RCSpin: Group of Spin-alike models

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#Friday, June 20, 2014
require(roxygen2)
roxygenize("RCSpin")
#Error in .Object$initialize(...) : object 'CrcRiskParams' not found

library(devtools)
document("RCSpin")
Updating RCSpin documentation
 Loading RCSpin
 Writing NAMESPACE
 Writing GenericModel-class.Rd
 Writing Test-class.Rd
 Writing ClinicalHistory-class.Rd
 Writing Person-class.Rd
 Writing Risk-class.Rd
 Writing lappend.Rd
 Writing CrcSpinModel-class.Rd
 Writing DukesAdenomaParams-class.Rd


############################################################
# Generated by roxygen2 (4.0.1): do not edit by hand

export(lappend)
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system("cp NAMESPACE RCSpin/NAMESPACE")
or svn revert RCSpin/NAMESPACE


system("R CMD build RCSpin")
system("sudo R CMD INSTALL RCSpin_0.1.tar.gz")
#restart

library(RCSpin)

cc<-GenericModel(iterations=99, num_subjects=10,base_seed=122)
cc<-CrcSpinModel$new(iterations=99, num_subjects=10,base_seed=122)
cc$run()
dd<-DukesCrcSpinModel$new(iterations=99, num_subjects=10, base_seed=125, commencement_age=20)
dd$run()
help(RCSpin)
help(death_rates)
help(GenericModel)  # takes the #' section at the tot of the file and add all the
                    # "" from each method
GenericModel$methods()
GenericModel$fields()
GenericModel$help()
GenericModel$help(updateSubject)

help(CrcSpinModel)  # takes the #' section just before setRefClass(CrcSpinModel ..)
                    #and adds all the  "" from each method
help(CrcRiskParams) #nothing


help(Test-class)#works if I type it in but not from emacs -- how can that happen?
Test$help()
help(Test)

help(ClinicalHistory)  # these are quite different. help(ClinicalHistory) gives the roxoygen help
ClinicalHistory$help() # this gives what appears to be some template of the function
help(Person)
Person$help()
Person$help(initialize)
help(PersonWithColon)        #nothing
help(Risk)
Risk$help()
help(lappend)
help(Adenoma) 
help(AdenomaParams)
help(Colon)  #nothing
help(CrcRisk)
help(DukesCrcSpinModel)
help(DukesAdenomaParams)     #nothing
help(DukesAdenoma)          #nothing
help(DukesColon)           #nothing
help(DukesPersonWithColon)  #nothing
DukesPersonWithColon$help()
help(SymptomaticPresentation)  #nothing
help(organize_results)#nothing
vignette("RCSpin")

system.time(cc<-GenericModel(iterations=99, num_subjects=1000,base_seed=122))
#   user  system elapsed
#   2.008   0.012   2.023
system.time(cc$run())
# 30.762   0.036  30.827
cc$study_group[1]


system.time(cc<-CrcSpinModel$new(iterations=99, num_subjects=1000,base_seed=122))
# 20.233   0.000  20.251
system.time(cc$run())
#107.987   0.040 108.160
cc$study_group[1]

system.time(dd<-DukesCrcSpinModel$new(iterations=99, num_subjects=1000, base_seed=125, commencement_age=20))
#20.778   0.012  20.808
system.time(dd$run())
#159.030   0.528 159.928

system.time(dd<-DukesCrcSpinModel$new(iterations=99, num_subjects=50000, base_seed=125, commencement_age=20))
system.time(dd$run())

dim(dd$study_results)




#######################################################################################
ccgm<-GenericModel(iterations=99, num_subjects=50,base_seed=122)
dim(ccgm$study_results)

res2<-ccgm$study_results
res.F<-res2[(1:99)*2-1,]
res.M<-res2[(1:99)*2,]

number.M<-sum(unlist (lapply(ccgm$study_group,f<-function(x){x$sex}))=="M")
number.F<-sum(unlist(lapply(ccgm$study_group,f<-function(x){x$sex}))=="F")

plot(1:99,res.M,col="blue",ylim=c(0,550),type="n",
     xlab="age",ylab="population")
temp<-rep(0,99)
temp[1]<-number.M
for ( ii in 2:99){
    temp[ii]<- temp[ii-1]-death_rate_male[ii-1]*temp[ii-1]
}
lines(temp,col="blue")
temp<-rep(0,99)
temp[1]<-number.F
for ( ii in 2:99){
    temp[ii]<- temp[ii-1]-death_rate_female[ii-1]*temp[ii-1]
}
lines(temp,col="red")
legend(20,300,c("male","female"),col=c("blue","red"),lty=1)




#ccsm<-CrcSpinModel$new(iterations=99, num_subjects=50000,base_seed=122)
#ccsm$run()
#dim(ccsm$study_results)# 198  18
#aa<-organize_results(ccsm)
#save(aa,file="aa_ccsm.Rdata")
load(file="aa_ccsm.Rdata")
attach(aa)
#png("CrcSpinModel.png")
plot(results.M$colon.state.large.adenoma/number.M,type="l",col="orange",lwd=2,xlab="age",axes=FALSE,
     ylab="proportion of population",ylim=c(0,0.1),
          main="CRC -- male population with no screening")
lines(results.M$colon.state.pre.symptomatic.CRC/number.M,col="plum4",lwd=2)
lines(results.M$colon.state.CRC/number.M,col="purple",lwd=2)
legend(20,0.07,c("population","large adenoma", "CRC","symptomatic CRC"), col=c(
"green","orange","plum4","purple"),lwd=2)
axis(2, pretty( c(0,0.1),10))
par(new=TRUE)
plot(pp<- number.M-cumsum(results.M$person.state.deceased),axes=FALSE,type="l",ylab="",xlab="",lty=1,col=3,lwd=2 )
axis(4, pretty(range(c(0,number.M),10)))
mtext(side=4, line=3, "population")

axis(1,pretty(range(1:99),10))
box() #- to make it look "as usual"
#dev.off()



#dddm<-DukesCrcSpinModel$new(iterations=99, num_subjects=50000, base_seed=125, commencement_age=20)
#dddm$run()
#dim(dddm$study_results)  #198  60
#aa<-organize_results(dddm)
#dim(dddm$study_results)  #198  60
#[1] 198  60
# aa<-organize_results(dddm)
#save(aa,file="aa_dddm.Rdata")

data(DukesCrcSpinModel_output)
attach(DukesCrcSpinModel_output)

png("DukesCrcSpinModel.png")
plot(results.M$colon.state.large.adenoma/number.M,type="l",col="orange",lwd=2,xlab="age",axes=FALSE,
     ylab="proportion of population",ylim=c(0,0.1),
          main="CRC -- male population with no screening")
lines(results.M$colon.state.CRC/number.M,col="plum4",lwd=2)
lines(results.M$colon.state.symptomatic.CRC/number.M,col="purple",lwd=2)
legend(20,0.07,c("population","large adenoma", "CRC","symptomatic CRC"), col=c(
"green","orange","plum4","purple"),lwd=2)
axis(2, pretty( c(0,0.1),10))
par(new=TRUE)
plot(pp<- number.M-cumsum(results.M$person.state.deceased),axes=FALSE,type="l",ylab="",xlab="",lty=1,col=3,lwd=2 )
axis(4, pretty(range(c(0,number.M),10)))
mtext(side=4, line=3, "population")
axis(1,pretty(range(1:99),10))
box() #- to make it look "as usual"


load(file="aa_ccsm.Rdata")
CrcSpinModel_output<-aa
save(CrcSpinModel_output,file="RCSpin/data/CrcSpinModel_output.RData")

load(file="aa_dddm.Rdata")
DukesCrcSpinModel_output<-aa
save(DukesCrcSpinModel_output,file="RCSpin/data/DukesCrcSpinModel_output.RData")



#http://win-builder.r-project.org/upload.aspx
#to create a windows library


svn export CRC-Spin2-R5-package test1
git config --global user.email "rob.dunne@csiro.au"
git config --global user.name "dun280"
cd test1
git init
git add .
git remote add origin https://github.com/parsifal9/test1.git
git push origin master
git pull https://github.com/parsifal9/test1.git/  #there is a README.md file on https://github.com/parsifal9/test1 that has to be pulled down first

tamar: git push origin master
#Counting objects: 32, done.
#Delta compression using up to 2 threads.
#Compressing objects: 100% (31/31), done.
#Writing objects: 100% (31/31), 141.14 KiB | 0 bytes/s, done.
#Total 31 (delta 3), reused 0 (delta 0)
#To https://github.com/parsifal9/test1.git
#   31fc568..18c666c  master -> master


git clone  https://github.com/csiro-crc-spin/RCSpin.git
R CMD build RCSpin 
R CMD INSTALL RCSpin_0.1.tar.gz -l ~/Downloads



library(devtools)
install_github("csiro-crc-spin/RCSpin",args=" -l /tmp")
library("RCSpin",lib.loc="/tmp")
cc<-GenericModel(iterations=99, num_subjects=10,base_seed=122)
cc<-CrcSpinModel$new(iterations=99, num_subjects=10,base_seed=122)
cc$run()
dd<-DukesCrcSpinModel$new(iterations=99, num_subjects=10, base_seed=125, commencement_age=20)
dd$run()
help(RCSpin)
#No documentation for ‘RCSpin’ in specified packages and libraries:
#you could try ‘??RCSpin’


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