inst/doc/introduction.R

In OddsPlotty: Odds Plot to Visualise a Logistic Regression Model

## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----inv_odds_plot------------------------------------------------------------
library(OddsPlotty)


## ----load_pack----------------------------------------------------------------
library(mlbench)
library(caret)
library(tibble)
library(ggplot2)
library(OddsPlotty)
library(e1071)
library(ggthemes)


## ----data---------------------------------------------------------------------
data("BreastCancer", package = "mlbench")
#Use complete cases of breast cancer
breast <- BreastCancer[complete.cases(BreastCancer), ] #Create a copy
breast <- breast[, -1]
head(breast, 10)
#Convert the class to a factor - Beningn (0) and Malignant (1)
breast$Class <- factor(breast$Class)
str(breast)


## ----data_loop----------------------------------------------------------------
for(i in 1:9) {
  breast[, i] <- as.numeric(as.character(breast[, i]))
}
#Loops through the first columns - 1 to 9 and changes them from factors to a numerical representation
str(breast)


## ----train_glm----------------------------------------------------------------
library(caret)
glm_model <- caret::train(Class ~ .,
                   data = breast,
                   method = "glm",
                   family = "binomial")

summary(glm_model)


## ----odds_plot, echo = FALSE--------------------------------------------------
plotty <- OddsPlotty::odds_plot(glm_model$finalModel,
                      title = "Odds Plot",
                      subtitle = "Showing odds of cancer based on various factors")


plotty$odds_plot

## ----oddstibble, echo = FALSE-------------------------------------------------
plotty$odds_data

## ----odds_plot_two, echo = FALSE----------------------------------------------
library(OddsPlotty)
library(ggthemes)
plotty <- OddsPlotty::odds_plot(glm_model$finalModel, 
                      title = "Odds Plot with ggthemes economist",
                      subtitle = "Showing odds of cancer based on various factors",
                      point_col = "#00f2ff",
                      error_bar_colour = "black",
                      point_size = .5,
                      error_bar_width = .8,
                      h_line_color = "red") 

plot <- plotty$odds_plot 
plot <- plot + ggthemes::theme_economist() + theme(legend.position = "NULL")

# Add odds ratios to labels by calling the data list element
# The round function is used to return 2 decimal place values
plot + geom_text(label=round(plotty$odds_plot$data$OR, digits=2), 
                             hjust=0.1, vjust=1, color="navy")


## ----themes-------------------------------------------------------------------
library(OddsPlotty)
library(ggthemes)
plotty <- OddsPlotty::odds_plot(glm_model$finalModel, 
                      title = "Odds Plot with ggthemes Tufte Theme",
                      subtitle = "Showing odds of cancer based on various factors",
                      point_col = "#00f2ff",
                      error_bar_colour = "black",
                      point_size = .5,
                      error_bar_width = .8,
                      h_line_color = "red")

plotty$odds_plot + ggthemes::theme_tufte()


## ----train_glm_tidymodels-----------------------------------------------------
library(tidymodels)
fitted_logistic_model<- logistic_reg() %>%
  # Set the engine
  set_engine("glm") %>%
  # Set the mode - this will always be classification for logstic regression 
  set_mode("classification") %>%
  # Fit the model
  fit(Class ~ ., data = breast)


## ----tm_oddsplot--------------------------------------------------------------
# Create odds plot for TidyModels object
tidy_odds_plot <- OddsPlotty::odds_plot(fitted_logistic_model$fit,
                                        title="TidyModels Odds Plot",
                                        point_col = "#6b95ff",
                                        h_line_color = "red")

# Output plot and data table
tidy_odds_plot$odds_plot + ggthemes::theme_gdocs()+ #Use ggthemes
                    theme(legend.position="none") #Turn off legend

#Generate tibble returning exp(odds) and 

tidy_odds_plot$odds_data