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Bland Altman Plot and initial report #42

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Bland Altman Plot and initial report
claudiavidalc Feb 6, 2024
8c9d214
Merge branch 'main' into claudia
ernestguevarra Feb 6, 2024
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22 changes: 22 additions & 0 deletions exercise1.R
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Original file line number Diff line number Diff line change
@@ -1,5 +1,27 @@
library(ggplot2)

ba = read.table("https://raw.githubusercontent.com/OxfordIHTM/teaching_datasets/main/ba.dat",header=TRUE)

average = rowMeans(ba)
ba$average = average
#Mean differences
difference <- ba$Wright - ba$Mini
ba$difference = difference
mean_difference = mean(difference)

#Confidence interval
lower <- mean_difference - 1.96*sd(ba$difference)
upper <- mean_difference + 1.96*sd(ba$difference)
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Good job here! Well done! This si a good example of a scripts-based approach to calculating all the elements that you need for creating a Bland and Altman plot.

I will add it here as a solution but this doesn't fully answer my task/issue because I was asking for a function. And the examples from Mariano and Clifford below is what I was really looking for.


#Create Bland Altman Plot
ggplot(ba, aes(x = average, y = difference)) +
geom_point() +
geom_hline(yintercept = mean_difference) +
geom_hline(yintercept = lower, color = "red", linetype="dashed") +
geom_hline(yintercept = upper, color = "red", linetype="dashed") +
ylab("PEFR (l/min) Mini Wright meter - Wright meter ") +
xlab("PEFR (l/min) Mini Wright meter + Wright meter / 2")
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Great! Amazing! Good work with the plot using ggplot. Well done!

Again, if I were to be strict with this task, my specific requirement was to create a function. Your script here is a good example of how to script the creation of a ggplot. I was wondering if you would like a challenge in converting this to a function?


BandA =function(W,M){
meanD=mean(abs(W-M))
SDD=sd(abs(W-M))
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37 changes: 37 additions & 0 deletions exercise1.Rmd
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Expand Up @@ -13,4 +13,41 @@ knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)

library(ggplot2)
ba = read.table("https://raw.githubusercontent.com/OxfordIHTM/teaching_datasets/main/ba.dat",header=TRUE)

average = rowMeans(ba)
ba$average = average

#Mean differences
difference <- ba$Wright - ba$Mini
ba$difference = difference
mean_difference = mean(difference)

#Confidence interval
lower <- mean_difference - 1.96*sd(ba$difference)
upper <- mean_difference + 1.96*sd(ba$difference)
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Good approach here for copying your script form the R file to this part of the RMarkdown. Well done!

```

# Task 4: Report

## 1. Table of the mean and difference of per subject measurements made by the Wright and the Mini-Wright



## 2. Bland and Altman plot
```{r plot}
plot = ggplot(ba, aes(x = average, y = difference)) +
geom_point() +
geom_hline(yintercept = mean_difference) +
geom_hline(yintercept = lower, color = "red", linetype="dashed") +
geom_hline(yintercept = upper, color = "red", linetype="dashed") +
ylab("PEFR (l/min) Mini Wright meter - Wright meter ") +
xlab("PEFR (l/min) Mini Wright meter + Wright meter / 2")

plot
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Good stuff! Good use of the code chunk and placement of plotting code inside.

My only main feedback and this is rather important so I will have to ask you to edit this before I approve it.

Here, you assigned the output of your ggplot script into an object called plot. The word plot is also the name of a function in R called plot. So, whilst the code will not cause an error, any code after you run these lines that needs/uses the plot function will not work properly anymore because within your code, the environment has changed and that plot is not a function anymore but an plotting object.

Generally, we try to avoid using a name of an existing function as an object name to store outputs. So I would suggest renaming this to maybe ba_plot instead.

Does this make sense?

```

## 3. Discussion of the findings with regard to the agreement between the Wright and Mini-Wright tools.

22 changes: 22 additions & 0 deletions exercise1.md
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# Task 4: Report

## 1. Table of the mean and difference of per subject measurements made by the Wright and the Mini-Wright

## 2. Bland and Altman plot

``` r
plot = ggplot(ba, aes(x = average, y = difference)) +
geom_point() +
geom_hline(yintercept = mean_difference) +
geom_hline(yintercept = lower, color = "red", linetype="dashed") +
geom_hline(yintercept = upper, color = "red", linetype="dashed") +
ylab("PEFR (l/min) Mini Wright meter - Wright meter ") +
xlab("PEFR (l/min) Mini Wright meter + Wright meter / 2")

plot
```

![](exercise1_files/figure-gfm/plot-1.png)<!-- -->

## 3. Discussion of the findings with regard to the agreement between the Wright and Mini-Wright tools.
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