time1<-date()
##################################################################
#                         START UP VMs                           #
##################################################################
#IF SOME THINGS NOT LOADED OR INSTALLED USE ...104.EVERYTHING...R#
##################################################################

#TURN OFF WARNINGS TO AVOID INCORRECT WARNINGS
#options(warn=-1)

# HOW MANY VMs TO USE 1,2 or 3
use.VMs<-2

#SET DEFAULT WORKING DIRECTORY
setwd("O:\\Documents\\pb51\\DATASHIELD.PROJECT\\STARTUP.AND.ANALYSIS.SCRIPTS")

#SOURCE CURRENT SET OF DEFAULT CLIENT FUNCTIONS THAT HAVE NOT BEEN ADDED TO dsBase.client
source("O:\\Documents\\pb51\\DATASHIELD.PROJECT\\STARTUP.AND.ANALYSIS.SCRIPTS\\CURRENT.EXTRA.CLIENT.SOURCE.FILES.R")


#PACKAGES: devtools
library(devtools)

#PACKAGES: opal, opaladmin
library(opal)
library(opaladmin) 


#When the current release is different to the most updated packages the
#following still work 
devtools::load_all("O:/Documents/pb51/DataSHIELD.PROJECT/DEVELOP.GITHUB/dsBaseClient")
devtools::load_all("O:/Documents/pb51/DataSHIELD.PROJECT/DEVELOP.GITHUB/dsStatsClient")
devtools::load_all("O:/Documents/pb51/DataSHIELD.PROJECT/DEVELOP.GITHUB/dsGraphicsClient")
#devtools::load_all("O:/Documents/pb51/DataSHIELD.PROJECT/DEVELOP.GITHUB/dsModellingClient")
#devtools::load_all("O:/Documents/pb51/DataSHIELD.PROJECT/DEVELOP.GITHUB/dsModellingClient-PB_ds.glm_bugfix")
devtools::load_all("O:/Documents/pb51/DataSHIELD.PROJECT/DEVELOP.GITHUB/dsModellingClient-master")


#otherwise when package release is up to date can use
#install.packages('dsBaseClient', repos='http://cran.obiba.org', type='source')
#install.packages('dsModellingClient', repos='http://cran.obiba.org', type='source')
#install.packages('dsGraphicsClient', repos='http://cran.obiba.org', type='source')
#install.packages('dsStatsClient', repos='http://cran.obiba.org', type='source')

#Do the same for server side functions
#LOAD SERVER SIDE PACKAGES INTO R
#devtools::load_all("O:/Documents/pb51/DataSHIELD.PROJECT/DEVELOP.GITHUB/dsBase/dsBase-master.110215")
#devtools::load_all("O:/Documents/pb51/DataSHIELD.PROJECT/DEVELOP.GITHUB/dsGraphics/dsGraphics-master.110215")
#devtools::load_all("O:/Documents/pb51/DataSHIELD.PROJECT/DEVELOP.GITHUB/dsModelling/dsModelling-master.110215")
#devtools::load_all("O:/Documents/pb51/DataSHIELD.PROJECT/DEVELOP.GITHUB/dsStats/dsStats-master.110215")


logindata<-ds.createLogindata(100,101,table="CNSIM.CNSIM")
logindata

opals <- datashield.login(logins=logindata,assign=TRUE)

#CHECK WHAT HAS BEEN READ IN
ds.dim('D')
ds.colnames('D')

############ 

#ds.class("D$LAB_TSC")   #ALL numeric until CVA
#ds.class("D$LAB_TRIG")          
#ds.class("D$LAB_HDL")
#ds.class("D$LAB_GLUC_ADJUSTED")
#ds.class("D$PM_BMI_CONTINUOUS")
#ds.class("D$DIS_CVA")    #ALL factor
#ds.class("D$MEDI_LPD")
#ds.class("D$DIS_DIAB")          
#ds.class("D$DIS_AMI")
#ds.class("D$GENDER")
#ds.class("D$PM_BMI_CATEGORICAL")


          
ds.assign("D$LAB_HDL","hdl")
ds.asNumeric("D$PM_BMI_CONTINUOUS","bmi.c")
ds.asNumeric("D$DIS_DIAB","diab")  
ds.asFactor("D$PM_BMI_CATEGORICAL","bmi.f")

time2<-date()

msg1<-ds.meanSdGp("hdl","bmi.f","both")

mod1<-ds.glm("hdl~bmi.f",family="gaussian")
mod1
mod2<-ds.glm("hdl~0+bmi.f",family="gaussian")
mod2

mod2
msg1

ds.glm("diab~hdl+bmi.f",family="binomial")

ds.rNorm(10000,100,5,"rvect")
ds.mean("rvect","split")
rrr<-ds.ex("DANGERprintDS(rvect)")
cbind(unlist(rrr[[1]]),unlist(rrr[[2]]))
ds.histogram("rvect","split")
plot(unlist(rrr[[1]]),unlist(rrr[[2]]))

time3<-date()