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#NDK 7: Beat Jaggi ; 
#must-spektren aus ueb-03-mu2a-3
#R

##    get functions and data
source("http://stat.ethz.ch/Teaching/Datasets/NDK/r-fns.R")
d.spec <- read.table("http://stat.ethz.ch/Teaching/Datasets/NDK/spec-reac.dat")
    ## dim(d.spec)   # 121 700
t.wl <- seq(1100,2492,length=ncol(d.spec)) # Wellenlaengen
names(d.spec) <- t.wl
## =======================================================================
##    GET DATA
s.datatitle <- s.title <- c.env$project <- "NIR spectra"
c.env$step <- "data"
s.sample <- "d.spec"

t.d <- f.getdata(a.series="", a.sd=1, a.plot=T,a.plotc=T) 
s.time <- 1:nrow(t.d)
t.d <- f.selwavel(t.d, 680, 1780)
## --------------------------------------------------------
##   PCA 
## --------------------------------------------------------
s.nc0 <- 10 # maximal number of dimensions
r.pca <- f.specpca(t.d)

s.nc <- 3
g.scpairs()
## labels should be readable
t.lab <- rep("-",121)
t.i <- seq(1,121,10)
t.lab[t.i] <- as.character(t.i)
g.scpairs(a.labels=t.lab)
## --------------------------------------------
##   Directions based on observed spectra
## --------------------------------------------
t.dir <- c(1,35,45,85,85,94,95,105) # 
r.sq <- f.rotation()
g.scpairs(r.sq)
g.scpairs(r.sq, a.nc=4)
g.finaldec(r.sq, a.nc=4)
## ---------------------------------------------