Package ‘cureplots’

December 6, 2023
Type Package
Title CURE (Cumulative Residual) Plots
Version 1.1.0
Description Creates 'ggplot2' Cumulative Residual (CURE) plots to check the goodness-of-
fit of a count model; or the tables to create a customized version. A dataset of crashes in Wash-
ington state is available for illustrative purposes.
License AGPL (>= 3)
Encoding UTF-8
LazyData true

URL https://github.com/gbasulto/cureplots,
https://gbasulto.github.io/cureplots/

BugReports https://github.com/gbasulto/cureplots/issues
Imports dplyr, ggplot2, glue
RoxygenNote 7.2.3
Depends R (>= 2.10)
Suggests testthat (>= 3.0.0)
Config/testthat/edition 3
Language en-US
NeedsCompilation no
Author Jonathan Wood [aut] (<https://orcid.org/0000-0003-0131-6384>),
Guillermo Basulto-Elias [aut, cre]
(<https://orcid.org/0000-0002-5205-2190>)
Maintainer Guillermo Basulto-Elias <[email protected]>
Repository CRAN
Date/Publication 2023-12-06 00:50:03 UTC

1
2 calculate_cure_dataframe

R topics documented:
calculate_cure_dataframe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
cure_plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
resample_residuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
washington_roads . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Index 7

calculate_cure_dataframe
Calculate CURE Dataframe

Description
Calculate CURE Dataframe

Usage
calculate_cure_dataframe(covariate_values, residuals)

Arguments
covariate_values
name to be plot. With or without quotes.
residuals Residuals.

Value
A data frame with five columns: independent variable, residuals, cumulative residuals, lower confi-
dence interval limit, and upper confidence interval limit.

Examples
set.seed(2000)

## Define parameters
beta <- c(-1, 0.3, 3)

## Simulate independent variables

n <- 900
AADT <- c(runif(n, min = 2000, max = 150000))
nlanes <- sample(x = c(2, 3, 4), size = n, replace = TRUE)
LNAADT <- log(AADT)

## Simulate dependent variable

theta <- exp(beta[1] + beta[2] * LNAADT + beta[3] * nlanes)
y <- rpois(n, theta)

## Fit model
cure_plot 3

mod <- glm(y ~ LNAADT + nlanes, family = poisson)

## Calculate residuals
res <- residuals(mod, type = "working")

## Calculate CURE plot data

cure_df <- calculate_cure_dataframe(AADT, res)

head(cure_df)

cure_plot CURE Plot

Description
CURE Plot

Usage
cure_plot(x, covariate = NULL, n_resamples = 0)

Arguments
x Either a data frame produced with calculate_cure_dataframe, in that case,
the first column is used to produce CURE plot; or regression model for count
data (e.g., Poisson) adjusted with glm or gam.
covariate Required when x is model fit.
n_resamples Number of resamples to overlay on CURE plot. Zero is the default.

Value
A CURE plot generated with ggplot2.

Examples
## basic example code

set.seed(2000)

## Define parameters
beta <- c(-1, 0.3, 3)

## Simulate independent variables

n <- 900
AADT <- c(runif(n, min = 2000, max = 150000))
nlanes <- sample(x = c(2, 3, 4), size = n, replace = TRUE)
LNAADT <- log(AADT)

## Simulate dependent variable

4 resample_residuals

theta <- exp(beta[1] + beta[2] * LNAADT + beta[3] * nlanes)

y <- rpois(n, theta)

## Fit model
mod <- glm(y ~ LNAADT + nlanes, family = poisson)

## Calculate residuals
res <- residuals(mod, type = "working")

## Calculate CURE plot data

cure_df <- calculate_cure_dataframe(AADT, res)

head(cure_df)

## Providing CURE data frame

cure_plot(cure_df)

## Providing glm object

cure_plot(mod, "LNAADT")

## Providing glm object adding resamples cumulative residuals

cure_plot(mod, "LNAADT", n_resamples = 3)

resample_residuals Resample residuals

Description
Resample residuals to compute several cumulative residual curves. Receives the covariate values,
residuals and number of samples and shuffles (i.e., samples without replacement a vector of the
same size) the residuals, and returns a stacked data frame.

Usage
resample_residuals(covariate_values, residuals, n_resamples)

Arguments
covariate_values
Covariate values.
residuals Residuals.
n_resamples Number of times to sample the residuals.

Value
Data frame of stacked
washington_roads 5

Examples
library(cureplots)
library(ggplot2)
## basic example
set.seed(2000)
## Define parameters.
beta <- c(-1, 0.3, 3)
## Simulate independent variables
n <- 900
AADT <- c(runif(n, min = 2000, max = 150000))
nlanes <- sample(x = c(2, 3, 4), size = n, replace = TRUE)
LNAADT <- log(AADT)
## Simulate dependent variable
theta <- exp(beta[1] + beta[2] * LNAADT + beta[3] * nlanes)
y <- rpois(n, theta)
## Fit model
mod <- glm(y ~ LNAADT + nlanes, family = poisson)
## Calculate residuals
res <- residuals(mod, type = "working")
## Calculate CURE plot data
cure_df <- calculate_cure_dataframe(AADT, res)
resampled_residuals_tbl <- resample_residuals(AADT, res, n_resamples = 3)
ggplot(data = cure_df) +
aes(AADT, cumres) +
geom_line(
data = resampled_residuals_tbl,
aes(group = sample),
col = "grey"
) +
geom_line(color = "darkgreen", linewidth = 0.8) +
geom_line(
aes(y = lower),
color = "magenta",
linetype = "dashed",
linewidth = 0.8) +
geom_line(
aes(y = upper),
color = "blue",
linetype = "dashed",
linewidth = 0.8) +
theme_bw()

washington_roads Washington Road Crashes

Description
Crashes on Washington primary roads from 2016, 2017, and 2018. Data acquired from Washington
Department of Transportation through the Highway Safety Information System (HSIS).
6 washington_roads

Usage
washington_roads

Format
The data frame washington_roads has 1,501 rows and 9 columns:
ID Anonymized road ID. Factor.
Year Year. Integer.
AADT Annual Average Daily Traffic (AADT). Double.
Length Segment length in miles. Double.
Total_crashes Total crashes. Integer.
lnaadt Natural logarithm of AADT. Double.
lnlength Natural logarithm of length in miles. Double.
speed50 Indicator of whether the speed limit is 50 mph or greater. Binary.
ShouldWidth04 Indicator of whether the shoulder is 4 feet or wider. Binary.

Source
<https://highways.dot.gov/research/safety/hsis>
Index

∗ datasets
washington_roads, 5

calculate_cure_dataframe, 2, 3
cure_plot, 3

gam, 3
glm, 3

resample_residuals, 4

washington_roads, 5