<syntaxhighlight lang="r">library(knitr)

1. figures makde will go to directory called figures, will make them as both png and pdf files

opts_chunk$set(fig.path='figures/',dev=c('png','pdf')) options(scipen = 2, digits = 3)

1. set echo and message to TRUE if you want to display code blocks and code output respectively

knitr::knit_hooks$set(inline = function(x) {

 knitr:::format_sci(x, 'md')

})

superpose.eb <- function (x, y, ebl, ebu = ebl, length = 0.08, ...)

 arrows(x, y + ebu, x, y - ebl, angle = 90, code = 3,
 length = length, ...)

se <- function(x) sd(x, na.rm=T)/sqrt(length(x))

1. load these packages, nearly always needed

library(tidyr) library(dplyr)</syntaxhighlight>

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

<syntaxhighlight lang="r"># sets maize and blue color scheme color.scheme <- c('#00274c', '#ffcb05')</syntaxhighlight>

<syntaxhighlight lang="r">#create seed for reproducibility set.seed(1265) test.data <- tibble(Treatment=c(rep("Experiment",6), rep("Control",6)),

          Result = rnorm(n=12, mean=10, sd=3))

1. test.data$Treatment <- as.factor(test.data$Treatment)

kable(test.data, caption="The test data used in the following examples")</syntaxhighlight>

<syntaxhighlight lang="r">#filter only for the control data control.data <- filter(test.data, Treatment=="Control")

1. The broom package makes the results of the test appear in a table, with the tidy command

library(broom)

1. run the Shapiro-Wilk test on the values

shapiro.test(control.data$Result) %>% tidy %>% kable(caption="Shapiro-Wilk test for normality of control data")</syntaxhighlight>

<syntaxhighlight lang="r">experiment.data <- filter(test.data, Treatment=="Experiment") shapiro.test(test.data$Result) %>% tidy %>% kable(caption="Shapiro-Wilk test for normality of the test data")</syntaxhighlight>

<syntaxhighlight lang="r">#load the car package library(car)</syntaxhighlight>

Loading required package: carData

Attaching package: 'car'

The following object is masked from 'package:dplyr':

    recode

<syntaxhighlight lang="r">#runs the test, grouping by the Treatment variable leveneTest(Result ~ Treatment, data=test.data) %>% tidy %>% kable(caption="Levene's test on test data")</syntaxhighlight>

Warning in leveneTest.default(y = y, group = group, ...): group coerced to
factor.

<syntaxhighlight lang="r">#The default for t.test in R is Welch's, so you need to set the var.equal variable to be TRUE t.test(Result~Treatment,data=test.data, var.equal=T) %>% tidy %>% kable(caption="Student's t test for test data")</syntaxhighlight>

<syntaxhighlight lang="r">#The default for t.test in R is Welch's, so you need to set the var.equal variable to be FALSE, or leave the default t.test(Result~Treatment,data=test.data, var.equal=F) %>% tidy %>% kable(caption="Welch's t test for test data")</syntaxhighlight>

<syntaxhighlight lang="r"># no need to specify anything about variance wilcox.test(Result~Treatment,data=test.data) %>% tidy %>% kable(caption="Mann-Whitney test for test data")</syntaxhighlight>

<syntaxhighlight lang="r">p.values <- c(0.023, 0.043, 0.056, 0.421, 0.012) data.frame(unadjusted = p.values, adjusted=p.adjust(p.values, method="BH")) %>%

 kable(caption="Effects of adjusting p-values by the method of Benjamini-Hochberg")</syntaxhighlight>

<syntaxhighlight lang="r">sessionInfo()</syntaxhighlight>

R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Detroit
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] car_3.1-2     carData_3.0-5 broom_1.0.6   dplyr_1.1.4   tidyr_1.3.1  
[6] knitr_1.48   

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5       cli_3.6.3         rlang_1.1.4       xfun_0.47        
 [5] purrr_1.0.2       generics_0.1.3    jsonlite_1.8.8    glue_1.7.0       
 [9] backports_1.5.0   htmltools_0.5.8.1 fansi_1.0.6       rmarkdown_2.28   
[13] abind_1.4-8       evaluate_0.24.0   tibble_3.2.1      fastmap_1.2.0    
[17] yaml_2.3.10       lifecycle_1.0.4   compiler_4.4.1    htmlwidgets_1.6.4
[21] pkgconfig_2.0.3   rstudioapi_0.16.0 digest_0.6.37     R6_2.5.1         
[25] tidyselect_1.2.1  utf8_1.2.4        pillar_1.9.0      magrittr_2.0.3   
[29] withr_3.0.1       tools_4.4.1