diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
index a83061b..f2c6f3b 100644
--- a/.github/workflows/rworkflows.yml
+++ b/.github/workflows/rworkflows.yml
@@ -32,10 +32,6 @@ jobs:
           cont: ~
           rspm: ~
     steps:
-    - name: Install Conda (macOS)
-      if: ${{ matrix.config.os == 'macOS-latest' }}
-      run: |
-        brew install zlib
     - uses: neurogenomics/rworkflows@master
       with:
         run_bioccheck: ${{ false }}
diff --git a/man/conservative_idr.Rd b/man/conservative_idr.Rd
index 6d3e2e6..d6c508e 100644
--- a/man/conservative_idr.Rd
+++ b/man/conservative_idr.Rd
@@ -24,15 +24,14 @@ files.}
 \item{is_paired}{Logical, specifying whether or not the BAM file is
 paired-end.}
 
-\item{idr_stringent}{Logical relating to the IDR threshold. If set to TRUE
-then the threshold used by IDR is 0.01. If set to FALSE then the threshold
-is 0.05. The default is TRUE.}
+\item{idr_stringent}{Logical. If set to TRUE then the threshold used by IDR
+is 0.01. If set to FALSE then the threshold is 0.05. The default is TRUE.}
 
 \item{out_dir}{Character specifying the name of the output directory in which
 a subdirectory containing the output files will be created.}
 
 \item{subdir_name}{Character specifying the name of the subdirectory that the
-output files will be written to.}
+output files will be placed.}
 
 \item{...}{
   Arguments passed on to \code{\link[MACSr:callpeak]{MACSr::callpeak}}
@@ -109,6 +108,5 @@ to the output files.
 }
 \description{
 \code{conservative_idr()} performs the conservative IDR analysis as defined
-by ENCODE. The function writes output files to a subdirectory in the
-specified \code{out_dir}.
+by ENCODE. The function writes a filtered set of peaks to a desired location.
 }
diff --git a/man/feature_counts_matrix.Rd b/man/feature_counts_matrix.Rd
index f6de09c..8e898ea 100644
--- a/man/feature_counts_matrix.Rd
+++ b/man/feature_counts_matrix.Rd
@@ -2,17 +2,16 @@
 % Please edit documentation in R/feature_counts_matrix.R
 \name{feature_counts_matrix}
 \alias{feature_counts_matrix}
-\title{Generate a featureCounts matrix for a set of peaks}
+\title{Generate a featureCounts matrix for a peak set}
 \usage{
-feature_counts_matrix(peak_file, treat_files)
+feature_counts_matrix(peak_file, bam_files)
 }
 \arguments{
 \item{peak_file}{Path to the peak file.}
 
-\item{treat_files}{Character vector of paths to the BAM files that the peak
-file is derived from.}
+\item{bam_files}{Path to the BAM file(s) that the peak file was derived from.}
 }
 \description{
 \code{feature_counts_matrix()} computes the number of reads from a BAM file
-that fall within the ranges of a peak within a set.
+that fall within each peak of your peak set.
 }
diff --git a/man/filter_bam.Rd b/man/filter_bam.Rd
index 9f8204f..07b5a81 100644
--- a/man/filter_bam.Rd
+++ b/man/filter_bam.Rd
@@ -7,12 +7,11 @@
 filter_bam(bam_file, out_dir)
 }
 \arguments{
-\item{bam_file}{Path to a paired-end BAM file}
+\item{bam_file}{Path to a paired-end BAM file.}
 
-\item{out_dir}{Path to where the output filtered BAM file will be written.}
+\item{out_dir}{Path to where the filtered BAM file will be written.}
 }
 \description{
-For Tn5-based methods like CUT&Tag and TIPseq, we recommend filtering
-paired-end BAM files to exclude the second mate in the read pair.
-If the BAM file does not have and index please run
+\code{filter_bam()} filters a paired-end BAM file to exclude the second
+mate in the read pair. The result is a single-ended BAM file.
 }
diff --git a/man/generate_pseudoreplicates.Rd b/man/generate_pseudoreplicates.Rd
index 21b003c..bcaa5c8 100644
--- a/man/generate_pseudoreplicates.Rd
+++ b/man/generate_pseudoreplicates.Rd
@@ -30,8 +30,8 @@ Generate pseudoreplicate BAM files
 \dontrun{
 pooled_bam <- testthat::test_path("testdata", "merged_treatment.bam")
 generate_pseudoreplicates(bam_file = pooled_bam,
-                          out_dir = tempdir(),
                           is_paired = FALSE,
-                          is_control = FALSE)
+                          is_control = FALSE,
+                          out_dir = tempdir())
                           }
 }
diff --git a/man/multiple_replicates_chipr.Rd b/man/multiple_replicates_chipr.Rd
index 2c34f6a..8f4eca7 100644
--- a/man/multiple_replicates_chipr.Rd
+++ b/man/multiple_replicates_chipr.Rd
@@ -7,8 +7,8 @@
 multiple_replicates_chipr(
   treat_files,
   control_files = NULL,
-  is_paired = FALSE,
-  out_dir = tempdir(),
+  is_paired,
+  out_dir,
   subdir_name = "chipr_analysis",
   minentries = 2,
   rankmethod = "pvalue",
@@ -34,7 +34,7 @@ paired-end.}
 a subdirectory containing the output files will be created.}
 
 \item{subdir_name}{Character specifying the name of the subdirectory that the
-output files will be written to.}
+output files will be placed.}
 
 \item{minentries}{The minimum number of intersections a given peak must
 satisfy.}
diff --git a/man/multiple_replicates_mspc.Rd b/man/multiple_replicates_mspc.Rd
index 2d222cd..df06a22 100644
--- a/man/multiple_replicates_mspc.Rd
+++ b/man/multiple_replicates_mspc.Rd
@@ -35,7 +35,7 @@ paired-end.}
 a subdirectory containing the output files will be created.}
 
 \item{subdir_name}{Character specifying the name of the subdirectory that the
-output files will be written to.}
+output files will be placed.}
 
 \item{replicateType}{Character string. This argument defines
 the replicate type. Possible values of the argument : 
@@ -146,7 +146,9 @@ A list containing a summary of the MSPC along with the path to the
 output files.
 }
 \description{
-\code{multiple_replicates_mspc()} is a wrapper of the MSPC function.
+\code{multiple_replicates_mspc()} runs multiple sample peak calling from the
+rmspc package. The function handles an arbitrary number of biological
+replicates.
 }
 \examples{
 \dontrun{
diff --git a/man/optimal_idr.Rd b/man/optimal_idr.Rd
index 066da64..8ae88fd 100644
--- a/man/optimal_idr.Rd
+++ b/man/optimal_idr.Rd
@@ -24,15 +24,14 @@ files.}
 \item{is_paired}{Logical, specifying whether or not the BAM file is
 paired-end.}
 
-\item{idr_stringent}{Logical relating to the IDR threshold. If set to TRUE
-then the threshold used by IDR is 0.01. If set to FALSE then the threshold
-is 0.05. The default is TRUE.}
+\item{idr_stringent}{Logical. If set to TRUE then the threshold used by IDR
+is 0.01. If set to FALSE then the threshold is 0.05. The default is TRUE.}
 
 \item{out_dir}{Character specifying the name of the output directory in which
 a subdirectory containing the output files will be created.}
 
 \item{subdir_name}{Character specifying the name of the subdirectory that the
-output files will be written to.}
+output files will be placed.}
 
 \item{...}{
   Arguments passed on to \code{\link[MACSr:callpeak]{MACSr::callpeak}}
@@ -108,6 +107,6 @@ Summary of the IDR output
 }
 \description{
 \code{optimal_idr()} runs the optimal IDR analysis. This involves pooling of
-the biological replicate BAM files, shuffling the reads splitting into
-pseudoreplicates.
+biological replicate BAM files, shuffling reads, splitting into
+pseudoreplicates and calling peaks on the pseudoreplicates.
 }
diff --git a/tests/testthat/test-feature_counts_matrix.R b/tests/testthat/test-feature_counts_matrix.R
index c7b04a7..2d15535 100644
--- a/tests/testthat/test-feature_counts_matrix.R
+++ b/tests/testthat/test-feature_counts_matrix.R
@@ -10,7 +10,7 @@ test_that("Filtered BAM file is created in the desired location", {
                       package = "ConsensusPeak")
 
   result <- feature_counts_matrix(peak_file = peak,
-                                  treat_files = c(treat_1, treat_2)
+                                  bam_files = c(treat_1, treat_2)
                                   )
 
   # Check if the feature counts matrix is created