oscar linares wrote:
Dear Wiza[R]ds,
I am very grateful to Duncan Murdoch for his assistance with this problem.
His help was invaluable. However, the problem has become a little more
complicated for me. Now, in each plot, I need to plot the observed and
fitted values of a supine and upright posture experiment. Here is what I
have and how far I got.
# tritiated (3H)-Norepinephrine(NE) disappearance from plasma
# concentrations supine and upright
# supine
datasu <- data.frame(
time=c(0,1,2,4,6,8,10,15,20),
concsu=c(385.61,265.88,173.87,99.47,66.7,55.27,48.29,39.85,40.66)
)
# upright
dataup <- data.frame(
time=c(0,1,2,4,6,8,10,15,20),
concup=c(767.27,529.03,328.13,225.94,164,151.1,132.02,121.15,70.88)
)
# fit supine
wt.su<- function(resp, time,A1,a1,A2,a2)
{
pred <- A1*exp(-a1*time)+A2*exp(-a2*time)
(resp - pred) / sqrt(pred)
}
fit.wt.su <- nls( ~ wt.su(concsu, time,A1,a1,A2,a2), data=datasu,
start=list(A1=500,a1=1,A2=100,a2=0.2),
trace = TRUE)
summary(fit.wt.su)
# fit upright
wt.up<- function(resp, time,B1,b1,B2,b2)
{
pred <- B1*exp(-b1*time)+B2*exp(-b2*time)
(resp - pred) / sqrt(pred)
}
fit.wt.up <- nls( ~ wt.up(concup, time,B1,b1,B2,b2), data=dataup,
start=list(B1=500,b1=1,B2=100,b2=0.1),
trace = TRUE)
summary(fit.wt.up)
# Function that returns predicted values and graphics
# by Duncan Murdoch
predictionssu <- function(fit, time) {
params <- summary(fit)$coefficients[, 1]
A1 <- params["A1"]
a1 <- params["a1"]
A2 <- params["A2"]
a2 <- params["a2"]
A1*exp(-a1*time)+A2*exp(-a2*time)
}
predictionsup <- function(fit, time) {
params <- summary(fit)$coefficients[, 1]
B1 <- params["B1"]
b1 <- params["b1"]
B2 <- params["B2"]
b2 <- params["b2"]
B1*exp(-b1*time)+B2*exp(-b2*time)
}
# plot observed and predicted values supine and upright in
# each plot type (linear and smi-log)
# this does supine
times <- seq(0,20, len=100)
par(mfrow=c(2,1))
plot(concsu ~ time, data=datasu)
lines(times, predictionssu(fit.wt.su, times))
plot(concsu ~ time, data=datasu, log="y")
lines(times, predictionssu(fit.wt.su, times))
# Need upright in same plots (e.g., dashed line)
Many thanks in advance...
Hi Oscar,
The "lines" and "points" commands add to the current plot, so adding
more points and dashed lines is straightforward (see the help page for
"par" for more details on how to customize the line type). The
following code plots the supine and upright graphs together. (obviously
it needs to go at the end of your code).
> par(mfrow=c(2,1))
> plot(c(datasu$concsu, dataup$concup) ~ c(datasu$time, dataup$time),
xlab = "time", ylab = "conc")
> lines(times, predictionssu(fit.wt.su, times))
> lines(times, predictionsup(fit.wt.up, times), lty = "dashed")
> plot(c(datasu$concsu, dataup$concup) ~ c(datasu$time, dataup$time),
xlab = "time", ylab = "conc", log = "y")
> lines(times, predictionssu(fit.wt.su, times))
> lines(times, predictionsup(fit.wt.up, times), lty = "dashed")
The 'plot' command is ugly and could be improved; also both "conc" and
"time" should be given better labels. Since you have different data
frames for "supine" and "upright", you don't need to distinguish the row
names; you could have "conc" be the row in both data frames. Even
better, you could have "supine" vs. "upright" as a factor, and store all
of your data in a single data frame; doing so would make it easier to
use the lattice graphics package for this sort of problem.
--
Gray Calhoun
Assistant Professor of Economics, Iowa State University
http://www.econ.iastate.edu/~gcalhoun/
467 Heady Hall
Ames, IA 50011
Phone: (515) 294-6271
Fax: (515) 294-0221
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