First attempt at merge

.gitignore

@@ -48,6 +48,7 @@ test/*/Makefile
 
 # RStudio files
 .Rproj.user/
+COVIDScenarioPipeline.Rproj
 
 # produced vignettes
 vignettes/*.html
@@ -72,3 +73,8 @@ packrat/lib*/
 build/
 dist/
 SEIR.egg-info/
+Outcomes.egg-info/
+.Rproj.user
+
+# R package manuals
+man/

R/pkgs/covidcommon/R/DataUtils.R

@@ -972,6 +972,12 @@ get_groundtruth_from_source <- function(
                                  run_parallel = FALSE) %>%
             dplyr::select(Update, FIPS, source, !!variables)
 
+    } else if((source == 'hhsCMU') && (scale == "US state")) {
+      warning("This code is almost certainly broken")
+      hosp <- get_hhsCMU_incidH_st_data()
+      hosp <- hosp %>% dplyr::select(-FIPS)
+      rc <- hosp
+      stop("This code is almost certainly broken")
     } else if(source == "file"){
 
         rc <- get_gt_file_data(source_file)

R/pkgs/hospitalization/DESCRIPTION

@@ -23,4 +23,4 @@ Description: Generate hospitalization scenarios corresponding to the infection s
 License: What license it uses
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1

R/pkgs/inference/NAMESPACE

@@ -1,6 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
 export(accept_reject_new_seeding_npis)
+export(add_perturb_column_hnpi)
+export(add_perturb_column_snpi)
 export(aggregate_and_calc_loc_likelihoods)
 export(calc_hierarchical_likadj)
 export(calc_prior_likadj)
@@ -18,13 +20,16 @@ export(logLikStat)
 export(multi_hosp_run)
 export(multi_loc_inference_test)
 export(npis_dataframe)
-export(perform_MCMC_step_copies)
+export(perform_MCMC_step_copies_chimeric)
+export(perform_MCMC_step_copies_global)
 export(periodAggregate)
 export(perturb_expand_npis)
 export(perturb_hnpi)
+export(perturb_hnpi_from_file)
 export(perturb_hpar)
 export(perturb_seeding)
 export(perturb_snpi)
+export(perturb_snpi_from_file)
 export(simulate_multi_epi)
 export(simulate_single_epi)
 export(single_hosp_run)