From 77dc95dacfc315032f9a82fd15d2c028fb330afd Mon Sep 17 00:00:00 2001
From: xec-cm <fcatala@irsicaixa.es>
Date: Thu, 27 Jul 2023 09:32:20 +0200
Subject: [PATCH] Update corncob.R

---
 R/corncob.R | 41 +++++++++++++++++++++--------------------
 1 file changed, 21 insertions(+), 20 deletions(-)

diff --git a/R/corncob.R b/R/corncob.R
index cc63ca8..0eeb7d0 100644
--- 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."),