Merge pull request #450 from mrc-ide/update-test-data

fix NA values in survey_hiv_indicators column std_error
mrc-ide · Nov 19, 2024 · 3b86ce9 · 3b86ce9
2 parents 998b725 + 3fc9b47
commit 3b86ce9
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Showing 7 changed files with 39 additions and 37 deletions.
diff --git a/R/run-model.R b/R/run-model.R
@@ -91,16 +91,15 @@ run_model <- function(data, options, validate) {
                  progress = progress)
 
 
-  if (fit$convergence !=0) {
+  if (fit$convergence != 0) {
 
-    if(fit$message == "false convergence (8)"){
+    if (fit$message == "false convergence (8)"){
       msg <- t_("WARNING_FALSE_CONVERGENCE")
     } else {
       msg <- t_("WARNING_CONVERGENCE", list(msg = fit$message))
     }
 
     naomi_warning(msg, "model_fit")
-
   }
 
   progress$finalise_fit()
@@ -131,7 +130,6 @@ run_model <- function(data, options, validate) {
     naomi_data = naomi_data,
     info = info
   )
-
 }
 
 build_hintr_output <- function(plot_data_path, model_output_path, warnings) {

diff --git a/data-raw/survey.R b/data-raw/survey.R
@@ -896,6 +896,8 @@ survey_hiv_indicators <- calc_survey_hiv_indicators(
   survey_biomarker,
   demo_area_hierarchy)
 
+filter(survey_hiv_indicators, is.na(std_error))
+survey_hiv_indicators$std_error[is.na(survey_hiv_indicators$std_error)] <- 0.0
 
 #' ## Save datasets
 #'

diff --git a/data/demo_survey_hiv_indicators.rda b/data/demo_survey_hiv_indicators.rda
diff --git a/inst/extdata/demo_survey_hiv_indicators.csv b/inst/extdata/demo_survey_hiv_indicators.csv
@@ -15908,7 +15908,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,both,Y045_049,177,240,1
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,both,Y050_054,129,162,120.54389037448695,0.7748599566807669,0.03905360222942496,0.6893738079387397,0.8422048964212699
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,both,Y055_059,88,109,80.85309273638147,0.7695115138884412,0.044489222350464,0.6712678191657072,0.8451667482868456
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,both,Y060_064,60,70,54.212237875912976,0.8091266443320001,0.055209812341668336,0.6778028857662217,0.8952003952540727
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,both,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,both,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,both,Y001_004,18,19,14.001704889638258,0.6569553204935843,0.12727378529840955,0.3876681553116353,0.8527877522680566
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,male,Y015_049,296,559,413.7810042594462,0.6025270373779054,0.024935000059006975,0.5527871489046333,0.6502351252266833
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,male,Y015_064,330,715,527.9651856480385,0.6349933905516871,0.021412824012724166,0.5920935512814668,0.6758514631593975
@@ -15957,7 +15957,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,female,Y045_049,109,134
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,female,Y050_054,79,92,67.26084291939691,0.7383353798552105,0.055047935218396404,0.6174825784892003,0.8314295014319167
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,female,Y055_059,54,58,40.980527410570545,0.8062973593393401,0.05865815216628626,0.6659698999459963,0.8968073503551113
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,female,Y060_064,31,35,28.865378277878452,0.8141291563780553,0.06993925587137714,0.6390399789700845,0.9155166554304044
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,female,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,female,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI,Malawi - Demo,all,female,Y001_004,8,8,7.125023177711781,0.450821665090431,0.2012542756391103,0.14300300695794438,0.8015270629465587
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_1_demo,Northern,all,both,Y015_049,47,149,129.9167754259742,0.7095078187744512,0.03299395227896437,0.6408924544039271,0.7697233867575317
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_1_demo,Northern,all,both,Y015_064,51,182,159.15510760305264,0.7271995528723063,0.02939191051171283,0.6659832380873617,0.7808877744617115
@@ -16123,7 +16123,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,both,Y045_049,99,14
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,both,Y050_054,76,95,71.33216353389295,0.7654317997684672,0.053298704879957075,0.6458560365159409,0.8537741512108593
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,both,Y055_059,41,48,35.16776879176661,0.8105785751619565,0.06359671606174175,0.6551955289951933,0.9059869905198982
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,both,Y060_064,44,53,42.27859686695561,0.792880355818035,0.06496072924156025,0.6380880359822956,0.8926093745184708
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,both,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,both,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,both,Y001_004,12,13,9.677498093333027,0.7020247557532454,0.14279478706913773,0.3820267319420337,0.8997879904178266
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,male,Y015_049,158,341,251.73162445844568,0.6280110059125654,0.030301399848660867,0.5669630915577909,0.6852307049151976
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,male,Y015_064,168,428,313.8365771888916,0.6539088283950566,0.02607980646571124,0.6011844780229604,0.703105168512981
@@ -16172,7 +16172,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,female,Y045_049,63,
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,female,Y050_054,47,54,40.356276767680704,0.7222581019604578,0.07329535690746976,0.5596057497573013,0.841818114403322
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,female,Y055_059,25,28,19.107157416862716,0.8298465119087445,0.08015581744009995,0.6158394863709681,0.9368584888491283
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,female,Y060_064,24,27,23.262461904120887,0.8269290431469299,0.07485386157110663,0.6315585086832759,0.9301584463389765
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,female,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,female,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_1_3_demo,Southern,all,female,Y001_004,4,4,3.8214178328274997,0.5808147855433148,0.26283549126771677,0.14310356057744214,0.9199734694284686
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_1_demo,Northern,all,both,Y015_049,47,149,129.9167754259742,0.7095078187744512,0.03299395227896437,0.6408924544039271,0.7697233867575317
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_1_demo,Northern,all,both,Y015_064,51,182,159.15510760305264,0.7271995528723063,0.02939191051171283,0.6659832380873617,0.7808877744617115
@@ -16478,7 +16478,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,both,Y045_049,62,
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,both,Y050_054,47,55,40.25105198063331,0.7702540336506881,0.07587604290389445,0.5913080679347493,0.8859594244748754
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,both,Y055_059,25,30,23.643309698961644,0.7846071237709136,0.07818954658150766,0.5952991473553306,0.900206663772158
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,both,Y060_064,30,35,28.54222819769796,0.8417338681594824,0.06840839294112025,0.6603221468549171,0.9356943668513962
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,both,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,both,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,both,Y001_004,6,6,5.062361470955532,0.7076824180773964,0.19608419347533246,0.2741558784349028,0.9394569697215944
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,male,Y015_049,102,240,185.62103250738627,0.631185482012857,0.033752889182644234,0.5629456597244568,0.6945517399000651
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,male,Y015_064,108,297,226.17645181697776,0.6553808467814354,0.03136168114855262,0.5916094824478016,0.7140079994019548
@@ -16527,7 +16527,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,female,Y045_049,4
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,female,Y050_054,27,30,22.310384504820178,0.7684727946846136,0.09428056599320409,0.5401951442385823,0.9036354199787159
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,female,Y055_059,14,17,12.967302486273946,0.8146617204899899,0.114543273456242,0.49842815021013287,0.9510826093278688
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,female,Y060_064,14,16,14.218776381233273,0.8129599303256666,0.1010522740650321,0.5416087994590735,0.9411381575613841
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,female,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,female,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_2_5_demo,South-West,all,female,Y001_004,1,1,1,1,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_1_demo,Chitipa,all,both,Y015_049,4,14,13.079921524097607,0.5697500395361266,0.09690420400556586,0.37896083604068515,0.7418534116545574
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_1_demo,Chitipa,all,both,Y015_064,4,15,13.962417971284841,0.5901693603411527,0.08628538364704366,0.41713662645085964,0.7434294300508175
@@ -17659,7 +17659,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,both,Y045_049,38,5
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,both,Y050_054,31,37,28.971021157532107,0.7578903195187772,0.08478863112371024,0.5586003626082315,0.8856250953721512
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,both,Y055_059,13,17,16.826643640957975,0.8229920644290639,0.08414212343243836,0.5998121049243477,0.9351616233325795
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,both,Y060_064,14,16,12.37343064787388,0.53422764153731,0.15381061635737578,0.25456619661424157,0.7939097299536315
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,both,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,both,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,both,Y001_004,3,3,2.9685669356661766,0.659421354577168,0.28378121752100083,0.1399316946654481,0.9584050086609006
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,male,Y015_049,63,151,117.2254133741664,0.5505924779260516,0.04582465796283461,0.4601074311530433,0.6378488857573587
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,male,Y015_064,65,184,140.99689221636893,0.5792052685775926,0.041926727264350025,0.49558802246015765,0.6585123948797179
@@ -17708,7 +17708,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,female,Y045_049,24
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,female,Y050_054,17,20,13.489097261708068,0.7636912670847119,0.12379844197501175,0.4572321114467524,0.9253622959017467
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,female,Y055_059,8,11,10.932092422559974,0.8292373699270147,0.10712500257861728,0.5243518087060408,0.9553395968870257
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,female,Y060_064,6,6,4.784013791501877,0.21706432603953751,0.15478125384609845,0.04445038412399939,0.62297608074363
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,female,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_23_demo,Blantyre,all,female,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_24_demo,Mwanza,all,both,Y015_049,3,17,16.253566102685422,0.6179858275360864,0.08388896390947519,0.4463448442931162,0.7644918446869419
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_24_demo,Mwanza,all,both,Y015_064,3,17,16.253566102685422,0.6179858275360864,0.08388479202422319,0.446353403492301,0.7644856086993684
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_3_24_demo,Mwanza,all,both,Y000_064,3,17,16.253566102685422,0.6179858275360864,0.08388413010421227,0.4463547615156104,0.7644846192740784
@@ -19393,7 +19393,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,both,Y045_049
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,both,Y050_054,28,33,30.399052972451507,0.7622677140135403,0.07993068973760899,0.5746015825273446,0.883875625599874
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,both,Y055_059,13,17,16.826643640957975,0.8229920644290639,0.08414212343243836,0.5998121049243477,0.9351616233325795
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,both,Y060_064,13,15,13.87136677542012,0.6513141948956539,0.14392886886733905,0.35039100923771527,0.8661064521174505
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,both,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,both,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,both,Y001_004,3,3,2.9685669356661766,0.659421354577168,0.28378121752100083,0.1399316946654481,0.9584050086609006
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,male,Y015_049,58,139,123.04362621121932,0.5208130984522058,0.04070545064155076,0.4411790635998353,0.5994032623510778
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,male,Y015_064,60,172,150.80269737778997,0.559343474613215,0.03769542445367252,0.4846920031573383,0.6314045665576387
@@ -19442,7 +19442,7 @@ art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,female,Y045_0
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,female,Y050_054,14,16,14.88670670542045,0.7800976185085934,0.10332952234736598,0.5214019678908002,0.9203278928842241
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,female,Y055_059,8,11,10.932092422559974,0.8292373699270147,0.10712500257861728,0.5243518087060408,0.9553395968870257
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,female,Y060_064,5,5,4.677033003604339,0.3292526499520002,0.20756938876381897,0.07217768246736284,0.7559450080669983
-art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,female,Y000_000,1,1,1,0,NA,NA,NA
+art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_29_demo,Blantyre City,all,female,Y000_000,1,1,1,0,0,NA,NA
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_30_demo,Thyolo,all,both,Y015_049,12,69,65.55932519254539,0.7074743010501984,0.04501746203468915,0.6122572491293277,0.7874273225463437
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_30_demo,Thyolo,all,both,Y015_064,13,77,73.20869482890575,0.7334283435031405,0.045281767402567695,0.6360233145445926,0.8124529446325933
 art_coverage,DEMO2016PHIA,CY2016Q1,MWI_4_30_demo,Thyolo,all,both,Y000_064,13,79,68.51317841292828,0.7519647646915016,0.042277439899731754,0.6603489780726222,0.8254024596619344

diff --git a/tests/testthat/test-outputs.R b/tests/testthat/test-outputs.R
@@ -164,16 +164,21 @@ test_that("subset_output_package() saves expected output package", {
   expect_setequal(indicator_sub, sub_keep_out$indicators$indicator)
 
 
+  ## Test that can **drop** selected indicators (rather than keep)
+
   sub_drop_file <- tempfile(fileext = ".zip")
 
-  sub_drop_return <- subset_output_package(out$path,
-                                           sub_drop_file,
-                                           area_id = area_id_sub,
-                                           sex = sex_sub,
-                                           age_group = age_group_sub,
-                                           calendar_quarter = calendar_quarter_sub,
-                                           indicator = indicator_sub,
-                                           drop = TRUE)
+  expect_warning(
+    sub_drop_return <- subset_output_package(out$path,
+                                             sub_drop_file,
+                                             area_id = area_id_sub,
+                                             sex = sex_sub,
+                                             age_group = age_group_sub,
+                                             calendar_quarter = calendar_quarter_sub,
+                                             indicator = indicator_sub,
+                                             drop = TRUE),
+    "Required indicators not in output: plhiv"
+  )
 
   sub_drop_out <- read_output_package(sub_drop_file)
 

diff --git a/tests/testthat/test-spectrum.R b/tests/testthat/test-spectrum.R
@@ -128,7 +128,7 @@ test_that("extract_pjnz_program_data() returns complete data", {
   expect_setequal(dat_old$anc_testing$spectrum_region_code, 0)
   expect_setequal(dat_old$anc_testing$indicator[dat_old$anc_testing$year == 2018],
                   c("anc_clients", "anc_tested", "anc_tested_pos", "anc_known_pos", "anc_already_art"))
-  expect_setequal(dat_old$anc_testing$indicator[dat_old$anc_testing$year == 2010],
+  expect_setequal(dat_old$anc_testing$indicator[dat_old$anc_testing$year == 2019],
                   c("anc_already_art"))
   expect_true(all(!is.na(dat_old$anc_testing$value)))
 
@@ -146,7 +146,7 @@ test_that("extract_pjnz_program_data() returns complete data", {
   expect_setequal(dat_new$anc_testing$spectrum_region_code, 0)
   expect_setequal(dat_new$anc_testing$indicator[dat_new$anc_testing$year == 2018],
                   c("anc_clients", "anc_tested", "anc_tested_pos", "anc_known_pos", "anc_known_neg", "anc_already_art"))
-  expect_setequal(dat_new$anc_testing$indicator[dat_new$anc_testing$year == 2010],
+  expect_setequal(dat_new$anc_testing$indicator[dat_new$anc_testing$year == 2019],
                   c("anc_already_art"))
   expect_true(all(!is.na(dat_new$anc_testing$value)))
 

diff --git a/tests/testthat/test-warning.R b/tests/testthat/test-warning.R
@@ -50,23 +50,20 @@ test_that("warning raised after false convergence", {
   a_fit_bad$convergence <- 1
   a_fit_bad$message <- "false convergence (8)"
 
-  a_fit_sample_bad <- a_fit_sample
-  a_fit_sample_bad$convergence <- 1
-  a_fit_sample_bad$message <- "false convergence (8)"
-
-  with_mocked_bindings(
-  {
-    out <- hintr_run_model(a_hintr_data, a_hintr_options, validate = FALSE)
-  },
-  fit_tmb = mockery::mock(a_fit_bad),
-  output_package = mockery::mock(a_output)
-  )
-
+  mock_fit_tmb <- mockery::mock(a_fit_bad)
+  mock_output_package <- mockery::mock(a_output)
+
+  with_mock(
+    fit_tmb = mock_fit_tmb,
+    output_package = mock_output_package, {
+      out <- hintr_run_model(a_hintr_data, a_hintr_options, validate = FALSE)
+    })
+
   expect_length(out$warnings, 3)
   expect_match(out$warnings[[1]]$text,
                "Naomi subnational data not equal to Spectrum national data. Check table on review inputs tab for: \nnumber_on_art: 2011;2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023")
   expect_match(out$warnings[[2]]$text,
-               "Naomi subnational data not equal to Spectrum national data. Check table on review inputs tab for: \nanc_already_art: 2011;2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023\nanc_clients: 2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023\nanc_known_neg: 2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023\nanc_known_pos: 2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023\nanc_tested: 2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023")
+               "Naomi subnational data not equal to Spectrum national data. Check table on review inputs tab for: \nanc_already_art: 2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023\nanc_clients: 2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023\nanc_known_neg: 2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023\nanc_known_pos: 2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023\nanc_tested: 2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022;2023")
   expect_equal(out$warnings[[3]]$text,
                "Model fitting to input data has not fully converged. Please review estimates of HIV prevalence and ART coverage across districts and the national distribution of key indicators by age and sex.")
 })