Dark.Rcheck/Dark/doc/Workflow.R

In emkayoh/Dark: The Analysis of Dark Adaptation Data

## ---- eval=FALSE---------------------------------------------------------
#  library(Dark)
#  tmp <- dark
#  names(tmp)

## ---- echo=FALSE---------------------------------------------------------
load("dark.rda")
tmp<-dark
Names <- c("time", "thrs", "fit", "resid", "R2", "Bootstrap", "weight", 
"valid", "Mod", "Pn", "AIC", "data", "opt", "call", "val")
print(Names)

## ---- fig.width=6, fig.height=6, fig.align='center'----------------------
par(las=1, bty='n',mfrow=c(1,1))
XL <- expression(bold(Time~(min)))
YL <- expression(bold(Threshold~(LU)))
plot(tmp$time, tmp$thrs, xlab = XL, ylab=YL)

## ---- eval=FALSE---------------------------------------------------------
#  set.seed(1234)
#  P <-Start(tmp, 2000)
#  head(P,3)

## ---- echo=FALSE---------------------------------------------------------
Pd <- structure(c(-1.93048394296102, -0.966243347355156, -0.990918795667905, 
0.253616641335044, 0.420301711722179, 1.32959014056482, 3.97646484343339, 
0.763150661132819, 0.905683974690625, -0.389894947473737, -0.4064032016008, 
-0.182491245622811, 2.52208104052026, 6.96883941970985, 3.12198099049525, 
0.130565282641321, 0.207403701850925, 0.0885442721360681, 32.5607121101566, 
32.9919673191487, 29.4211741886944), .Dim = c(3L, 7L), .Dimnames = list(
    NULL, c("CT", "CC", "Tau", "S2", "Alph", "S3", "Beta")))
print.table(Pd,3)

## ---- eval=FALSE---------------------------------------------------------
#  MSC<-ModelSelect(tmp,P)
#  MSC

## ---- echo=FALSE---------------------------------------------------------

MSCd <- structure(list(AIC = c(0, 0, -347.688152541027, 0, -353.337417397606, 
-556.296993756504, -561.687551083725), param = structure(c(-7.03677859813905, 
-4.84533369033486, -5.52767312215107, -1.97221068357342, 6.23084047079413, 
4.01859727139177, 1.43155445018767, 1.39834034016783, 28.1212523680337, 
17.2254594347471, 0.557811726205019, 1.62283784201578, 0, -0.0365810342284519, 
9.61920222958987, -0.227896945728703, 0, 9.40371211032976, 3.50297041829524, 
8.73599874809917, 0, 0, 0.0972021474126348, 0.180809685149208, 
0, 0, 0, 19.4250494832971), .Dim = c(4L, 7L))), .Names = c("AIC", 
"param"))
print(MSCd, 3)

## ---- eval =FALSE--------------------------------------------------------
#  tmp<-BestFit(tmp,MSC)

## ---- eval=FALSE---------------------------------------------------------
#  tmp<-MultiStart(tmp,repeats = 25)
#  tmp<-BootDark(tmp,R = 500)

## ---- fig.width=6, fig.height=6, fig.align='center', echo=FALSE----------
source("../R/H.R")
source("../R/P7c.R")
par(las=1, bty='n',mfrow=c(1,1))
XL <- expression(bold(Time~(min)))
YL <- expression(bold(Threshold~(LU)))
plot(tmp$time, tmp$thrs, xlab = XL, ylab=YL)
X <- tmp$time
lines(X, tmp$fit)
lines(X, P7c(tmp$Bootstrap[,1], X), col = 2)
lines(X, P7c(tmp$Bootstrap[,3], X), col = 2)


## ------------------------------------------------------------------------
print(tmp,2)