From 662dae1025ba80c0634fde204c2ea62726770877 Mon Sep 17 00:00:00 2001
From: Casey Novak <cnovak@nd.edu>
Date: Fri, 19 Nov 2021 12:43:55 -0500
Subject: [PATCH 1/2] Version of code from after tutorial class

---
 Exercise9.R | 43 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 Exercise9.R

diff --git a/Exercise9.R b/Exercise9.R
new file mode 100644
index 0000000..dd74298
--- /dev/null
+++ b/Exercise9.R
@@ -0,0 +1,43 @@
+# Exercise 09 
+
+setwd("~/Desktop/Fall-2021/Biocomputing")
+# Name of function and arguments
+
+dir="~/Desktop/Fall-2021/Biocomputing/Biocomp_tutorial11/Example/"
+column=1
+
+# Takes directory as argument, specifies which column from each file to be used in calculations 
+exercise9 <- function(dir, column, rows=50, override=FALSE){
+# Reads data from each file in the specified directory
+  file_list <- list.files(path=dir) # This function assumes that all of the files in the directory are .csv files 
+  results<-NA
+  for (i in 1:length(file_list)){
+    data <- read.table(file_list[i])
+    if(nrow(data)<rows){
+      print("Error because number of rows in file does not meet the minimum requirement.")
+      if (override==TRUE){
+        # Save data and calculate coefficient of variation 
+        stdev <- sd(data[,column])
+        mean <- mean(data$column[i]==column)
+        print("Coefficient of variation will be added to results even though file did not meet row requirement.")
+        results <- c(results, (stdev/mean))
+      }else{
+        results <- c(results, NA) 
+        }
+    }else{
+      # Calculate the standard deviation 
+      stdev <- sd(data[,column])
+      mean <- mean(data$column[i]==column)
+      results <- c(results, (stdev/mean))
+    } 
+  }
+  return(results[-1])
+}
+
+
+  
+
+
+
+
+# Create directory with two csv files and have one column for each 
\ No newline at end of file

From 911bfee7ad87c0afb818b27985f89e499ae256b9 Mon Sep 17 00:00:00 2001
From: Casey Novak <cnovak@nd.edu>
Date: Fri, 19 Nov 2021 17:17:45 -0500
Subject: [PATCH 2/2] Final answers for exercise 9

---
 Exercise9.R | 39 +++++++++++++++++----------------------
 1 file changed, 17 insertions(+), 22 deletions(-)

diff --git a/Exercise9.R b/Exercise9.R
index dd74298..e6c0971 100644
--- a/Exercise9.R
+++ b/Exercise9.R
@@ -1,43 +1,38 @@
 # Exercise 09 
 
-setwd("~/Desktop/Fall-2021/Biocomputing")
+setwd("~/Desktop/Fall-2021/Biocomputing/Biocomp_tutorial11")
 # Name of function and arguments
 
-dir="~/Desktop/Fall-2021/Biocomputing/Biocomp_tutorial11/Example/"
-column=1
-
-# Takes directory as argument, specifies which column from each file to be used in calculations 
+# Takes a directory path and column number, default arguments are set for rows and override 
 exercise9 <- function(dir, column, rows=50, override=FALSE){
 # Reads data from each file in the specified directory
   file_list <- list.files(path=dir) # This function assumes that all of the files in the directory are .csv files 
-  results<-NA
-  for (i in 1:length(file_list)){
+  results<-NA # Creates results vector 
+  for(i in 1:length(file_list)){ 
     data <- read.table(file_list[i])
-    if(nrow(data)<rows){
-      print("Error because number of rows in file does not meet the minimum requirement.")
-      if (override==TRUE){
-        # Save data and calculate coefficient of variation 
+    if(nrow(data)<rows){ # Tests whether the number of rows in each file meets the specified row requirement
+      print(paste0("Error because number of rows in ", file_list[i], " does not meet the minimum requirement."))
+      if (override==TRUE){ # If override is true, then the coefficient of standard deviation will still be calculated 
+        print(paste0("Coefficient of variation for ", file_list[i], " will be added to results vector even though file did not meet row requirement."))
         stdev <- sd(data[,column])
-        mean <- mean(data$column[i]==column)
-        print("Coefficient of variation will be added to results even though file did not meet row requirement.")
+        mean <- mean(data[,column])
         results <- c(results, (stdev/mean))
-      }else{
+      }else{ # If override is false and rows do not meet the requirement, NA will be added to the results vector 
         results <- c(results, NA) 
         }
     }else{
-      # Calculate the standard deviation 
+      # If rows are greater than 50, add the coefficient of standard deviation to the results vector for each file 
       stdev <- sd(data[,column])
-      mean <- mean(data$column[i]==column)
+      mean <- mean(data[,column])
       results <- c(results, (stdev/mean))
     } 
   }
   return(results[-1])
 }
 
-
+# Call function 
+## Give path to directory for dir argument
+## Give number of column for column argument 
+## Optional to change default number of rows and override
+exercise9(dir,column)
   
-
-
-
-
-# Create directory with two csv files and have one column for each 
\ No newline at end of file