### R code from vignette source 'flu.Rnw'
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### code chunk number 1: startup
###################################################
#system ("mkdir fig")
options(SweaveHooks=list(fig=function() {
par(mar = c (4.1, 4.1, 1, .6))
trellis.pars <- trellis.par.get ("layout.heights")
trellis.pars [grep ("padding", names (trellis.pars))] <- 0
trellis.par.set(layout.heights = trellis.pars)
trellis.pars <- trellis.par.get ("layout.widths")
trellis.pars [grep ("padding", names (trellis.pars))] <- 0
trellis.par.set(layout.widths = trellis.pars)
}))
options ("width" = 100, "digits" = 5)
library (hyperSpec)
# redefine lattice functions so that the result is printed without external print command
setMethod ("plot",
signature (x = "hyperSpec", y = "character"),
function (x, y, ...){
tmp <- hyperSpec:::.plot (x, y, ...)
if (is (tmp, "trellis"))
print (tmp)
invisible (tmp)
})
plotmap <- function (...) print (hyperSpec:::plotmap (...))
setMethod ("levelplot", signature (x = "hyperSpec", data = "missing"),
function (x, data, ...) {
l <- hyperSpec:::.levelplot (x = formula (spc ~ x * y), data = x, ...)
print (l)
}
)
setMethod ("levelplot", signature (x = "formula", data = "hyperSpec"),
function (x, data, ...) print (hyperSpec:::.levelplot (x, data, ...))
)
plotc <- function (...){
call <- match.call ()
call [[1]] <- hyperSpec:::plotc
print (eval (call))
}
ploterrormsg <- function (fn, pkg) {
plot (0, 0, type = "n", axes = FALSE, bty = "n", xlab = "", ylab = "")
text (0, 0, paste ("Function", fn, "not available:\npackage", pkg, "needed."))
}
griderrormsg <- function (fn, pkg) {
require (grid)
grid.text (label = paste ("Function", fn, "not available:\npackage", pkg, "needed."))
NA
}
texterrormsg <- function (fn, pkg) {
cat ("Function", fn, "not available:\npackage", pkg, "needed.\n")
}
nice.paste <- function (...){
fnames <- c (...)
if (length (fnames) == 2L)
fnames <- paste (fnames, collapse = " and ")
if (length (fnames) > 1L){
fnames [length (fnames)] <- paste ("and", tail (fnames, 1))
fnames <- paste (fnames, collapse = ", ")
}
fnames
}
check.req.pkg <- function (pkg = stop ("pkg needed"),
texterrors = NULL, ploterrors = NULL, griderrors = NULL,
hynstext = NULL, hynsplot = NULL, hynsgrid = NULL,
donothing = NULL, special = NULL, v = TRUE){
if (v) cat ("\\item[\\Rpackage{", pkg, "}:] ", sep = "")
dummies <- list ()
if (pkg.exists (pkg)){
if (v) cat ("available\n")
} else {
for (fn in as.character (texterrors))
dummies <- c (dummies, bquote (.(fn) <- function (...) texterrormsg (.(fn), .(pkg))))
for (fn in as.character (ploterrors))
dummies <- c (dummies, bquote (.(fn) <- function (...) ploterrormsg (.(fn), .(pkg))))
for (fn in as.character (griderrors))
dummies <- c (dummies, bquote (.(fn) <- function (...) griderrormsg (.(fn), .(pkg))))
for (fn in as.character (hynstext))
assignInNamespace (x = fn,
value = eval (bquote (function (...) texterrormsg (.(fn), .(pkg)))),
ns = "hyperSpec")
for (fn in as.character (hynsplot))
assignInNamespace (x = fn,
value = eval (bquote (function (...) ploterrormsg (.(fn), .(pkg)))),
ns = "hyperSpec")
for (fn in as.character (hynsgrid))
assignInNamespace (x = fn,
value = eval (bquote (function (...) griderrormsg (.(fn), .(pkg)))),
ns = "hyperSpec")
fnames <- nice.paste (texterrors, ploterrors, griderrors, hynstext, hynsplot, hynsgrid, names (special))
if (v && length (fnames) > 0L) cat (fnames, "replaced.")
for (fn in as.character (donothing))
dummies <- c (dummies, bquote (.(fn) <- function (...) invisible (NULL)))
fnames <- nice.paste (donothing)
if (v && length (fnames) > 0L) cat (fnames, "missing.")
if (v) cat ("\n")
}
invisible (dummies)
}
plotvoronoi <- function (...) print (hyperSpec:::plotvoronoi (...))
# set standardized color palettes
seq.palette <- colorRampPalette (c ("white", "dark green"), space = "Lab")
YG.palette <- function (n = 20) rgb (colorRamp (c("#F7FCF5", "#E5F5E0", "#C7E9C0", "#A1D99B", "#74C476",
"#41AB5D", "#238B45", "#006D2C", "#00441B"), space = "Lab")
# was: brewer.pal (9, "Greens")
(seq (1/3, 1, length.out = n)^2), maxColorValue = 255)
div.palette <- colorRampPalette (c("#00008B", "#351C96", "#5235A2", "#6A4CAE", "#8164BA", "#967CC5",
"#AC95D1", "#C1AFDC", "#D5C9E8", "#E0E3E3", "#F8F8B0", "#F7E6C2",
"#EFCFC6", "#E6B7AB", "#DCA091", "#D08977", "#C4725E", "#B75B46",
"#A9432F", "#9A2919", "#8B0000"), space = "Lab")
pkgSuggests <- function (...)
strsplit (packageDescription (..., fields="Suggests"), ",\\s*")[[1]]
pkg.exists <- function (pkg = stop ("package name needed"), lib.loc = NULL){
dir <- sapply (pkg, function (p) system.file (package = p, lib.loc = lib.loc))
nzchar (dir) > 0L
}
is.basepkg <- function (pkg){
pkg.exists (pkg) && grepl ("^base$", packageDescription (pkg, fields = "Priority"))
}
pkg.or.base <- function (pkg){
pkg [sapply (pkg, is.basepkg)] <- "base"
pkg
}
citation.or.file <- function (pkg, svd.cit = sprintf ("%s.CITATION", pkg)){
if (pkg.exists (pkg))
citation (pkg)
else if (file.exists (svd.cit))
readCitationFile (file = svd.cit)
else
NULL
}
make.cite.keys <- function (pkg, entries){
pkg <- pkg.or.base (pkg)
if (! pkg.exists (pkg))
return (pkg)
if (missing (entries))
entries <- citation.or.file (pkg)
keys <- sapply (unclass (entries), attr, "key")
noname <- which (sapply (keys, is.null))
if (length (keys) == 1L && noname == 1L) {
keys <- pkg
} else {
for (i in noname)
keys [[i]] <- paste (pkg, i, sep = ".")
}
keys <- make.unique (unlist (keys))
keys
}
citation.with.key <- function (pkg = "base"){
pkg <- pkg.or.base (pkg)
tmp <- citation.or.file (pkg)
keys <- make.cite.keys (pkg, tmp)
for (entry in seq_along (tmp))
tmp [entry]$"key" <- keys [[entry]]
tmp
}
cite.pkg <- function (p, entries, citefun = "cite"){
paste ("\\\\", citefun, "{", paste (make.cite.keys (p, entries), collapse = ", "), "}", sep = "")
}
make.bib <- function (..., file = NULL) {
pkg <- c (...)
if (length (pkg) == 0L) {
pkg <- loadedNamespaces()
pkg <- unique (pkg.or.base (pkg))
}
l <- lapply (pkg, citation.with.key)
l <- do.call ("c", l [! sapply (l, is.null)])
if (!is.null (file))
if (is.null (l))
cat (NULL, file = file) # touches file
else
cat (toBibtex (l), file = file, sep = "\n")
invisible (l)
}
###################################################
### code chunk number 2: mailme
###################################################
cat ("\\newcommand{\\mailme}{\\href{mailto:",
packageDescription ("hyperSpec")$Maintainer,
"}{\\texttt{",
packageDescription ("hyperSpec")$Maintainer,
"}}}\n",
sep = "")
###################################################
### code chunk number 3: listfunctions
###################################################
texListFun <- function (pattern){
funs <- ls (envir = getNamespace ("hyperSpec"), pattern = pattern)
funs <- paste ("\\\\Rfunction{", funs, "}", sep ="")
nice.paste (funs)
}
###################################################
### code chunk number 4: cleanup (eval = FALSE)
###################################################
## sessionInfo ()
## rm (list = ls ())
## library (tools)
###################################################
### code chunk number 5: read.txt.PE
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source ("scan.txt.PerkinElmer.R")
flu <- scan.txt.PerkinElmer ("rawdata/flu?.txt", skip = 54)
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### code chunk number 6: rawspc
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flu
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### code chunk number 7: rawfig
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getOption("SweaveHooks")[["fig"]]()
plot (flu)
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### code chunk number 8: newdata
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flu$c <- seq (from = 0.05, to = 0.30, by = 0.05)
labels (flu, "c") <- "c / (mg / l)"
flu
save (flu, file = 'flu.rda')
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### code chunk number 9: newc
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flu$c
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### code chunk number 10: delcol
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flu$file <- NULL
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### code chunk number 11: calplot1
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getOption("SweaveHooks")[["fig"]]()
plotc (flu[,,450])
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### code chunk number 12: cutspc
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flu <- flu [,,450]
labels (flu, "spc") <- expression (I ["450 nm"] / a.u.)
###################################################
### code chunk number 13: calplot2
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getOption("SweaveHooks")[["fig"]]()
plotc (flu, xlim = range (0, flu$c), ylim = range (0, flu$spc))
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### code chunk number 14: abbrev
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flu[[]]
flu$.
flu$..
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### code chunk number 15: cal
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calibration <- lm (c ~ spc, data = flu$.)
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### code chunk number 16: summarymodel
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summary (calibration)
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### code chunk number 17: pred
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I <- c (125, 400)
conc <- predict (calibration, newdata = list (spc = as.matrix(I)), interval = "prediction",
level = .99)
conc
###################################################
### code chunk number 18: calplot3
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getOption("SweaveHooks")[["fig"]]()
int <- list (spc = as.matrix(seq (min (flu), max(flu), length.out = 25)))
ci <- predict (calibration, newdata = int, interval = "confidence", level = 0.99)
panel.ci <- function (x, y, ...,
intensity, ci.lwr, ci.upr, ci.col = "#606060") {
panel.xyplot (x, y, ...)
panel.lmline (x, y,...)
panel.lines (ci.lwr, intensity, col = ci.col)
panel.lines (ci.upr, intensity, col = ci.col)
}
plotc (flu, panel = panel.ci,
intensity = int$spc, ci.lwr = ci [, 2], ci.upr = ci [, 3])
## # extrapolate to lower intensities
## int <- list (spc = as.matrix(0 : min (flu)))
## ci <- predict (calibration, newdata = int, interval = "confidence", level = 0.99)
## matlines (ci, int$spc, col = c ("red","#606060","#606060"), lty = 3)
# our example
#lines (conc[-1], rep(I, 2), col = "blue")
#points (conc[1], I, col = "blue", pch = 4, cex = 0.5)
###################################################
### code chunk number 19: calplot4.1
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flu$type <- "data points"
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### code chunk number 20: calplot4.2
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tmp <- new ("hyperSpec", spc = as.matrix(seq (min (flu), max(flu), length.out = 25)),
wavelength = 450)
ci <- predict (calibration, newdata = tmp$., interval = "confidence", level = 0.99)
tmp <- tmp [rep (seq (tmp, index = TRUE), 3)]
tmp$c <- as.numeric (ci)
tmp$type <- rep (colnames (ci), each = 25)
flu <- rbind (flu, tmp)
###################################################
### code chunk number 21: calplot4
###################################################
getOption("SweaveHooks")[["fig"]]()
panel.predict <- function (x, y, ...,
intensity, ci, pred.col = "red", pred.pch = 19, pred.cex = 1) {
panel.xyplot (x, y, ...)
mapply (function (i, lwr, upr, ...) {
panel.lines (c (lwr, upr), rep (i, 2), ...)
},
intensity, ci [, 2], ci [, 3], MoreArgs = list (col = pred.col))
panel.xyplot (ci [, 1], intensity, col = pred.col, pch = pred.pch, cex = pred.cex, type = "p")
}
plotc (flu, groups = type, type = c("l", "p"),
col = c ("black", "black", "#606060", "#606060"),
pch = c (19, NA, NA, NA), cex = 0.5,
lty = c (0, 1, 1, 1),
panel = panel.predict,
intensity = I,
ci = conc,
pred.cex = 0.5)
###################################################
### code chunk number 22: flu.Rnw:239-240
###################################################
sessionInfo ()
rm (list = ls ())
library (tools)
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