example2.R
## ----message=FALSE, warning=FALSE, include=FALSE-------------------------
library(bayestestR)
data(iris)
library(knitr)
options(knitr.kable.NA = '')
knitr::opts_chunk$set(comment=">")
knitr::opts_chunk$set(dpi=300)
options(digits=2)
set.seed(333)
## ----message=FALSE, warning=FALSE, eval=TRUE-----------------------------
result <- cor.test(iris$Sepal.Width, iris$Sepal.Length)
result
## ----message=FALSE, warning=FALSE, results='hide'------------------------
library(BayesFactor)
result <- correlationBF(iris$Sepal.Width, iris$Sepal.Length)
## ----message=FALSE, warning=FALSE, eval=FALSE----------------------------
# describe_posterior(result)
## ----echo=FALSE----------------------------------------------------------
structure(list(Parameter = "rho", Median = -0.114149129692488,
CI = 89, CI_low = -0.240766308855643, CI_high = 0.00794997655649642,
pd = 91.6, ROPE_CI = 89, ROPE_low = -0.1, ROPE_high = 0.1,
ROPE_Percentage = 42.0949171581017, BF = 0.509017511647702,
Prior_Distribution = "cauchy", Prior_Location = 0, Prior_Scale = 0.333333333333333), row.names = 1L, class = "data.frame")
## ----message=FALSE, warning=FALSE, eval=TRUE-----------------------------
bayesfactor(result)
## ----echo=FALSE, fig.cap="Wagenmakers' pizza poking analogy. From the great 'www.bayesianspectacles.org' blog.", fig.align='center', out.width="100%"----
knitr::include_graphics("https://github.com/easystats/easystats/raw/master/man/figures/bayestestR/LetsPokeAPizza.jpg")
## ----message=FALSE, warning=FALSE, eval=TRUE-----------------------------
library(see)
plot(bayesfactor(result)) +
scale_fill_pizza()
## ----message=FALSE, warning=FALSE, eval=TRUE-----------------------------
library(dplyr)
library(ggplot2)
# Select only two relevant species
data <- iris %>%
filter(Species != "setosa") %>%
droplevels()
# Visualise distributions and observations
data %>%
ggplot(aes(x = Species, y = Sepal.Width, fill = Species)) +
geom_violindot(fill_dots = "black", size_dots = 1) +
scale_fill_material() +
theme_modern()
## ----message=FALSE, warning=FALSE----------------------------------------
result <- BayesFactor::ttestBF(formula = Sepal.Width ~ Species, data = data)
describe_posterior(result)
## ----message=FALSE, warning=FALSE, eval=FALSE----------------------------
# library(rstanarm)
#
# model <- stan_glm(Species ~ Sepal.Width, data = data, family = "binomial")
## ----message=FALSE, warning=FALSE, echo=FALSE----------------------------
library(rstanarm)
model <- stan_glm(Species ~ Sepal.Width, data = data, family = "binomial", refresh = 0)
## ----message=FALSE, warning=FALSE----------------------------------------
library(performance)
model_performance(model)
## ----message=FALSE, warning=FALSE----------------------------------------
describe_posterior(model, test = c("pd", "ROPE", "BF"))
## ----message=FALSE, warning=FALSE----------------------------------------
# plot(rope(result))