRC; ZAF2016DHS,ZAF2017HSRC,ZAF2017HSRC,FALSE,,TRUE,TRUE,TRUE,2024,12,2017,2024,2017,2024,subnational,TRUE,250,1000,17,TRUE,-4,TRUE,1,TRUE,1,FALSE,1,subnational,sex_age_group,subnational,sex_age_group,subnational,sex_age_group,subnational,sex_age_group,logistic,1,TRUE,TRUE,TRUE,TRUE,TRUE,TRUE,CY2026Q3,CY2027Q3,2 +ZMB,ZMB,2,CY2024Q4,CY2025Q3,CY2021Q3,ZMB2021PHIA,ZMB2021PHIA,,FALSE,,TRUE,TRUE,TRUE,2024,12,2021,2024,2021,2024,national,TRUE,250,1000,1000,TRUE,-3,TRUE,1,TRUE,1,TRUE,1,national,sex_age_group,national,sex_age_group,national,sex_age_group,national,sex_age_group,logistic,1,TRUE,TRUE,TRUE,FALSE,FALSE,TRUE,CY2026Q3,CY2027Q3,2 +ZWE,ZWE,2,CY2024Q4,CY2025Q3,CY2020Q1,ZWE2020PHIA,ZWE2020PHIA,,FALSE,,TRUE,TRUE,TRUE,2024,12,2020,2024,2020,2024,subnational,TRUE,250,1000,1000,TRUE,-4,TRUE,1,TRUE,1,TRUE,1,subnational,sex_age_group,subnational,sex_age_group,subnational,sex_age_group,subnational,sex_age_group,logistic,1,TRUE,TRUE,TRUE,FALSE,FALSE,TRUE,CY2026Q3,CY2027Q3,1 diff --git a/tests/testthat/test-options.R b/tests/testthat/test-options.R index 54ad29c..9baa5fc 100644 --- a/tests/testthat/test-options.R +++ b/tests/testthat/test-options.R @@ -205,7 +205,7 @@ describe("when getting controls for unknown country", { it("has override defaults for non country specific options", { calendar_quarter_t2 <- get_control(out, "calendar_quarter_t2") - expect_equal(calendar_quarter_t2$value, "CY2023Q4") + expect_equal(calendar_quarter_t2$value, "CY2024Q4") }) it("has no value for country specific options", { From fc5db8f0015adc367830c8a08be516a4bd6e6cfb Mon Sep 17 00:00:00 2001 From: Rob Ashton Date: Fri, 15 Nov 2024 13:10:34 +0000 Subject: [PATCH 4/5] Bump version number and add news item --- DESCRIPTION | 2 +- NEWS.md | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0212c64..20e7437 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: naomi.options Title: Contains model and calibration options and helper functions for Naomi -Version: 1.2.1 +Version: 1.3.0 Authors@R: person(given = "Robert", family = "Ashton", diff --git a/NEWS.md b/NEWS.md index ce0dbf0..d5f89d7 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# naomi.options 1.3.0 + +* Update default for 2024/2025 HIV estimates + # naomi.options 1.2.1 * Update default calibration options: From 6e7e83441ce9b24702ba6654d49cadd4a73b20b8 Mon Sep 17 00:00:00 2001 From: Rob Ashton Date: Mon, 18 Nov 2024 09:47:09 +0000 Subject: [PATCH 5/5] Add more details into NEWS --- NEWS.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/NEWS.md b/NEWS.md index d5f89d7..e607bed 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,14 @@ # naomi.options 1.3.0 * Update default for 2024/2025 HIV estimates + - Calendar quaters T2 - T5 updated to 2024 - 2027 + - ANC T2 options set to 2025 + - include_art_t1: blank (force select) + - include_art_t2: TRUE + - artattend: TRUE + - artattend_t2: TRUE + - Calibration method set to logistic + - For CAF, CMR, STP, MWI and ZAF default options from prior year were used # naomi.options 1.2.1