Hotfix/issue 80 sdm likelihood evaluation explodes for extremely high kappa

R/bmm_model_sdmSimple.R

@@ -108,9 +108,13 @@ configure_model.sdmSimple <- function(model, data, formula) {
      # fix mu to 0 (when I change mu to be the center, not c)
      brms::prior_("constant(0)", class = "Intercept", dpar = "mu")
 
+   # set initial values to be sampled between [-1,1] to avoid extreme SDs that
+   # can cause the sampler to fail // TODO: test extensively if this works in
+   # all cases
+   init = 1
 
    # return the list
-   out <- nlist(formula, data, family, prior, stanvars)
+   out <- nlist(formula, data, family, prior, stanvars, init)
    return(out)
 }
 

R/fit_model.R

@@ -89,12 +89,11 @@ fit_model <- function(formula, data, model, parallel = FALSE, chains = 4, prior
 
   # estimate the model
   dots <- list(...)
-  fit_args <- c(config_args, opts, dots)
+  fit_args <- combine_args(nlist(config_args, opts, dots))
   fit <- call_brm(fit_args)
 
   # model postprocessing
   fit <- postprocess_brm(model, fit)
 
   return(fit)
 }
-

R/utils.R

@@ -131,3 +131,23 @@ call_brm <- function(fit_args) {
   }
   return(fit)
 }
+
+
+# function to ensure that if the user wants to overwrite an argument (such as
+# init), they can
+combine_args <- function(args) {
+  config_args <- args$config_args
+  opts <- args$opts
+  dots <- args$dots
+  if (is.null(dots)) {
+    return(c(config_args, opts))
+  }
+  for (i in names(dots)) {
+    if (not_in(i, c('family'))) {
+      config_args[[i]] <- dots[[i]]
+    } else {
+      stop('You cannot provide a family argument to fit_model. Please use the model argument instead.')
+    }
+  }
+  c(config_args, opts)
+}