Merge feat/vpc

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: bbr
 Title: R package for bbi
-Version: 1.10.0.8007
+Version: 1.10.0.8010
 Authors@R: 
     c(person(given = "Seth",
              family = "Green",
@@ -66,11 +66,12 @@ Imports:
     magrittr,
     Matrix,
     mrgmisc,
-    nmrec,
+    nmrec (>= 0.3.0),
     processx,
     purrr,
     readr,
     rlang,
+    stringfish,
     stringr,
     stringi,
     tibble,

NAMESPACE

@@ -12,25 +12,29 @@ S3method(check_nonmem_finished,bbi_base_model)
 S3method(check_nonmem_finished,list)
 S3method(check_output_dir,bbi_model)
 S3method(check_output_dir,character)
+S3method(check_up_to_date,bbi_base_model)
 S3method(check_up_to_date,bbi_log_df)
-S3method(check_up_to_date,bbi_nonmem_model)
+S3method(check_up_to_date,bbi_nmboot_model)
 S3method(check_up_to_date,bbi_nonmem_summary)
 S3method(config_log_make_entry,bbi_nonmem_model)
 S3method(config_log_make_entry,default)
 S3method(copy_model_from,bbi_nonmem_model)
 S3method(cov_cor,bbi_nonmem_model)
 S3method(cov_cor,bbi_nonmem_summary)
 S3method(create_model_hook,bbi_nmboot_model)
+S3method(create_model_hook,bbi_nmsim_model)
 S3method(create_model_hook,bbi_nonmem_model)
 S3method(create_model_hook,default)
 S3method(get_based_on,bbi_run_log_df)
 S3method(get_based_on,character)
 S3method(get_based_on,default)
 S3method(get_config_path,bbi_log_df)
 S3method(get_config_path,bbi_model)
+S3method(get_config_path,bbi_nonmem_summary)
 S3method(get_data_path,bbi_log_df)
 S3method(get_data_path,bbi_model)
 S3method(get_data_path,bbi_nmboot_model)
+S3method(get_data_path,bbi_nmsim_model)
 S3method(get_data_path,bbi_nonmem_model)
 S3method(get_data_path,bbi_nonmem_summary)
 S3method(get_model_ancestry,bbi_run_log_df)
@@ -39,19 +43,22 @@ S3method(get_model_ancestry,default)
 S3method(get_model_id,bbi_model)
 S3method(get_model_id,character)
 S3method(get_model_path,bbi_log_df)
-S3method(get_model_path,bbi_nmboot_model)
-S3method(get_model_path,bbi_nonmem_model)
+S3method(get_model_path,bbi_model)
 S3method(get_model_path,bbi_nonmem_summary)
 S3method(get_model_status,default)
 S3method(get_output_dir,bbi_log_df)
-S3method(get_output_dir,bbi_nmboot_model)
-S3method(get_output_dir,bbi_nonmem_model)
+S3method(get_output_dir,bbi_model)
 S3method(get_output_dir,bbi_nonmem_summary)
 S3method(get_yaml_path,bbi_log_df)
 S3method(get_yaml_path,bbi_model)
-S3method(model_diff,default)
+S3method(get_yaml_path,bbi_nonmem_summary)
+S3method(model_diff,bbi_nmboot_model)
+S3method(model_diff,bbi_nmsim_model)
+S3method(model_diff,bbi_nonmem_model)
 S3method(model_summaries,bbi_run_log_df)
 S3method(model_summaries,list)
+S3method(model_summary,bbi_nmboot_model)
+S3method(model_summary,bbi_nmsim_model)
 S3method(model_summary,bbi_nonmem_model)
 S3method(nm_file,bbi_model)
 S3method(nm_file,character)
@@ -65,16 +72,17 @@ S3method(print,bbi_nmboot_summary)
 S3method(print,bbi_nonmem_summary)
 S3method(print,bbi_process)
 S3method(print_model_files,default)
+S3method(submit_model,bbi_base_model)
 S3method(submit_model,bbi_nmboot_model)
-S3method(submit_model,bbi_nonmem_model)
+S3method(submit_model,bbi_nmsim_model)
 S3method(submit_models,bbi_nonmem_models)
 S3method(submit_models,default)
 S3method(submit_models,list)
 S3method(tags_diff,bbi_model)
 S3method(tags_diff,bbi_run_log_df)
-S3method(tail_lst,bbi_nonmem_model)
+S3method(tail_lst,bbi_base_model)
 S3method(tail_lst,character)
-S3method(tail_output,bbi_nonmem_model)
+S3method(tail_output,bbi_base_model)
 S3method(tail_output,character)
 S3method(wait_for_nonmem,default)
 export("%>%")
@@ -84,6 +92,7 @@ export(add_bbi_args)
 export(add_config)
 export(add_description)
 export(add_notes)
+export(add_simulation)
 export(add_star)
 export(add_summary)
 export(add_tags)
@@ -129,8 +138,10 @@ export(get_model_status)
 export(get_omega)
 export(get_output_dir)
 export(get_sigma)
+export(get_simulation)
 export(get_theta)
 export(get_yaml_path)
+export(has_simulation)
 export(inherit_param_estimates)
 export(initial_estimates)
 export(mod_ext)
@@ -143,8 +154,10 @@ export(new_ext)
 export(new_model)
 export(nm_data)
 export(nm_file)
+export(nm_file_multi_tab)
 export(nm_grd)
 export(nm_join)
+export(nm_join_sim)
 export(nm_par_tab)
 export(nm_tab)
 export(nm_table_files)

R/aaa.R

@@ -197,11 +197,12 @@ BBI_ARGS = list(
 # models _and_ summary objects. BBI_BASE_MODEL_CLASS ("bbi_base_model") came
 # later and applies only to regular models, not summary objects.
 BBI_PARENT_CLASS <- "bbi_model" # SHARED with bbr.bayes
-BBI_BASE_MODEL_CLASS <- "bbi_base_model"
+BBI_BASE_MODEL_CLASS <- "bbi_base_model" # SHARED with bbr.bayes
 NM_MOD_CLASS <- "bbi_nonmem_model" # SHARED with bbr.bayes
 NM_SUM_CLASS <- "bbi_nonmem_summary" # SHARED with bbr.bayes
 NMBOOT_MOD_CLASS <- "bbi_nmboot_model"
 NMBOOT_SUM_CLASS <- "bbi_nmboot_summary"
+NMSIM_MOD_CLASS <- "bbi_nmsim_model"
 SL_CLASS <- "bbi_summary_list"
 PROC_CLASS <- "bbi_process"
 RUN_LOG_CLASS <- "bbi_run_log_df"
@@ -217,7 +218,7 @@ YAML_TAGS <- "tags" # SHARED with bbr.bayes
 YAML_NOTES <- "notes"
 YAML_BBI_ARGS <- "bbi_args"
 YAML_MOD_TYPE <- "model_type" # SHARED with bbr.bayes
-YAML_STAR <- 'star'
+YAML_STAR <- "star"
 
 YAML_REQ_INPUT_KEYS <- c(
   YAML_MOD_TYPE
@@ -226,6 +227,24 @@ YAML_REQ_INPUT_KEYS <- c(
 ABS_MOD_PATH <- "absolute_model_path" # SHARED with bbr.bayes
 RUN_ID_COL <- "run" # SHARED with bbr.bayes
 
+# SPEC keys that are hard-coded
+SPEC_NMSIM_NSIM <- "n_sim"
+
+SPEC_NMBOOT_NSAMPLE <- "n_samples"
+SPEC_NMBOOT_STRAT <- "strat_cols"
+
+# List of keys required to print a bbi_nmsim_model object
+SPEC_NMSIM_KEYS <- c(
+  SPEC_NMSIM_NSIM
+)
+
+# List of keys required to print a bbi_nmboot_model object
+SPEC_NMBOOT_KEYS <- c(
+  SPEC_NMBOOT_NSAMPLE,
+  SPEC_NMBOOT_STRAT
+)
+
+
 # keys required to create a model object
 MODEL_REQ_INPUT_KEYS <- c(
   ABS_MOD_PATH,
@@ -268,6 +287,7 @@ YAML_SCALAR_TO_LIST_KEYS <- c(
   YAML_STAR
 )
 
+
 SUMMARY_DETAILS <- "run_details"
 SUMMARY_HEURISTICS <- "run_heuristics"
 SUMMARY_COND_NUM <- "condition_number"
@@ -288,6 +308,9 @@ CONFIG_MODEL_MD5 <- "model_md5" # SHARED with bbr.bayes
 CONFIG_DATA_PATH <- "data_path" # SHARED with bbr.bayes
 CONFIG_DATA_MD5 <- "data_md5" # SHARED with bbr.bayes
 
+# keys for bootstrap runs
+CONFIG_DATA_BASED_ON_MD5 <- "based_on_data_md5"
+
 # keys required for a summary object to have
 SUMMARY_REQ_KEYS <- c(
   ABS_MOD_PATH,

R/bootstrap-model.R

@@ -10,6 +10,18 @@
 #'  Both default to `TRUE`.
 #'
 #' @seealso setup_bootstrap_run summarize_bootstrap_run
+#' @examples
+#' \dontrun{
+#'
+#' # Create new bootstrap object
+#' .boot_run <- new_bootstrap_run(.mod)
+#'
+#' # Optionally inherit final parameter estimates
+#' .boot_run <- inherit_param_estimates(.boot_run)
+#'
+#' # Set up the run
+#' setup_bootstrap_run(.boot_run)
+#' }
 #' @return S3 object of class `bbi_nmboot_model`.
 #' @export
 new_bootstrap_run <- function(
@@ -44,12 +56,10 @@ new_bootstrap_run <- function(
 
   # Optionally remove $TABLE and $COV statements here
   if(isTRUE(remove_cov)) remove_records(boot_run, type = "covariance")
-  if(isTRUE(remove_tables)){
-    remove_records(boot_run, type = "table")
-  }else{
-    # Update table names if present (not used, but for consistency)
-    boot_run <- update_model_id(boot_run) %>% suppressMessages()
-  }
+  if(isTRUE(remove_tables)) remove_records(boot_run, type = "table")
+
+  # Update table and estimation record file paths
+  boot_run <- update_model_id(boot_run) %>% suppressMessages()
 
   # Return read-in model to get the updated class as part of the model object
   return(read_model(file.path(model_dir, boot_dir)))
@@ -74,7 +84,12 @@ new_bootstrap_run <- function(
 #'
 #' # Setup
 #' .boot_run <- new_bootstrap_run(.mod)
-#' .boot_run <- setup_bootstrap_run(.boot_run, n = 1000, seed = 1234)
+#' .boot_run <- setup_bootstrap_run(
+#'   .boot_run,
+#'   n = 1000,
+#'   seed = 1234,
+#'   strat_cols = c("STUDY", "ETN")
+#' )
 #'
 #' # Submit
 #' submit_model(.boot_run)
@@ -574,6 +589,7 @@ get_boot_models <- function(.boot_run){
     .boot_run <- read_model(.boot_run[[ABS_MOD_PATH]])
   }
 
+  boot_dir <- .boot_run[[ABS_MOD_PATH]]
   output_dir <- get_output_dir(.boot_run, .check_exists = FALSE)
   if(!fs::file_exists(output_dir)){
     verbose_msg(
@@ -590,29 +606,39 @@ get_boot_models <- function(.boot_run){
   }
 
   boot_spec <- get_boot_spec(.boot_run)
-  boot_models <- tryCatch(
-    purrr::map(boot_spec$bootstrap_runs$mod_path_abs, read_model),
-    error = function(cond){
-      # Suppress 'does not exist' message - handle separately
-      if(!stringr::str_detect(cond$parent$message, "does not exist")){
-        # Likely would only happen if there was a bbi/submission issue
-        message(cond$parent$message)
-      }
-      return(NULL)
+  boot_model_ids <- fs::path_ext_remove(basename(boot_spec$bootstrap_runs$mod_path_abs))
+
+  boot_models <- tryCatch({
+    find_models(.boot_run[[ABS_MOD_PATH]], .recurse = FALSE, .include = boot_model_ids)
+  }, warning = function(cond){
+    if(!stringr::str_detect(cond$message, "All models excluded|Found no valid model")){
+      warning(cond)
     }
-  )
+    return(NULL)
+  })
+
 
   # This shouldnt happen, but could if the directory existed and models
   # referenced in the spec file aren't found for any reason _other than_
   # cleaning up the run
   if(is.null(boot_models) || rlang::is_empty(boot_models)){
-    boot_dir <- .boot_run[[ABS_MOD_PATH]]
-    rlang::warn(
+    rlang::abort(
       c(
         glue("At least one bootstrap run model does not exist in `{boot_dir}`")
       )
     )
+  }else{
+    if(length(boot_model_ids) != length(boot_models)){
+      rlang::warn(
+        c(
+          glue("Found an unexpected number of models in {boot_dir}"),
+          glue("Expected number of models: {length(boot_model_ids)}"),
+          glue("Discovered number of models: {length(boot_models)}")
+        )
+      )
+    }
   }
+
   return(boot_models)
 }
 
@@ -672,7 +698,7 @@ cleanup_bootstrap_run <- function(.boot_run, .force = FALSE){
   }
 
   # Overwrite spec file
-  spec_path <- get_boot_spec_path(.boot_run)
+  spec_path <- get_spec_path(.boot_run)
   boot_spec <- jsonlite::read_json(spec_path, simplifyVector = TRUE)
   # Set cleaned up - impacts status checking
   boot_spec$bootstrap_spec$cleaned_up <- TRUE