From 30edfa28af01f4600a86a5c5db36e5eb975b3d21 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Feb 2026 17:51:24 +0000
Subject: [PATCH 1/3] Initial plan


From 295b6c59f817cf31a80dfdf8350747b13fa93c09 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Feb 2026 17:52:55 +0000
Subject: [PATCH 2/3] Replace deprecated add_rownames() with
 rownames_to_column()

Co-authored-by: Ulthran <14882396+Ulthran@users.noreply.github.com>
---
 DESCRIPTION        | 3 ++-
 vignettes/zibr.Rmd | 9 +++++----
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6303627..f1021b1 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -20,7 +20,8 @@ Suggests:
     nlme,
     knitr,
     rmarkdown,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    tibble
 Config/testthat/edition: 3
 Depends: 
     R (>= 2.10),
diff --git a/vignettes/zibr.Rmd b/vignettes/zibr.Rmd
index cafcc67..c1bfed5 100755
--- a/vignettes/zibr.Rmd
+++ b/vignettes/zibr.Rmd
@@ -18,6 +18,7 @@ knitr::opts_chunk$set(
 library(ZIBR)
 library(dplyr)
 library(nlme)
+library(tibble)
 
 set.seed(19683)
 ```
@@ -171,14 +172,14 @@ sample.info <- read.csv(sample.info.file, row.names = 1)
 #### Time, antiTNF+EEN
 reg.cov <-
   data.frame(Sample = rownames(taxa.data), stringsAsFactors = FALSE) %>%
-  left_join(add_rownames(sample.info, var = "Sample"), by = "Sample") %>%
+  left_join(rownames_to_column(sample.info, var = "Sample"), by = "Sample") %>%
   dplyr::filter(Treatment.Specific != "PEN") %>%
   dplyr::select(Sample, Time, Subject, Response, Treatment.Specific) %>%
   group_by(Subject) %>%
   summarise(count = n()) %>%
   dplyr::filter(count == 4) %>%
   dplyr::select(Subject) %>%
-  left_join(add_rownames(sample.info, var = "Sample"), by = "Subject") %>%
+  left_join(rownames_to_column(sample.info, var = "Sample"), by = "Subject") %>%
   mutate(Treat = ifelse(Treatment.Specific == "antiTNF", 1, 0)) %>%
   dplyr::select(Sample, Subject, Time, Response, Treat) %>%
   dplyr::mutate(Subject = paste("S", Subject, sep = "")) %>%
@@ -246,14 +247,14 @@ for (spe in spe.all) {
 #### adjust p values
 p.species.zibr <- t(as.data.frame(p.species.list.zibr))
 p.species.zibr.adj <-
-  add_rownames(as.data.frame(p.species.zibr), var = "Species") %>% mutate_each(funs(p.adjust(., "fdr")), -Species)
+  rownames_to_column(as.data.frame(p.species.zibr), var = "Species") %>% mutate_each(funs(p.adjust(., "fdr")), -Species)
 
 # write.csv(p.species.zibr.adj,file=paste('4_Results/Real_Data_Estimation_Results_antiTNF_EEN_ZIBR.csv',sep=''))
 
 
 p.species.lme <- t(as.data.frame(p.species.list.lme))
 p.species.lme.adj <-
-  add_rownames(as.data.frame(p.species.lme), var = "Species") %>% mutate_each(funs(p.adjust(., "fdr")), -Species)
+  rownames_to_column(as.data.frame(p.species.lme), var = "Species") %>% mutate_each(funs(p.adjust(., "fdr")), -Species)
 
 # write.csv(p.species.lme.adj,file=paste('4_Results/Real_Data_Estimation_Results_antiTNF_EEN_LME.csv',sep=''))
 

From 7ec0ac14cb1e59784afcb55a2c7ea21d01a3f4b9 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Feb 2026 20:46:23 +0000
Subject: [PATCH 3/3] Replace deprecated mutate_each() with mutate(across())

Co-authored-by: Ulthran <14882396+Ulthran@users.noreply.github.com>
---
 vignettes/zibr.Rmd | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/vignettes/zibr.Rmd b/vignettes/zibr.Rmd
index c1bfed5..876f038 100755
--- a/vignettes/zibr.Rmd
+++ b/vignettes/zibr.Rmd
@@ -247,14 +247,14 @@ for (spe in spe.all) {
 #### adjust p values
 p.species.zibr <- t(as.data.frame(p.species.list.zibr))
 p.species.zibr.adj <-
-  rownames_to_column(as.data.frame(p.species.zibr), var = "Species") %>% mutate_each(funs(p.adjust(., "fdr")), -Species)
+  rownames_to_column(as.data.frame(p.species.zibr), var = "Species") %>% mutate(across(-Species, ~p.adjust(., "fdr")))
 
 # write.csv(p.species.zibr.adj,file=paste('4_Results/Real_Data_Estimation_Results_antiTNF_EEN_ZIBR.csv',sep=''))
 
 
 p.species.lme <- t(as.data.frame(p.species.list.lme))
 p.species.lme.adj <-
-  rownames_to_column(as.data.frame(p.species.lme), var = "Species") %>% mutate_each(funs(p.adjust(., "fdr")), -Species)
+  rownames_to_column(as.data.frame(p.species.lme), var = "Species") %>% mutate(across(-Species, ~p.adjust(., "fdr")))
 
 # write.csv(p.species.lme.adj,file=paste('4_Results/Real_Data_Estimation_Results_antiTNF_EEN_LME.csv',sep=''))