CODEWITHSUNDEEP
rmarkdownr-markdown
Íris Aníta Eyþórsdóttir
Íris Aníta Eyþórsdóttir

Reputation: 21

How do i embed only certain parts of my R command into R markdown document using `r `?

I am creating a hypothesis test and confidence interval using this command: 

```{r}
t.test(urtak1$fermetraverd ~ urtak1$matssvaedi)
```

And I need to embed the t-value and p-value as well as the confidence interval (seperately) into text for my R markdown document. How do I do this using ' r ' ?

Here is my output: 

Welch Two Sample t-test

data:  urtak1$fermetraverd by urtak1$matssvaedi
t = 1.0812, df = 96.784, p-value = 0.2823
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -12.02648  40.80856
sample estimates:
   mean in group Hagar mean in group Kringlan 
          348.5697               334.1787

Upvotes: 2

Views: 241

Answers (1)

FvD
FvD

Reputation: 3794

You can do this using the broom package. I do not have the data you are using your questione, so I set up something quickly with iris.

In a first chunk you do the analysis and create an object that holds the "tidy" version of your t-test output. For example

```{r}
library(dplyr)
library(broom)

example <- iris %>% 
  filter(Species != "setosa") %>% 
  droplevels()

result <- t.test(example$Sepal.Length ~ example$Species)

tidy_result <- tidy(result)

```

Have a look at tidy_result: the magic of the broom package is that it extracts all the output of your t-test (and many others!) in a tidy dataframe, that you can use elsewhere.

Now you can use this in your text, evaluating r tidy_result$statistic to show your t-statistic and r tidy_result$p.value to show your p-value (the back-ticks are not showing correctly, but should be placed in front of the 'r' expressions in with the tidy_result objects.

In your Rmarkdown it might look like this:

the t-test resulted in a t-statistic of `r tidy_result$statistic` 
with a p-value of `r tidy_result$p.value`

To look at all the parameters you can include, evaluate tidy_result in your console. You will see:

> tidy_result
  estimate estimate1 estimate2 statistic      p.value parameter   conf.low  conf.high                  method alternative
1   -0.652     5.936     6.588 -5.629165 1.866144e-07  94.02549 -0.8819731 -0.4220269 Welch Two Sample t-test   two.sided

So you can choose any of the following:

"estimate"    "estimate1"   "estimate2"   
"statistic"   "p.value"     "parameter"    
"conf.low"    "conf.high"   "method"      "alternative"

Notice that your to get your confidence interval, you have the low (conf.low) and the high (conf.high) value at your disposal.

Upvotes: 1

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