Update corncob.R

MicrobialGenomics-IrsicaixaOrg · Jul 27, 2023 · 77dc95d · 77dc95d
1 parent 5972240
commit 77dc95d
Showing 1 changed file with 21 additions and 20 deletions.
diff --git a/R/corncob.R b/R/corncob.R
@@ -236,28 +236,29 @@ run_corncob <- function(rec,
             dplyr::filter(!!dplyr::sym(var) %in% comparison) %>% 
             dplyr::pull(sample_id) %>% 
             phyloseq::prune_samples(phy)
-
-          corncob_res <- rlang::catch_cnd(
-            corncob::differentialTest(
-              formula = glue::glue("~ { var }") %>% stats::formula(),
-              data = f_phy,
-              phi.formula = phi.formula,
-              formula_null = formula_null,
-              phi.formula_null = phi.formula_null,
-              link = link,
-              phi.link = phi.link,
-              test = test,
-              boot = boot,
-              B = 10e4,
-              filter_discriminant = filter_discriminant,
-              fdr_cutoff = Inf,
-              fdr = fdr
-            )
-          )
 
+          corncob_res <- 
+            tryCatch({
+              corncob::differentialTest(
+                formula = glue::glue("~ { var }") %>% stats::formula(),
+                data = f_phy,
+                phi.formula = phi.formula,
+                formula_null = formula_null,
+                phi.formula_null = phi.formula_null,
+                link = link,
+                phi.link = phi.link,
+                test = test,
+                boot = boot,
+                B = 10e4,
+                filter_discriminant = filter_discriminant,
+                fdr_cutoff = Inf,
+                fdr = fdr
+              )
+            }, error = function(e) { conditionMessage(e) })
+
           ## Skip error for no convergenc
-          if (is(corncob_res, "error")) {
-            if (stringr::str_detect(corncob_res$message, "failed to converge")) {
+          if (!is(corncob_res, "differentialTest")) {
+            if (stringr::str_detect(corncob_res, "failed to converge")) {
               rlang::abort(c(
                 glue::glue("{crayon::bgMagenta('corncob')}: All models failed to converge!"),
                 glue::glue("{crayon::bgMagenta('corncob')}: If you are seeing this, it is likely that your model is overspecified. This occurs when your sample size is not large enough to estimate all the parameters of your model. This is most commonly due to categorical variables that include many categories."),