update Rd files

man/metrics_plot.Rd

@@ -14,7 +14,7 @@ values include "AIC", "BIC", "logLik", "deviance", "df.resid", and
 "dispersion". If \code{NULL}, all available metrics will be plotted.}
 }
 \value{
-A ggplot object displaying density plots for the specified metrics.
+A ggplot object displaying histogram plots for the specified metrics.
 }
 \description{
 This function generates a density plot of the specified metrics for the given

man/simulationReport.Rd

@@ -7,10 +7,10 @@
 simulationReport(
   mock_obj,
   list_tmb = NULL,
-  dds_obj = NULL,
   coeff_threshold = 0,
   alt_hypothesis = "greaterAbs",
-  report_file = NULL
+  report_file = NULL,
+  dds_obj = NULL
 )
 }
 \arguments{
@@ -18,13 +18,13 @@ simulationReport(
 
 \item{list_tmb}{A list of model results.}
 
-\item{dds_obj}{a DESeq2 object}
-
 \item{coeff_threshold}{A threshold for comparing estimates.}
 
 \item{alt_hypothesis}{The alternative hypothesis for comparisons ("greater", "less", "greaterAbs").}
 
 \item{report_file}{File name to save the generated report. If NULL, the report will not be exported.}
+
+\item{dds_obj}{a DESeq2 object}
 }
 \value{
 A list containing settings, plots, and evaluation results.