# Paul Johnson <pauljohn@ku.edu> 2005-08-31
# This should update and then install all packages, except for
# ones I exclude because they don't work or we don't want them.


#options(repos = "http://lib.stat.cmu.edu/R/CRAN/")
options(repos = "http://cran.cnr.berkeley.edu/")


#update the ones you want to keep
update.packages(ask=F, checkBuilt=T)


###  Note vital role of dependencies in this approach

desiredPackages <- c("Rcmdr","reshape")

## dependencies grabbed include most of the things that we
## use in regression analysis & reporting

## abind
## acepack
## scatterplot3d
## fBasics
## Hmisc
## quadprog
## oz
## mlbench
## xtable
## leaps
## strucchange
## randForest
## SparseM
## chron
## DAAG
## e1071
## zoo
## mvtnorm
## car
## effects
## relimp
## Rcmdr
## fCalendar
## its
## tseries
## sandwich
## dynlm
## lmtest
## multcomp
## strucchange


### rgl needed for 3d graphics in Rcmdr
desiredPackages <- union(desiredPackages, c("rgl","gregmisc","tkrplot","TeachingDemos","misc3d","ggplot"))

desiredPackages <- union(desiredPackages,c("JGR"))

## dependencies grabbed include sub-packages of bundle gregmisc

## gdata
## gmodels
## gplots 


desiredPackages <- union(desiredPackages, c("Design","doBy"))
### Would need Hmisc too, but it got grabbed by Rcmdr dependencies
### doBy is a convenience

desiredPackages <- union(desiredPackages, c("coda","betareg", "segmented", "lme4","MEMSS"))
## dependencies grabbed include

##  Matrix
##  coda
##  mlmRev

### Neat Bayesian things
desiredPackages <- union(desiredPackages, c("R2WinBUGS","MCMCpack", "BMA"))
### We would need coda if it had not already been grabbed
## rrcov
## forward


### More Neat Bayesian things
desiredPackages <- union(desiredPackages, c("bayesm","bayesmix","mcmc","mcgibbsit","scapeMCMC","survBayes"))

### Misc. things I spotted while scanning package list
desiredPackages <- union(desiredPackages, c("dse", "akima", "JointGLM", "aod", "gee","geepack","cslogistic"))

## These ones have datasets or support for books
desiredPackages <- union(desiredPackages, c("Devore6","Devore5", "faraway", "ISwR","SASmixed","StatDataML","UsingR"))
# for ecology
desiredPackages <- union(desiredPackages, c("spatstat","ecodist","cocorresp","ade4","adehabitat","eiPack","grasper","sp","spatclus","spatialCovariance","spatialkernel","spdep","splancs","DCluster"))

desiredPackages <- union(desiredPackages, c("ffmanova"))

desiredPackages <- union(desiredPackages, c("fields", "flexmix","quantreg", "gamlss", "geoRglm","glmmML", "eha", "HyperbolicDist")) 

### data and missing value related
desiredPackages <- union (desiredPackages, c("lmeSplines", "zicounts","ZIGP", "locfit", "MNP", "norm", "hdf5", "Amelia", "impute", "mix",  "pan", "mice", "micEcon", "systemfit", "mitools", "sem","pspline")) 

desiredPackages <- union (desiredPackages, c("SemiPar","sm", "statmod","stepwise","subselect","survey"))

desiredPackages <- union (desiredPackages, c("Zelig","pscl","wnominate", "rattle", "rggobi"))

# VGAM is not in CRAN yet, but Zelig will use it.

desiredPackages <- union (desiredPackages, c("mmlcr", "tree","adapt","lars"))

# list of all currently installed packages

installedPackages <- rownames (installed.packages() )

# TRUE/FALE indicator for each desiredPackage
alreadyHave <- desiredPackages %in% installedPackages

#install non blacklisted packages that are in theNew list
if (sum(!alreadyHave) > 0) install.packages( desiredPackages[!alreadyHave],dependencies=T)
                         

if ( "VGAM" %in% installedPackages) 
  update.packages(repos="http://www.stat.auckland.ac.nz/~yee",ask=F) else 
  install.packages("VGAM", repos="http://www.stat.auckland.ac.nz/~yee")