From b364dd5445375ede755efce66edcfb4a2a5a48b7 Mon Sep 17 00:00:00 2001 From: sebastiz Date: Sat, 28 Sep 2019 09:18:29 +0000 Subject: [PATCH 1/2] Updated documentation --- docs/reference/BarrettsBxQual.html | 10 ++++---- docs/reference/EndoBasicGraph.html | 14 +++++++----- docs/reference/PatientFlow_CircosPlots.html | 8 +++++-- docs/reference/index.html | 4 +--- docs/reference/sanity.html | 16 ++++++++----- docs/reference/scale_colour_Publication.html | 8 +++++-- docs/reference/scale_fill_Publication.html | 24 ++++++++------------ docs/reference/theme_Publication.html | 8 +++++-- man/BarrettsBxQual.Rd | 5 ++-- man/EndoBasicGraph.Rd | 9 ++++---- man/PatientFlow_CircosPlots.Rd | 4 +++- man/sanity.Rd | 8 ++++--- man/scale_colour_Publication.Rd | 4 +++- man/scale_fill_Publication.Rd | 10 ++++---- man/theme_Publication.Rd | 4 +++- 15 files changed, 78 insertions(+), 58 deletions(-) diff --git a/docs/reference/BarrettsBxQual.html b/docs/reference/BarrettsBxQual.html index 9cc504d..5c8177a 100644 --- a/docs/reference/BarrettsBxQual.html +++ b/docs/reference/BarrettsBxQual.html @@ -34,11 +34,12 @@ - +of biopsies being taken. The output is the shortfall per endoscopist" /> @@ -160,11 +161,12 @@

Get the number of Barrett's biopsies taken

-

This function gets the biopsies taken per endoscopy and compares to the +

This function gets the number of biopsies taken per +endoscopy and compares it to the Prague score for that endoscopy.Endoscopists should be taking a certain number of biopsies given the length of a Barrett's segment so it should be straightforward to detect a shortfall in the number -of biopsies being taken.

+of biopsies being taken. The output is the shortfall per endoscopist

diff --git a/docs/reference/EndoBasicGraph.html b/docs/reference/EndoBasicGraph.html index fbf2be4..052c15e 100644 --- a/docs/reference/EndoBasicGraph.html +++ b/docs/reference/EndoBasicGraph.html @@ -34,7 +34,8 @@ - + @@ -156,7 +157,8 @@

Basic graph creation using the template specified in theme_Publication.

-

This creates a basic graph using the template specified in theme_Publication.

+

This creates a basic graph using the template specified in theme_Publication. +It takes a numeric column and plots it against any non-numeric x axis in a ggplot

@@ -171,7 +173,7 @@

Arg xdata -

The Time column

+

The x column

number @@ -181,13 +183,13 @@

Arg

Value

-

Myplot the EDA final plot

+

Myplot This is the final plot

Myplot

Examples

- 
# This function plot numeric y vs non-numeric x
-# Get some numeric columns eg number of biopsies and size
+    
# This function plots numeric y vs non-numeric x
+# Get some numeric columns e.g. number of biopsies and size
 Mypath$Size <- HistolBxSize(Mypath$Macroscopicdescription)
 Mypath$NumBx <- HistolNumbOfBx(Mypath$Macroscopicdescription, "specimen")
 Mypath2 <- Mypath[, c("NumBx", "Size")]
diff --git a/docs/reference/PatientFlow_CircosPlots.html b/docs/reference/PatientFlow_CircosPlots.html
index 741ef7c..a791bdc 100644
--- a/docs/reference/PatientFlow_CircosPlots.html
+++ b/docs/reference/PatientFlow_CircosPlots.html
@@ -35,7 +35,9 @@
 
 
 
+type of procedure to another using circos plots. A good example of it's 
+use might be to see how patients move from one state (e.g. having an
+EMR), to another state (e.g. undergoing RFA)" />
 
 
 
@@ -158,7 +160,9 @@ 
Create a Circos plot for patient flow

     

     
     
This allows us to look at the overall flow from one
-type of procedure to another using circos plots.

+type of procedure to another using circos plots. A good example of it's 
+use might be to see how patients move from one state (e.g. having an
+EMR), to another state (e.g. undergoing RFA)

     
     

 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index feba95d..62eafad 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -493,9 +493,7 @@ 
scale_fill_Publication() 

         
-        
#' Set the fill theme for all the ggplots
-#'
-#'

+        
Set the fills for all the ggplots

       
         
         
diff --git a/docs/reference/sanity.html b/docs/reference/sanity.html
index a1517de..e2d44dd 100644
--- a/docs/reference/sanity.html
+++ b/docs/reference/sanity.html
@@ -34,9 +34,11 @@
   
 
 
-
+
 
 
 
@@ -158,9 +160,11 @@ 
Create a basic consort diagram from dataframes

 
     

     
-    
The idea of the package is that it creates a consort diagram using 
-diagrammeR but all the dataframes are automatically filled with the dataframes
-in the script. The user just provides a pathname for the script

+    
This function creates a consort diagram using 
+diagrammeR by assessing all of the dataframes in your script
+and populating each box in the consort diagram with the 
+number of rows in each dataframe as well as how the dataframes are linked
+together. The user just provides a pathname for the script

     
     

 
diff --git a/docs/reference/scale_colour_Publication.html b/docs/reference/scale_colour_Publication.html
index d482460..4ec7d74 100644
--- a/docs/reference/scale_colour_Publication.html
+++ b/docs/reference/scale_colour_Publication.html
@@ -34,7 +34,9 @@
   
 
 
-
+
 
 
 
@@ -156,7 +158,9 @@ 
Set the colour theme for all the ggplots

 
     

     
-    
Set the colour theme for all the ggplots

+    
This standardises the colours for any ggplot plot produced.
+If you do use it, like all ggplots it can be extended using the 
+"+" to add whatever else is necessary

     
     

 
diff --git a/docs/reference/scale_fill_Publication.html b/docs/reference/scale_fill_Publication.html
index 65e2c89..58fcad4 100644
--- a/docs/reference/scale_fill_Publication.html
+++ b/docs/reference/scale_fill_Publication.html
@@ -6,9 +6,7 @@
 
 
 
-#' Set the fill theme for all the ggplots
-#'
-#' — scale_fill_Publication • EndoMineR
+Set the fills for all the ggplots — scale_fill_Publication • EndoMineR
 
 
 
@@ -34,13 +32,11 @@
 
   
   
-
+
 
-
+
 
 
 
@@ -155,18 +151,16 @@
 

   

     

-    
#' Set the fill theme for all the ggplots
-#'
-#'

+    
Set the fills for all the ggplots

     Source: R/Graphics.R
     
     

 
     

     
-    
#' Set the fill theme for all the ggplots
-#'
-#'

+    
This standardises the fills for any ggplot plot produced.
+If you do use it, like all ggplots it can be extended using the 
+"+" to add whatever else is necessary

     
     

 
diff --git a/docs/reference/theme_Publication.html b/docs/reference/theme_Publication.html
index e9f49c1..e8e2521 100644
--- a/docs/reference/theme_Publication.html
+++ b/docs/reference/theme_Publication.html
@@ -34,7 +34,9 @@
   
 
 
-
+
 
 
 
@@ -156,7 +158,9 @@ 
Set the publication theme for all the ggplots

 
     

     
-    
Set the publication theme for all the ggplots

+    
This standardises the theme for any ggplot plot produced.
+If you do use it, like all ggplots it can be extended using the 
+"+" to add whatever else is necessary

     
     

 
diff --git a/man/BarrettsBxQual.Rd b/man/BarrettsBxQual.Rd
index e22fa11..9647857 100644
--- a/man/BarrettsBxQual.Rd
+++ b/man/BarrettsBxQual.Rd
@@ -16,11 +16,12 @@ BarrettsBxQual(dataframe, Endo_ResultPerformed, PatientID, Endoscopist)
 \item{Endoscopist}{name of the column with the Endoscopist names}
 }
 \description{
-This function gets the biopsies taken per endoscopy and compares to the
+This function gets the number of biopsies taken per 
+endoscopy and compares it to the
 Prague score for that endoscopy.Endoscopists should be taking a certain
 number of biopsies given the length of a Barrett's segment so it
 should be straightforward to detect a shortfall in the number
-of biopsies being taken.
+of biopsies being taken. The output is the shortfall per endoscopist
 }
 \examples{
 # Firstly relevant columns are extrapolated from the
diff --git a/man/EndoBasicGraph.Rd b/man/EndoBasicGraph.Rd
index 95bb38b..05d7156 100644
--- a/man/EndoBasicGraph.Rd
+++ b/man/EndoBasicGraph.Rd
@@ -9,21 +9,22 @@ EndoBasicGraph(dataframe, xdata, number)
 \arguments{
 \item{dataframe}{dataframe}
 
-\item{xdata}{The Time column}
+\item{xdata}{The x column}
 
 \item{number}{The numeric column}
 }
 \value{
-Myplot the EDA final plot
+Myplot This is the final plot
 
 Myplot
 }
 \description{
 This creates a basic graph using the template specified in theme_Publication.
+It takes a numeric column and plots it against any non-numeric x axis in a ggplot
 }
 \examples{
-# This function plot numeric y vs non-numeric x
-# Get some numeric columns eg number of biopsies and size
+# This function plots numeric y vs non-numeric x
+# Get some numeric columns e.g. number of biopsies and size
 Mypath$Size <- HistolBxSize(Mypath$Macroscopicdescription)
 Mypath$NumBx <- HistolNumbOfBx(Mypath$Macroscopicdescription, "specimen")
 Mypath2 <- Mypath[, c("NumBx", "Size")]
diff --git a/man/PatientFlow_CircosPlots.Rd b/man/PatientFlow_CircosPlots.Rd
index dd9b52f..e849d89 100644
--- a/man/PatientFlow_CircosPlots.Rd
+++ b/man/PatientFlow_CircosPlots.Rd
@@ -20,7 +20,9 @@ any dscription of a procedure you desire)}
 }
 \description{
 This allows us to look at the overall flow from one
-type of procedure to another using circos plots.
+type of procedure to another using circos plots. A good example of it's 
+use might be to see how patients move from one state (e.g. having an
+EMR), to another state (e.g. undergoing RFA)
 }
 \examples{
 # This function builds a circos plot which gives a more aggregated
diff --git a/man/sanity.Rd b/man/sanity.Rd
index 43455fe..b46d713 100644
--- a/man/sanity.Rd
+++ b/man/sanity.Rd
@@ -10,9 +10,11 @@ sanity(pathName)
 \item{pathName}{The string in the Indication to search for}
 }
 \description{
-The idea of the package is that it creates a consort diagram using 
-diagrammeR but all the dataframes are automatically filled with the dataframes
-in the script. The user just provides a pathname for the script
+This function creates a consort diagram using 
+diagrammeR by assessing all of the dataframes in your script
+and populating each box in the consort diagram with the 
+number of rows in each dataframe as well as how the dataframes are linked
+together. The user just provides a pathname for the script
 }
 \examples{
 #pathName<-paste0(here::here(),"/inst/TemplateProject/munge/PreProcessing.R")
diff --git a/man/scale_colour_Publication.Rd b/man/scale_colour_Publication.Rd
index 9286843..8b67242 100644
--- a/man/scale_colour_Publication.Rd
+++ b/man/scale_colour_Publication.Rd
@@ -7,7 +7,9 @@
 scale_colour_Publication(...)
 }
 \description{
-Set the colour theme for all the ggplots
+This standardises the colours for any ggplot plot produced.
+If you do use it, like all ggplots it can be extended using the 
+"+" to add whatever else is necessary
 }
 \examples{
 # None needed
diff --git a/man/scale_fill_Publication.Rd b/man/scale_fill_Publication.Rd
index 1549ee5..a843d3d 100644
--- a/man/scale_fill_Publication.Rd
+++ b/man/scale_fill_Publication.Rd
@@ -2,16 +2,14 @@
 % Please edit documentation in R/Graphics.R
 \name{scale_fill_Publication}
 \alias{scale_fill_Publication}
-\title{#' Set the fill theme for all the ggplots
-#'
-#'}
+\title{Set the fills for all the ggplots}
 \usage{
 scale_fill_Publication(...)
 }
 \description{
-#' Set the fill theme for all the ggplots
-#'
-#'
+This standardises the fills for any ggplot plot produced.
+If you do use it, like all ggplots it can be extended using the 
+"+" to add whatever else is necessary
 }
 \examples{
 # None needed
diff --git a/man/theme_Publication.Rd b/man/theme_Publication.Rd
index 266e67d..348b0c8 100644
--- a/man/theme_Publication.Rd
+++ b/man/theme_Publication.Rd
@@ -12,7 +12,9 @@ theme_Publication(base_size = 14, base_family = "Helvetica")
 \item{base_family}{the base family}
 }
 \description{
-Set the publication theme for all the ggplots
+This standardises the theme for any ggplot plot produced.
+If you do use it, like all ggplots it can be extended using the 
+"+" to add whatever else is necessary
 }
 \examples{
 # None needed

From c52da165a33eba371c2b7bdb45a3f4adba5bc9a4 Mon Sep 17 00:00:00 2001
From: sebastiz 
Date: Sat, 28 Sep 2019 09:37:30 +0000
Subject: [PATCH 2/2] seealso tag introduced

---
 R/Module_Barretts.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/Module_Barretts.R b/R/Module_Barretts.R
index 9747da8..1a1a0cb 100644
--- a/R/Module_Barretts.R
+++ b/R/Module_Barretts.R
@@ -262,6 +262,7 @@ Barretts_FUType <- function(dataframe, CStage, MStage, IMorNoIM) {
 #' @importFrom dplyr case_when
 #' @export
 #' @return Newdf
+#' @seealso [Barretts_PragueScore()] [Barretts_PathStage()] [Barretts_FUType()]
 #' @examples
 #' Barretts_df <- BarrettsAll(Myendo, "Findings", "OGDReportWhole", Mypath, "Histology")
 BarrettsAll <- function(Endodataframe, EndoReportColumn, EndoReportColumn2, Pathdataframe, PathColumn) {