VRPM: Visualizing Risk Prediction Models

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This is a package to visualize risk prediction models. For each predictor, a color bar represents the contribution to the linear predictor or latent variable. A conversion from the linear predictor to the estimated risk or survival is also given. (Cumulative) contribution charts enable to visualize how the estimated risk for one particular observation is obtained by the model. Several options allow to choose different color maps, and to select the zero level of the contributions. The package is able to deal with 'glm', 'coxph', 'mfp', 'multinom' and 'ksvm' objects. For 'ksvm' objects, the visualization is not always exact. Functions providing tools to indicate the accuracy of the approximation are provided in addition to the visualization.

Author
Vanya Van Belle
Date of publication
2016-09-01 15:41:33
Maintainer
Vanya Van Belle <vanya.vanbelle@esat.kuleuven.be>
License
GPL-3
Version
1.1

View on CRAN

Man pages

ccchart
Cumulative contribution chart.
cchart
Contribution chart.
colplot
Visualize a risk prediction model by means of colored bars.
HTMLsummary
Summarize the risk prediction plots.
plotperf
Performance plots for the approximation of an SVM model.
preplotperf
Preprocess a 'ksvm' object
runVRPMexample
Run R Shiny app

Files in this package

VRPM
VRPM/inst
VRPM/inst/examples
VRPM/inst/examples/HTMLsummaryex.R
VRPM/inst/examples/plotperfex.R
VRPM/inst/examples/colplotex.R
VRPM/inst/examples/cchartex.R
VRPM/inst/examples/ccchartex.R
VRPM/inst/examples/Appex.R
VRPM/inst/NEWS
VRPM/inst/shiny-examples
VRPM/inst/shiny-examples/Iris
VRPM/inst/shiny-examples/Iris/ui.R
VRPM/inst/shiny-examples/Iris/server.R
VRPM/inst/shiny-examples/Iris/lps.png
VRPM/inst/shiny-examples/Iris/colplot.png
VRPM/inst/shiny-examples/Iris/www
VRPM/inst/shiny-examples/Iris/www/empty.png
VRPM/inst/shiny-examples/Iris/probs.png
VRPM/inst/shiny-examples/Iris/ROC.png
VRPM/inst/shiny-examples/Iris/links.png
VRPM/inst/shiny-examples/Iris/contributions2.png
VRPM/inst/shiny-examples/Iris/outcomes.png
VRPM/inst/shiny-examples/Iris/ccchart.png
VRPM/inst/shiny-examples/Iris/cchart.png
VRPM/inst/shiny-examples/Iris/corrplot.png
VRPM/inst/shiny-examples/Iris/ff.png
VRPM/inst/shiny-examples/IntermittentClaudication
VRPM/inst/shiny-examples/IntermittentClaudication/ui.R
VRPM/inst/shiny-examples/IntermittentClaudication/server.R
VRPM/inst/shiny-examples/IntermittentClaudication/colplot.png
VRPM/inst/shiny-examples/IntermittentClaudication/www
VRPM/inst/shiny-examples/IntermittentClaudication/www/empty.png
VRPM/inst/shiny-examples/IntermittentClaudication/helpers.R
VRPM/inst/shiny-examples/IntermittentClaudication/ccchart.png
VRPM/inst/shiny-examples/IntermittentClaudication/cchart.png
VRPM/inst/shiny-examples/xsnz
VRPM/inst/shiny-examples/xsnz/ui.R
VRPM/inst/shiny-examples/xsnz/server.R
VRPM/inst/shiny-examples/xsnz/ccchartp_widowed_ccchart.png
VRPM/inst/shiny-examples/xsnz/colplotp_married.png
VRPM/inst/shiny-examples/xsnz/www
VRPM/inst/shiny-examples/xsnz/www/empty.png
VRPM/inst/shiny-examples/xsnz/colplot_patientsummary.png
VRPM/inst/shiny-examples/xsnz/ccchart_divorced_ccchart.png
VRPM/inst/shiny-examples/xsnz/colplotp_married_wing.png
VRPM/inst/shiny-examples/xsnz/cchart_divorced_cchart.png
VRPM/inst/shiny-examples/xsnz/colplotp_divorced.png
VRPM/inst/shiny-examples/xsnz/colplotp_single.png
VRPM/inst/shiny-examples/xsnz/ccchartp_divorced_ccchart.png
VRPM/inst/shiny-examples/xsnz/colplot_widowed.png
VRPM/inst/shiny-examples/xsnz/colplotp_widowed.png
VRPM/inst/shiny-examples/xsnz/colplot_divorced.png
VRPM/inst/shiny-examples/xsnz/colplot_patientsummary2.png
VRPM/inst/shiny-examples/xsnz/ccchart_widowed_ccchart.png
VRPM/inst/shiny-examples/xsnz/cchart_married_cchart.png
VRPM/inst/shiny-examples/xsnz/cchartp_divorced_cchart.png
VRPM/inst/shiny-examples/xsnz/ccchartp_married_ccchart.png
VRPM/inst/shiny-examples/xsnz/cchartp_single_cchart.png
VRPM/inst/shiny-examples/xsnz/ccchartp_single_ccchart.png
VRPM/inst/shiny-examples/xsnz/cchartp_widowed_cchart.png
VRPM/inst/shiny-examples/xsnz/cchart_widowed_cchart.png
VRPM/inst/shiny-examples/xsnz/colplotp_divorced_wing.png
VRPM/inst/shiny-examples/xsnz/ccchart_married_ccchart.png
VRPM/inst/shiny-examples/xsnz/cchartp_married_cchart.png
VRPM/inst/shiny-examples/xsnz/colplot_married.png
VRPM/inst/shiny-examples/xsnz/colplotp_widowed_wing.png
VRPM/inst/shiny-examples/Pima
VRPM/inst/shiny-examples/Pima/ui.R
VRPM/inst/shiny-examples/Pima/server.R
VRPM/inst/shiny-examples/Pima/lps.png
VRPM/inst/shiny-examples/Pima/colplot.png
VRPM/inst/shiny-examples/Pima/www
VRPM/inst/shiny-examples/Pima/www/empty.png
VRPM/inst/shiny-examples/Pima/probs.png
VRPM/inst/shiny-examples/Pima/colplot_B.png
VRPM/inst/shiny-examples/Pima/ROC.png
VRPM/inst/shiny-examples/Pima/links.png
VRPM/inst/shiny-examples/Pima/contributions2.png
VRPM/inst/shiny-examples/Pima/outcomes.png
VRPM/inst/shiny-examples/Pima/ccchart.png
VRPM/inst/shiny-examples/Pima/cchart.png
VRPM/inst/shiny-examples/Pima/corrplot.png
VRPM/inst/shiny-examples/Pima/ff.png
VRPM/NAMESPACE
VRPM/R
VRPM/R/patientchartcode.R
VRPM/R/colplotcode.R
VRPM/R/cumpatientchartcode.R
VRPM/R/svm_code.R
VRPM/R/glmcoxphcode.R
VRPM/R/APPcode.R
VRPM/R/multinomLRcode.R
VRPM/R/generalcode.R
VRPM/MD5
VRPM/DESCRIPTION
VRPM/man
VRPM/man/HTMLsummary.Rd
VRPM/man/plotperf.Rd
VRPM/man/cchart.Rd
VRPM/man/preplotperf.Rd
VRPM/man/runVRPMexample.Rd
VRPM/man/colplot.Rd
VRPM/man/ccchart.Rd