Added note for reproducibility

Brief explanation given to run the code if the audit is to be auditable

audit-snippets.Rmd

@@ -1,16 +1,22 @@
 ---
 title: "Code Snippets Audit"
-output: html_notebook
+output:
+  html_document:
+    df_print: paged
 ---
 
 
+
+
+<!--This code imports the data from a validly labelled and named csv file, runs mathematical calculations on the data, and also generates charts to present the data. It is provided with my audit for reproducibility purposes if necessary. It requires the 'R' runtime environment to work and Rstudio is the recommended program to run it. -->
+
 # collection of snippets for the data collection
 
 # Setup and calculations
 
 
 
-```{r setup, include=FALSE, echo=FALSE}
+```{r setup, include=TRUE, echo=TRUE}
 library(readr)
 library(ggplot2)
 library(dplyr)
@@ -299,7 +305,7 @@ FinalIncluded <- nrow(HtnDataold[HtnDataold$Inclusion_Crit == 1, ])
 # Flow Chart
 
 
-```{r flowchart, include=TRUE, echo=FALSE, fig.cap="Case Selection for Kimberley Hypertension Audit of 2022 Patients"}
+```{r flowchart, include=TRUE, echo=TRUE, fig.cap="Case Selection for Kimberley Hypertension Audit of 2022 Patients"}
 # Define ineligibles, all others defined before
 Ineligibles <- nrow(HtnDataold) - FinalIncluded
 
@@ -341,7 +347,7 @@ ggflowchart(
 
 # Table of age categories
 
-```{r tableofage, echo=FALSE, include=TRUE, warning=FALSE, fig.cap='Age Distribution of Patient Sample', fig.pos ='H', message=FALSE}
+```{r tableofage, echo=TRUE, include=TRUE, warning=FALSE, fig.cap='Age Distribution of Patient Sample', fig.pos ='H', message=FALSE}
 library(kableExtra)
 # Summarise data
 AgeTable <- HtnData %>% 
@@ -366,7 +372,7 @@ kable(AgeTable, digits = 2, caption = "Age distribution of Patient Sample", alig
 # Converting variables to in text references
 
 
-```{r calculatingstandards-results, echo=FALSE}
+```{r calculatingstandards-results, echo=TRUE}
 
 OldSt1Text <- round(mean(as.numeric(HtnData$Old_Std_1_Met)) * 100, 1)
 OldSt2Text <- round(mean(as.numeric(HtnData$Old_Std_2_Met)) * 100, 1)
@@ -378,7 +384,7 @@ OldASt2Text <- mean(as.numeric(HtnData$Old_audit_Std_2_Met)) * 100
  
 # Bar graph comparing previous and current audit results
 
-```{r bargraphStandardOld, echo=FALSE, include=TRUE, fig.cap="Comparison of Previous and Present Audit Based on Previous Standard"}
+```{r bargraphStandardOld, echo=TRUE, include=TRUE, fig.cap="Comparison of Previous and Present Audit Based on Previous Standard"}
 # Unite the columns into one dataframe
 standards <- HtnData %>%
   select(Old_Std_1_Met, Old_Std_2_Met, Old_audit_Std_1_Met, Old_audit_Std_2_Met) %>%
@@ -409,7 +415,7 @@ ggplot(standards, aes(x = Standard_No, y = Percentage, fill = Condition)) +
 
 # New standard Pie Chart
 
-```{r newstandard1, echo=FALSE, include=TRUE, fig.cap = "Proportion Of Present Audit Adherence With Standard 1"}
+```{r newstandard1, echo=TRUE, include=TRUE, fig.cap = "Proportion Of Present Audit Adherence With Standard 1"}
 generate_pie_chart <- function(data, column, title) {
   # Count TRUE and FALSE instances
   counts <- table(data[[column]])
@@ -453,7 +459,7 @@ print(newstandard1)
 
 # Baseline investigations 
 
-```{r AdherenceBaselineFull, echo=FALSE, include=TRUE, fig.cap="Adherence to Standard for Baseline Investigations"}
+```{r AdherenceBaselineFull, echo=TRUE, include=TRUE, fig.cap="Adherence to Standard for Baseline Investigations"}
 
 
 columns_to_run <- c("HbA1c" = "HbA1c", "Lipid" = "Lipids", "U_E" = "U&Es", "Dip_Urine" = "Urine Dipstick", "ACR_Urine" = "Urine ACR")
@@ -505,7 +511,7 @@ ggplot(adherence_inv_perc, aes(x = pretty_label, y = adherence, fill = color)) +
   
 # Other management bar graph
 
-```{r OtherManagement, include=TRUE, echo=FALSE, fig.cap="Adherence of Remaining Criteria"}
+```{r OtherManagement, include=TRUE, echo=TRUE, fig.cap="Adherence of Remaining Criteria"}
 
 # Calculate adherence
 counts_715 <- table(HtnData$c715_Check)
@@ -542,7 +548,7 @@ print(p)
 
 # Standard 2 Pie chart
 
-```{r newstandard2, echo=FALSE, include=TRUE, fig.cap="Proportion of Present Audit Adherence with Standard 2"}
+```{r newstandard2, echo=TRUE, include=TRUE, fig.cap="Proportion of Present Audit Adherence with Standard 2"}
 generate_pie_chart <- function(data, column, title) {
   # Get proportions of true and false
   counts <- table(data[[column]])
@@ -585,7 +591,7 @@ print(newstandard1)
 
 # Follow up criteria
 
-```{r followupfinal, include=TRUE, echo=FALSE, fig.cap="Adherence to Criteria for Followup"}
+```{r followupfinal, include=TRUE, echo=TRUE, fig.cap="Adherence to Criteria for Followup"}
 # Calculate adherence to followup
 HtnData$initial_flwp <- (HtnData$c3_MO_RVW_LFSTL | HtnData$c2_4_WK_RVW_ACE)
 HtnData$complete_followup_adherence <- HtnData$initial_flwp & HtnData$c3_MO_FLWP_STBL_WITHNA & HtnData$c6_MO_BP
@@ -631,7 +637,7 @@ ggplot(adherence_flwp_perc, aes(x = pretty_label, y = adherence, fill = pretty_l
 
 # More in text references for variables
 
-```{r calculatingstandards-discussion, echo=FALSE}
+```{r calculatingstandards-discussion, echo=TRUE}
 
 OldSt1Text <- round(mean(as.numeric(HtnData$Old_Std_1_Met)) * 100)
 OldSt2Text <- round(mean(as.numeric(HtnData$Old_Std_2_Met)) * 100)
@@ -655,7 +661,7 @@ texturin <- round(sum(counts_urin["TRUE"]) /sum(counts_urin) * 100, 1)
 
 ## Action Plan
 
-```{r actionplan, echo=FALSE, include=TRUE, message=FALSE, fig.pos ='H', fig.cap="Action Plan following 2023 Audit of Adherence to Kimberley Hypertension Guidelines"}
+```{r actionplan, echo=TRUE, include=TRUE, message=FALSE, fig.pos ='H', fig.cap="Action Plan following 2023 Audit of Adherence to Kimberley Hypertension Guidelines"}
 
 library(readxl)
 library(kableExtra)
@@ -674,4 +680,10 @@ kableExtra::kable(df, format = "latex", booktabs = TRUE, linesep = "\\addlinespa
 ```
 
 
+Copyright 2023 Liam Jones
 
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.