SHIPP tool integration

.gitignore

@@ -20,3 +20,4 @@ vignettes_src/model-workflow.Rmd
 tests/testthat/testdata/fit.RDS
 .vscode
 .Rprofile
+.idea

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: naomi
 Title: Naomi Model for Subnational HIV Estimates
-Version: 2.9.18
+Version: 2.9.19
 Authors@R:
     person(given = "Jeff",
            family = "Eaton",
@@ -13,7 +13,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Additional_repositories:
     https://mrc-ide.r-universe.dev
 Imports:
@@ -36,7 +36,9 @@ Imports:
     knitr,
     magrittr,
     mvtnorm,
+    naomi.resources (>= 0.0.2),
     naomi.options (>= 1.2.0),
+    openxlsx,
     plotly,
     prettyunits,
     qs,
@@ -50,7 +52,6 @@ Imports:
     traduire,
     utils,
     withr,
-    writexl,
     yaml,
     zip,
     zoo

NAMESPACE

@@ -5,6 +5,7 @@ export(add_output_labels)
 export(age_bar_plotly)
 export(aggregate_anc)
 export(aggregate_art)
+export(agyw_format_naomi)
 export(align_inputs_outputs)
 export(anc_testing_artcov_mf)
 export(anc_testing_clients_mf)
@@ -59,8 +60,6 @@ export(naomi_objective_function_r)
 export(naomi_output_frame)
 export(output_package)
 export(pop_pyramid_outputs)
-export(prepare_input_time_series_anc)
-export(prepare_input_time_series_art)
 export(prepare_tmb_inputs)
 export(quarter_id_to_calendar_quarter)
 export(quarter_labels)

NEWS.md

@@ -1,3 +1,9 @@
+# naomi 2.9.19
+
+* Generate PSE workbook from naomi outputs.
+* Add function `extract_kp_workbook()` to extract key population totals from the Spectrum PJNZ file. Data are extracted from summary table saved in AIM Programme Statistics input for key populations.
+
+
 # naomi 2.9.18
 
 * Change PEPFAR Data Pack file name to `pepfar_datapack_indicators_2024.csv`.