## ------------------------------------------------------------------------
suppressPackageStartupMessages(library(diseaseRiskPredictor))
# copy depression disease model into current environment
lDis <- diseaseRiskPredictor::lDisDepression
# report the depression disease model
lDis
## ------------------------------------------------------------------------
# calculate disease model
lDis <- fnCalcDiseaseModel( lDis )
names(lDis)
## ------------------------------------------------------------------------
# copy 3 generation pedigree into current environment
dfPed <- diseaseRiskPredictor::dfPed3Gen1Aff
dfPed
## ------------------------------------------------------------------------
# validate pedigree (also performs type conversion on some columns, hence the returned object)
dfPed <- fnValidatePedigree( dfPed )
## ---- fig.width=7, fig.height=4------------------------------------------
# construct pedigree object
oPedigree <- fnConstructPedigree( dfPed )
# plot pedigree diagram
plot(oPedigree)
## ------------------------------------------------------------------------
lPedDis <- fnPrepareForRiskPrediction( dfPed, lDis )
# calculate pedigree members' risks of depression
lRes <- fnPredictRisk( lPedDis )
# report contents of the results object
names(lRes)
## ---- fig.width=7, fig.height=4------------------------------------------
# report pedigree members' risks
lRes$dfPedRisk[,c(2,3,5:7,11:12)]
# plot pedigree members' risks
fnBarPlotRisk( lRes$dfPedRisk )
## ------------------------------------------------------------------------
lRes$lDis$categoricalRiskFactors[,1:7]
## ---- fig.width=7, fig.height=4------------------------------------------
# report pedigree members' risks
lRes$dfPedRisk[,c(2,3,5:7,13,18)]
## ----eval=FALSE----------------------------------------------------------
# # install it
# install.packages("Rcpp")
#
# # attach it
# library(Rcpp)
#
# # test c++ code for adding 1 plus 1
# evalCpp('1+1',showOutput=1,rebuild=1)
## ----eval=FALSE----------------------------------------------------------
# # install it
# install.packages("devtools")
#
# # attach it
# library(devtools)
#
# # test for Rtools installation
# find_rtools()
## ----eval=FALSE----------------------------------------------------------
# install.packages("devtools")
#
# devtools::install_github("DesmondCampbell/diseaseRiskPredictor")
## ----eval=FALSE----------------------------------------------------------
# # attach it
# library("diseaseRiskPredictor")
#
# assignInNamespace( "plot.pedigree", diseaseRiskPredictor:::plot.pedigree.FIXED, ns="kinship2")
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