fix minor issues in document and examples in last release

R/help.R

@@ -26,9 +26,7 @@
 #' Before creating a new issue, 
 #' please read the guideline (\href{https://chiliubio.github.io/microeco_tutorial/notes.html#github-issues}{https://chiliubio.github.io/microeco_tutorial/notes.html#github-issues}).
 #' 
-#' To cite microeco package in publications, please run the following command to get the reference: \code{citation("microeco")}\cr
-#' To read the paper, please turn to the publication website 
-#' (\href{https://academic.oup.com/femsec/article/97/2/fiaa255/6041020}{https://academic.oup.com/femsec/article/97/2/fiaa255/6041020}).
+#' To cite microeco package in publications, please run the following command to get the reference: \code{citation("microeco")}
 #' 
 #' Reference:\cr
 #' Chi Liu, Yaoming Cui, Xiangzhen Li and Minjie Yao. 2021. microeco: an R package for data mining in microbial community ecology. 

R/trans_diff.R

@@ -1448,7 +1448,7 @@ trans_diff <- R6Class(classname = "trans_diff",
 		#' @param annotation_shape_size default 5; size used in the annotation legend.
 		#' @return ggplot.
 		#' @examples
-		#' \donttest{
+		#' \dontrun{
 		#' t1$plot_diff_cladogram(use_taxa_num = 100, use_feature_num = 30, select_show_labels = NULL)
 		#' }
 		plot_diff_cladogram = function(

R/trans_func.R

@@ -72,7 +72,6 @@ trans_func <- R6Class(classname = "trans_func",
 		#' @examples
 		#' \donttest{
 		#' t1$cal_spe_func(prok_database = "FAPROTAX")
-		#' t1$cal_spe_func(fungi_database = "FungalTraits")
 		#' }
 		cal_spe_func = function(
 			prok_database = c("FAPROTAX", "NJC19")[1],