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

Correlation Analysis

Codes for generating correlation analysis.^[See childRmd/_20correlation.Rmd file for other codes]

#  https://easystats.github.io/correlation/
# install.packages("devtools")
# devtools::install_github("easystats/correlation")
library("correlation")

correlation::correlation(iris)

library(dplyr)

iris %>% 
  select(Species, starts_with("Sepal")) %>% 
  group_by(Species) %>% 
  correlation::correlation() %>% 
  filter(r < 0.9)

correlation::correlation(select(iris, Species, starts_with("Sepal")),
            select(iris, Species, starts_with("Petal")),
            partial=TRUE)

correlation(iris, bayesian=TRUE)

library(report)
iris %>% 
  select(starts_with("Sepal")) %>% 
  correlation::correlation(bayesian=TRUE) %>% 
  report()

report::report(cor.test(iris$Sepal.Length, iris$Petal.Length))

https://stat.ethz.ch/R-manual/R-patched/library/stats/html/cor.test.html

iris %>% 
  group_by(Species) %>% 
  correlation() %>% 
  report() %>% 
  to_table()

iris %>% explore(Sepal.Length, Petal.Length)

iris$is_versicolor <- ifelse(iris$Species == "versicolor", 1, 0)
iris %>% explore(Sepal.Length, Petal.Length, target = is_versicolor)

dlookr::correlate(carseats)
dlookr::correlate(carseats, Sales, CompPrice, Income)
dlookr::correlate(carseats, Sales:Income)
dlookr::correlate(carseats, -(Sales:Income))
carseats %>%
  dlookr::correlate(Sales:Income) %>%
  dplyr::filter(as.integer(var1) > as.integer(var2))
carseats %>%
  dplyr::filter(ShelveLoc == "Good") %>%
  group_by(Urban, US) %>%
  dlookr::correlate(Sales) %>%
  dplyr::filter(abs(coef_corr) > 0.5)

dlookr::plot_correlate(carseats)
dlookr::plot_correlate(carseats, Sales, Price)
carseats %>%
  dplyr::filter(ShelveLoc == "Good") %>%
  dplyr::group_by(Urban, US) %>%
  dlookr::plot_correlate(Sales)

## Summary statistics by – overall with correlation
SmartEDA::ExpNumStat(
  Carseats,
  by = "A",
  gp = "Price",
  Qnt = seq(0, 1, 0.1),
  MesofShape = 1,
  Outlier = TRUE,
  round = 2
)

# https://alastairrushworth.github.io/inspectdf/articles/pkgdown/inspect_cor_exampes.html
inspectdf::inspect_cor(storms)

inspectdf::inspect_cor(storms) %>% inspectdf::show_plot()

inspectdf::inspect_cor(storms, storms[-c(1:200), ])

inspectdf::inspect_cor(storms, storms[-c(1:200), ]) %>% 
  slice(1:20) %>%
  inspectdf::show_plot()

https://neuropsychology.github.io/psycho.R/2018/05/20/correlation.html

devtools::install_github("neuropsychology/psycho.R")  # Install the newest version

remove.packages("psycho")
renv::install("neuropsychology/psycho.R@0.4.0")
# devtools::install_github("neuropsychology/psycho.R@0.4.0")

library(psycho)
<!-- library(tidyverse) -->

cor <- psycho::affective %>% 
  correlation()

summary(cor)


plot(cor)


print(cor)

cor %>% 
    report::to_values()

summary(cor) %>% 
  knitr::kable(format = "latex") %>% 
  kableExtra::kable_styling(latex_options="scale_down")


ggplot(mydata, aes(x = tx_zamani_verici_yasi, y = trombosit)) +
  geom_point() + 
  geom_smooth(method = lm, size = 1)

mydata %>%
  select(continiousVariables,
         -dateVariables) %>% 
visdat::vis_cor()

sbalci/histopathology-template documentation built on June 29, 2023, 5:52 a.m.