Merge pull request #219 from mrc-ide/naomi-v2.3.1

Naomi v2.3.1
mrc-ide · Feb 1, 2021 · 554633b · 554633b
2 parents 30c1d6e + 798f209
commit 554633b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: naomi
 Title: Naomi Model for Subnational HIV Estimates
-Version: 2.3.0
+Version: 2.3.1
 Authors@R: 
     person(given = "Jeff",
            family = "Eaton",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# naomi 2.3.1
+
+* Set default for `calibrate_method` model option in user interface via JSON metadata.
+* Fix swapped indicator_code and indicator_id for Data Pack metadata which were swapped.
+* Refactor [`calibrate_outputs()`]; handle uncertainty ranges for proportion adjustments.
+
 # naomi 2.3.0
 
 * Implement 'logistic' scaling option for [`calibrate_outputs()`] such that estimates are

diff --git a/R/outputs.R b/R/outputs.R
diff --git a/inst/datapack/datapack_indicator_mapping.csv b/inst/datapack/datapack_indicator_mapping.csv
@@ -11,4 +11,4 @@ anc_tested_neg,tAE7ZD7p9zu,PMTCT_STAT_SUBNAT.N.New.Neg.T_1,# Pregnant Women who
 anc_tested_pos,tAE7ZD7p9zu,PMTCT_STAT_SUBNAT.N.New.Pos.T_1,# Pregnant Women who are newly tested and found HIV-positive at ANC1,TRUE
 art_current,xghQXueYJxu,TX_CURR_SUBNAT.T_1,Total # of PLHIV on ART,TRUE
 art_coverage,TX_CURR_SUBNAT.Rt.T_1,TX_CURR_SUBNAT.Rt.T_1,ART coverage,FALSE
-aware_plhiv_num,DIAGNOSED_SUBNAT.T_1,nF19GOjcnoD,Number of PLHIV aware of HIV positive status,TRUE
+aware_plhiv_num,nF19GOjcnoD,DIAGNOSED_SUBNAT.T_1,Number of PLHIV aware of HIV positive status,TRUE
diff --git a/inst/metadata/calibration_run_options.json b/inst/metadata/calibration_run_options.json
@@ -220,6 +220,7 @@
         {
           "name": "calibrate_method",
           "type": "select",
+          "value": "logistic",
           "required": true,
           "options": [
             {

diff --git a/man/calibrate_outputs.Rd b/man/calibrate_outputs.Rd
diff --git a/man/scale_gmrf_precision.Rd b/man/scale_gmrf_precision.Rd
diff --git a/tests/testthat/test-run-model.R b/tests/testthat/test-run-model.R
@@ -423,6 +423,7 @@ test_that("input data types can be formatted", {
 })
 
 test_that("model run can be calibrated", {
+
   ## Calibration makes no modification of existing files.
   output_hash <- tools::md5sum(a_hintr_output$output_path)
   spectrum_hash <- tools::md5sum(a_hintr_output$spectrum_path)