In sbalci/histopathology-template: Template of R Codes Used in Histopathology Research.

Codes for generating hypothesis tests.^[See childRmd/_15hypothesisTests.Rmd file for other codes]

Hypothesis Tests

Tests of Normality

dlookr::normality(carseats)
dlookr::normality(carseats, Sales, CompPrice, Income)
dlookr::normality(carseats, Sales:Income)
dlookr::normality(carseats, -(Sales:Income))
carseats %>%
  dlookr::normality() %>%
  dplyr::filter(p_value <= 0.01) %>% 
  arrange(abs(p_value))
carseats %>%
  group_by(ShelveLoc, US) %>%
  dlookr::normality(Income) %>% 
  arrange(desc(p_value))
carseats %>%
  mutate(log_income = log(Income)) %>%
  group_by(ShelveLoc, US) %>%
  dlookr::normality(log_income) %>%
  dplyr::filter(p_value > 0.01)

dlookr::plot_normality(carseats, Sales, CompPrice)
carseats %>%
  dplyr::filter(ShelveLoc == "Good") %>%
  group_by(US) %>%
  dlookr::plot_normality(Income)

jamovi

mytable <- jmv::ttestIS(
    formula = Age ~ Sex,
    data = mydata,
    vars = Age,
    students = FALSE,
    mann = TRUE,
    norm = TRUE,
    meanDiff = TRUE,
    desc = TRUE,
    plots = TRUE)

cat("<pre class='jamovitable'>")
print(jtable(mytable$ttest))
cat("</pre>")

Categorical

categ <- dlookr::target_by(carseats, US)
cat_cat <- dlookr::relate(categ, ShelveLoc)
cat_cat
summary(cat_cat)
plot(cat_cat)

Chi-Square Cramer Association Predictive Power

## Summary statistics of categorical variables
SmartEDA::ExpCatStat(
  Carseats,
  Target = "Urban",
  result = "Stat",
  clim = 10,
  nlim = 5,
  Pclass = "Yes"
)

inspectdf::inspect_cat(star_1, star_2)

Continious

num <- dlookr::target_by(carseats, Sales)
num_num <- dlookr::relate(num, Price)
num_num
summary(num_num)
plot(num_num)
plot(num_num, hex_thres = 350)

https://stat.ethz.ch/R-manual/R-devel/library/stats/html/t.test.html

t.test(mtcars$mpg ~ mtcars$am) %>% report::report()

report(t.test(iris$Sepal.Length, iris$Petal.Length))

Odds

## Inforamtion value and Odds value
SmartEDA::ExpCatStat(
  Carseats,
  Target = "Urban",
  result = "IV",
  clim = 10,
  nlim = 5,
  Pclass = "Yes"
)

Frequently Used Statistical Tests By Pathologists

Frequently Used Statistical Tests^[Statistical Literacy Among Academic Pathologists: A Survey Study to Gauge Knowledge of Frequently Used Statistical Tests Among Trainees and Faculty. Archives of Pathology & Laboratory Medicine: February 2017, Vol. 141, No. 2, pp. 279-287. https://doi.org/10.5858/arpa.2016-0200-OA] by [@Schmidt2017]