Greg: Regression Helper Functions

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Methods for manipulating regression models and for describing these in a style adapted for medical journals. Contains functions for generating an HTML table with crude and adjusted estimates, plotting hazard ratio, plotting model estimates and confidence intervals using forest plots, extending this to comparing multiple models in a single forest plots. In addition to the descriptives methods, there are addons for the robust covariance matrix provided by the sandwich package, a function for adding non-linearities to a model, and a wrapper around the Epi package's Lexis functions for time-spliting a dataset when modeling non-proportional hazards in Cox regressions.

Author
Max Gordon [aut, cre], Reinhard Seifert [aut] (Author of original plotHR)
Date of publication
2016-03-28 23:24:58
Maintainer
Max Gordon <max@gforge.se>
License
GPL (>= 3)
Version
1.2
URLs

View on CRAN

Man pages

addNonlinearity
Add a nonlinear function to the model
bread.ols
Getting the bread for the vcovHC
caDescribeOpts
A function for gathering all the description options
confint.ols
A confint function for the ols
confint_robust
The confint function adapted for vcovHC
estfun.ols
Fix for the Extract Empirical Estimating Functions
forestplotCombineRegrObj
Compares different scores in different regression objects.
forestplotRegrObj
Forest plot for multiple models
GetCoefAndCI
Get the confidence intervals
getCrudeAndAdjustedModelData
This function helps with printing regression models
getModelData4Forestplot
Get model data
Greg-package
Regression Helper Functions
hatvalues.ols
Get the hat matrix for the OLS
isFitFn
Functions for checking regression type
model.matrix.ols
A fix for the model.matrix
plotHR
Plot a spline in a Cox regression model
prCaAddRefAndStat
Add reference according to the model
prCaAddReference
Adds a reference to value matrix
prCaAddUserReferences
Adds references
prCaGetImputationCols
Function for retrieving the imputation arguments
prCaGetRowname
Gets the labelled rowname if it exists
prCaGetVnStats
Gets the variable stats
prCaPrepareCrudeAndAdjusted
Prettify the text
prCaReorder
Reorder according to the requested variables
prCaReorderReferenceDescribe
Adds the ordering, references, and descriptions
prCaSelectAndOrderVars
Re-order variables
prCaSetRownames
Sets the rownames of the reordered_groups
prClearPCAclass
Removes the printCrudeAndAdjusted class from arguments
prConvertShowMissing
A functuon for converting a useNA variable
prEnvModelCall
Runs an 'fastDoCall' within the environment of the model
prExtractOutcomeFromModel
Get model outcome
prFindRownameMatches
Looks for unique rowname match without grep
prGetFpDataFromFit
Gets the confidence interval, p-values, coefficients from a...
prGetFpDataFromGlmFit
Gets the boundaries for a GLM fit that is poisson or...
prGetFpDataFromSurvivalFit
Gets the boundaries for a survival fit
prGetModelData
Get model data.frame
prGetModelVariables
Get the models variables
prGetStatistics
Get statistics according to the type
printCrudeAndAdjustedModel
Output crude and adjusted model data
prMapVariable2Name
A function that tries to resolve what variable corresponds to...
prNlChooseDf
Chooses the degrees of freedom for the non-linearity
prPhConfIntPlot
Plots the confidence intervals
prPhDensityPlot
Plot a density on the datapoints
prPhEstimate
Gets the non-linear function's estimate
prPhNewData
A function for retrieving new_data argument for predict
prPhRugPlot
Plot a rug on the datapoints
prPrintCAstring
Prep for printing
robcov_alt
Robust covariance matrix based upon the sandwich-package
SimpleRmsAnova
A simpler latex output of the latex.anova.rms
timeSplitter
A function for splitting a time according to time periods

Files in this package

Greg
Greg/inst
Greg/inst/examples
Greg/inst/examples/printCrudeAndAdjustedModel_example.R
Greg/inst/examples/plotHR_example.R
Greg/inst/examples/forestplotRegrObj_example.R
Greg/inst/examples/getCphRegrObjData_example.R
Greg/inst/examples/timeSplitter_example.R
Greg/inst/examples/simpleRmsAnova_example.R
Greg/inst/examples/addNonlinearity_example.R
Greg/inst/examples/printSimpleFit_example.R
Greg/inst/examples/rms_SandwichAddon_example.R
Greg/inst/examples/getCrudeAndAdjustedModelData_example.R
Greg/inst/examples/isFitLogit_example.R
Greg/inst/examples/forestplotCombineRegrObj_example.R
Greg/inst/examples/isFitCoxPH_example.R
Greg/inst/examples/confint_robust_example.R
Greg/inst/doc
Greg/inst/doc/Print_crude_and_adjusted_models.html
Greg/inst/doc/Print_crude_and_adjusted_models.Rmd
Greg/inst/doc/timeSplitter.Rmd
Greg/inst/doc/timeSplitter.html
Greg/inst/doc/Print_crude_and_adjusted_models.R
Greg/inst/doc/timeSplitter.R
Greg/tests
Greg/tests/test-interval-timeSplitter.R
Greg/tests/test-nonlin_4_coxph.R
Greg/tests/testthat.R
Greg/tests/testthat
Greg/tests/testthat/test-plotHR.R
Greg/tests/testthat/test-addNonlinearity.R
Greg/tests/testthat/test-private_functions.R
Greg/tests/testthat/test-getCrudeAndAdjustedModelData.R
Greg/tests/testthat/test-simpleRmsAnova.R
Greg/tests/testthat/test-forestplotRegrObj.R
Greg/tests/testthat/test-confint_robust.R
Greg/tests/testthat/test-printCrudeAndAdjustedModel.R
Greg/tests/testthat/test-fit.mult.impute-C&A.R
Greg/tests/testthat/test-isFit.R
Greg/tests/testthat/test-timeSplitter.R
Greg/tests/testthat/test-forestplotCombineRegrObj.R
Greg/NAMESPACE
Greg/NEWS
Greg/R
Greg/R/isFitCoxPH.R
Greg/R/confint_robust.R
Greg/R/simpleRmsAnova.R
Greg/R/forestplotRegrObj.R
Greg/R/rms_SandwichAddon.R
Greg/R/getModelData4Forestplot.R
Greg/R/getCrudeAndAdjustedModelData.rms.R
Greg/R/printCrudeAndAdjustedModel.R
Greg/R/private_printCaA.R
Greg/R/forestplotCombineRegrObj.R
Greg/R/addNonlinearity.R
Greg/R/private_functions.R
Greg/R/private_plotHR.R
Greg/R/plotHR.R
Greg/R/private_getCaA.R
Greg/R/isFitLogit.R
Greg/R/Greg.R
Greg/R/timeSplitter.R
Greg/R/getCrudeAndAdjustedModelData.R
Greg/vignettes
Greg/vignettes/Print_crude_and_adjusted_models.Rmd
Greg/vignettes/timeSplitter.Rmd
Greg/README.md
Greg/MD5
Greg/build
Greg/build/vignette.rds
Greg/DESCRIPTION
Greg/man
Greg/man/prGetFpDataFromSurvivalFit.Rd
Greg/man/timeSplitter.Rd
Greg/man/prCaAddRefAndStat.Rd
Greg/man/SimpleRmsAnova.Rd
Greg/man/prCaPrepareCrudeAndAdjusted.Rd
Greg/man/bread.ols.Rd
Greg/man/prPhDensityPlot.Rd
Greg/man/prEnvModelCall.Rd
Greg/man/prGetModelData.Rd
Greg/man/prGetFpDataFromFit.Rd
Greg/man/prFindRownameMatches.Rd
Greg/man/prPhEstimate.Rd
Greg/man/prCaSelectAndOrderVars.Rd
Greg/man/prCaReorder.Rd
Greg/man/prPhNewData.Rd
Greg/man/model.matrix.ols.Rd
Greg/man/prCaAddReference.Rd
Greg/man/prClearPCAclass.Rd
Greg/man/prGetStatistics.Rd
Greg/man/plotHR.Rd
Greg/man/forestplotRegrObj.Rd
Greg/man/prCaAddUserReferences.Rd
Greg/man/prPrintCAstring.Rd
Greg/man/prMapVariable2Name.Rd
Greg/man/isFitFn.Rd
Greg/man/estfun.ols.Rd
Greg/man/prCaReorderReferenceDescribe.Rd
Greg/man/prCaSetRownames.Rd
Greg/man/Greg-package.Rd
Greg/man/getCrudeAndAdjustedModelData.Rd
Greg/man/addNonlinearity.Rd
Greg/man/caDescribeOpts.Rd
Greg/man/forestplotCombineRegrObj.Rd
Greg/man/getModelData4Forestplot.Rd
Greg/man/confint.ols.Rd
Greg/man/prExtractOutcomeFromModel.Rd
Greg/man/prGetFpDataFromGlmFit.Rd
Greg/man/prCaGetVnStats.Rd
Greg/man/prNlChooseDf.Rd
Greg/man/prGetModelVariables.Rd
Greg/man/printCrudeAndAdjustedModel.Rd
Greg/man/prCaGetRowname.Rd
Greg/man/prConvertShowMissing.Rd
Greg/man/confint_robust.Rd
Greg/man/robcov_alt.Rd
Greg/man/prPhRugPlot.Rd
Greg/man/prPhConfIntPlot.Rd
Greg/man/hatvalues.ols.Rd
Greg/man/prCaGetImputationCols.Rd
Greg/man/GetCoefAndCI.Rd