From da1c02694e0fabcd0092f469b5a617641b285e16 Mon Sep 17 00:00:00 2001
From: Givanna Putri <ghar1821@users.noreply.github.com>
Date: Sat, 25 May 2024 08:24:30 +1000
Subject: [PATCH] redo docs

---
 .github/workflows/check-standard.yaml | 2 +-
 R/BatchAdjust.R                       | 9 ++++-----
 R/do.add.cols.R                       | 1 -
 R/do.zscore.R                         | 3 +--
 R/read.spatial.files.R                | 1 -
 man/do.add.cols.Rd                    | 7 +++++--
 man/do.zscore.Rd                      | 4 ++++
 man/run.pca.Rd                        | 6 +++---
 8 files changed, 18 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
index 99a0a486..90f6e6e4 100644
--- a/.github/workflows/check-standard.yaml
+++ b/.github/workflows/check-standard.yaml
@@ -30,7 +30,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v2
+      # - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
diff --git a/R/BatchAdjust.R b/R/BatchAdjust.R
index 3730f863..e0a6e753 100755
--- a/R/BatchAdjust.R
+++ b/R/BatchAdjust.R
@@ -1,8 +1,7 @@
-#' BatchAdjust
-#' 
-#' Functions provided for BatchAdjust
-#' 
-#' @export
+# BatchAdjust
+# 
+# Functions provided for BatchAdjust
+# 
 
 ######## Version from https://github.com/i-cyto/CytofBatchAdjust/edit/master/BatchAdjust.R to allow on windows
 
diff --git a/R/do.add.cols.R b/R/do.add.cols.R
index 491a04ac..0624dd5c 100755
--- a/R/do.add.cols.R
+++ b/R/do.add.cols.R
@@ -198,7 +198,6 @@ do.add.cols <- function(dat, # the list of dataframes (samples) where each dataf
 #'
 #' @references \url{https://sydneycytometry.org.au/spectre}.
 #'
-#' @examples
 #'
 #' @import data.table
 #'
diff --git a/R/do.zscore.R b/R/do.zscore.R
index 072fe11d..a8a067a7 100755
--- a/R/do.zscore.R
+++ b/R/do.zscore.R
@@ -10,8 +10,7 @@
 #' @return Returns a new data.table with z-score calculations for each selected column
 #'
 #' @examples
-# res <- do.zscore(dat = Spectre::demo.sum,
-#                  use.cols = names(Spectre::demo.sum)[c(4:15)])
+#' res <- do.zscore(dat = Spectre::demo.sum, use.cols = names(Spectre::demo.sum)[c(4:15)])
 #' 
 #' @import data.table
 #'
diff --git a/R/read.spatial.files.R b/R/read.spatial.files.R
index 462663a5..d2c03533 100755
--- a/R/read.spatial.files.R
+++ b/R/read.spatial.files.R
@@ -10,7 +10,6 @@
 #'
 #' @return Returns a list of spatial data objects.
 #'
-#' @examples
 #'
 #' @import data.table
 #'
diff --git a/man/do.add.cols.Rd b/man/do.add.cols.Rd
index 62e0b6a2..8ac9e50d 100644
--- a/man/do.add.cols.Rd
+++ b/man/do.add.cols.Rd
@@ -26,10 +26,13 @@ Returns the data.table with new columns embedded.
 do.add.cols
 }
 \examples{
-add.dt <- data.table('Files' = unique(Spectre::demo.asinh$FileName),
+
+dat <- Spectre::demo.clustered[,1:19]
+
+add.dt <- data.table('Files' = unique(dat$FileName),
                      'SampleNumber' = c(1:12))
 
-cell.dat <- do.add.cols(dat = Spectre::demo.asinh,
+cell.dat <- do.add.cols(dat = dat,
                         base.col = "FileName",
                         add.dat = add.dt,
                         add.by = "Files")
diff --git a/man/do.zscore.Rd b/man/do.zscore.Rd
index 57f4abcc..3e7e1293 100644
--- a/man/do.zscore.Rd
+++ b/man/do.zscore.Rd
@@ -21,3 +21,7 @@ Returns a new data.table with z-score calculations for each selected column
 \description{
 do.zscore - Calculate z.score for a dataset
 }
+\examples{
+res <- do.zscore(dat = Spectre::demo.sum, use.cols = names(Spectre::demo.sum)[c(4:15)])
+
+}
diff --git a/man/run.pca.Rd b/man/run.pca.Rd
index d5aba273..98c82986 100644
--- a/man/run.pca.Rd
+++ b/man/run.pca.Rd
@@ -112,20 +112,20 @@ Spectre::run.pca(dat = Spectre::demo.clustered,
                  )
         
 # When prompted, type in "5" and click enter to continue function 
-(this selects the elbow point based off the scree plot)
+# (this selects the elbow point based off the scree plot)
 
 ## Possible issues ##
 # Remove any NA present
 na.omit(dat)
 
 # Remove columns that have zero variance (e.g. if MFI is the same for all 
-samples for a marker)
+# samples for a marker)
 dat <- data.table::as.data.table(dat)
 dat <- dat[ , lapply(.SD, function(v) if(data.table::uniqueN(v, na.rm = TRUE) > 1) v)] 
 
 
 # Ellipses are only generated in 'plot.ind.group' when there are at least 
-2 samples per group ('group.ind')
+# 2 samples per group ('group.ind')
 
 }
 \author{