Date repository last updated: February 01, 2023
Overview
The sparrpowR
package is a suite of R
functions to calculate the statistical power to detect clusters using
the kernelbased spatial relative risk function that is estimated using
the sparr
package. Basic visualization is also supported.
Installation
To install the release version from CRAN:
install.packages("sparrpowR")
To install the development version from GitHub:
devtools::install_github("machielalab/sparrpowR")
Available functions
Function  Description 

spatial_power

Main function. Compute the statistical power of a spatial relative risk function using randomly generated data. 
spatial_data

Generate random bivariate data for a spatial relative risk function. 
jitter_power

Compute the statistical power of a spatial relative risk function using previously collected data. 
spatial_plots

Easily make multiple plots from spatial_power ,
spatial_data , and jitter_power outputs.

pval_correct

Called within spatial_power and jitter_power ,
calculates various multiple testing corrections for the alpha level.

Authors
Ian D. Buller  Social & Scientific Systems, Inc., a division of DLH Corporation, Silver Spring, Maryland (current)  Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland (original)  GitHub  ORCID
Derek W. Brown  Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland (original)  GitHub  ORCID
See also the list of contributors who participated in this package, including:
set.seed(1234) # for reproducibility
#  #
# Necessary packages #
#  #
library(sparrpowR)
library(spatstat.geom)
library(stats)
#  #
# Run spatial_power #
#  #
# Circular window with radius 0.5
# Uniform case sampling within a disc of radius of 0.1 at the center of the window
# Complete Spatial Randomness control sampling
# 20% prevalence (n = 300 total locations)
# Statistical power to detect both case and control relative clustering
# 100 simulations (more recommended for power calculation)
< spatstat.geom::disc(radius = 0.5, centre = c(0.5,0.5))
unit.circle
< sparrpowR::spatial_power(win = unit.circle,
foo sim_total = 100,
x_case = 0.5,
y_case = 0.5,
samp_case = "uniform",
samp_control = "CSR",
r_case = 0.1,
n_case = 50,
n_control = 250)
#  #
# Outputs from iterations #
#  #
# Mean and standard deviation of simulated sample sizes and bandwidth
::mean(foo$n_con); stats::sd(foo$n_con) # controls
stats::mean(foo$n_cas); stats::sd(foo$n_cas) # cases
stats::mean(foo$bandw); stats::sd(foo$bandw) # bandwidth of case density (if fixed, same for control density)
stats
# Global Test Statistics
## Global maximum relative risk: Null hypothesis is mu = 1
::t.test(x = foo$s_obs, mu = 0, alternative = "two.sided")
stats
## Integral of log relative risk: Null hypothesis is mu = 0
::t.test(x = foo$t_obs, mu = 1, alternative = "two.sided")
stats
#  #
# Run spatial_plots #
#  #
# Statistical power for caseonly clustering (onetailed test)
::spatial_plots(foo) sparrpowR
# Statistical power for case clustering and control
clustering (twotailed test)
## Only showing second and third plot
sparrpowR::spatial_plots(foo, cascon = TRUE)
#  #
# Multiple Testing Correction #
#  #
# Same parameters as above
# Apply a conservative Bonferroni correction
set.seed(1234) # reset RNG
# Run spatial_power()
foo < sparrpowR::spatial_power(win = unit.circle,
sim_total = 100,
x_case = 0.5,
y_case = 0.5,
samp_case = "uniform",
samp_control = "CSR",
r_case = 0.1,
n_case = 50,
n_control = 250,
alpha = 0.05,
p_correct = "Bonferroni")
median(foo$alpha) # critical pvalue of 3e6
# Run spatial_plots() for caseonly clustering
## Only showing third plot
sparrpowR::spatial_plots(foo, cascon = TRUE)
This package was developed while the authors were originally postdoctoral fellows supported by the Cancer Prevention Fellowship Program at the National Cancer Institute. Any modifications since December 05, 2022 were made while the author I.D.B. was an employee of Social & Scientific Systems, Inc., a division of DLH Corporation.
When citing this package for publication, please follow:
citation("sparrpowR")
For questions about the package please contact the maintainer Dr. Ian D. Buller or submit a new issue.