Small corrections if start_levels are specified

seroanalytics · May 17, 2024 · e8c7313 · e8c7313
1 parent 7aa296a
commit e8c7313
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Showing 2 changed files with 14 additions and 5 deletions.
diff --git a/R/plot_antibody_model.R b/R/plot_antibody_model.R
@@ -168,10 +168,15 @@ plot_model_fits <- function(chain, infection_histories,
       possible_exposure_times <- possible_exposure_times_tmp
     }
   } 
-
+  if(class(start_level) == "character"){
   start_levels <- create_start_level_data(antibody_data %>% 
                                             dplyr::filter(individual %in% individuals),start_level,FALSE) %>% 
                                             dplyr::arrange(individual, biomarker_group, sample_time, biomarker_id, repeat_number)
+  } else if(class(start_level) %in% c("tibble","data.frame")){
+    start_levels <- start_levels
+  } else {
+    start_levels <- NULL
+  }
   ## Generate antibody predictions
   antibody_preds <- get_antibody_level_predictions(
     chain, infection_histories, antibody_data, 
@@ -417,9 +422,14 @@ plot_antibody_predictions <- function(chain, infection_histories,
       possible_exposure_times <- possible_exposure_times_tmp
     }
   } 
-
-  start_levels <- create_start_level_data(antibody_data,start_level,FALSE) %>% 
+  if(class(start_level) == "character"){
+    start_levels <- create_start_level_data(antibody_data,start_level,FALSE) %>% 
     dplyr::arrange(individual, biomarker_group, sample_time, biomarker_id, repeat_number)
+  } else if(class(start_level) %in% c("tibble","data.frame")){
+    start_levels <- start_levels
+  } else {
+    start_levels <- NULL
+  }
   ## Generate antibody predictions
   x <- get_antibody_level_predictions(
     chain, infection_histories, antibody_data, individuals=unique(antibody_data$individual),

diff --git a/R/posteriors.R b/R/posteriors.R
@@ -76,8 +76,7 @@ create_posterior_func <- function(par_tab,
       if(verbose) message(cat("Note: no biomarker_group detected in measurement_bias Assuming all biomarker_group as 1.\n"))
       measurement_bias$biomarker_group <- 1
     }
-
-    if(verbose){
+    if(verbose & any(class(start_level) == "character")){
       message(cat("Setting starting antibody levels based on data using command:", start_level, "; and randomizing starting antibody levels set to:", start_level_randomize, "\n"))
     }