screenr | R Documentation |
The screenr
package enables construction of binary test-screening
tools. It is designed to enable those with only a basic familiarity with
R
to develop, validate and implement screening tools for diagnostic
tests. screenr
integrates the capabilities of the glm
,
glmpath
and pROC
packages for convenience and ease of use.
Consider the situation where a diagnostic test for some condition is
relatively expensive, and the condition is rare. In that case, universal
testing would not be efficient in terms of the yield of postive results per
test performed. Now suppose that responses to a set of simple screening
questions may be predictive of the condition. Package screenr
enables
estimation of thresholds for making decisions about when to test in order to
screen in/out individuals based on Receiver Operating Characteristics (ROC)
estimated from an initial sample. The choice of a particular screening
threshold is left to the user, and should be based on careful consideration
of application-specific tradeoffs between sensitivity and specificity.
screenr
also enables easy construction of screening tools.
A tutorial is available from vignette("screenr_Tutorial", package = "screenr")
.
The pdf versions of the package manual and the tutorial are available at https://github.com/sgutreuter/screenr.
The high-level functions in the screenr
package are:
lasso_screenr
Selection of logistic models based on GLM path regularization
logreg_screenr
Test-screening based maximum-likelhood estimation of logistic models
gee_screenr
Test-screening based GEE estimation of logistic models accounting for cluster sampling
easy_tool
Easy implementation of test-screening tools
simple_screenr
(Too) simple un-optimized test-screening
rescale_to_int
Rescale a strictly positive vector of real numbers to integers
sens_spec_plus
Sensitivity, specificity and friends
screenr
provides the usual plot
, print
, summary
,
predict
methods for the objects produced by lasso_screenr
,
logreg_screenr
, gee_screenr
, simple_screenr
and
easy_tool
, and also
coef
and confint
methods for lasso_screenr
,
gee_screenr
and logreg_screenr
objects.
screenr
also provides get_what
methods to extract object
components, and ntpp
methods for computation of the average number of
tests required to detect a single positive result and the residual
positivity among those screened out of testing.
The canonical source repository for screenr
is
https://github.com/sgutreuter/screenr
Steve Gutreuter: sgutreuter@gmail.com
Teferi W, Gutreuter S, Bekele A et al. Adapting strategies for effective and efficient pediatric HIV case finding: Risk screening tool for testing children presenting at high-risk entry points. BMC Infectious Diseases. 2022; 22:480. http://doi.org/10.1186/s12879-022-07460-w
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