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Plotting observed vs. Predicted values, change of symbols
3 messages · oscar linares, David Winsemius
On Nov 29, 2009, at 8:51 AM, oscar linares wrote:
Dear Wiz[R]ds, I am deeply grateful for the help from Duncan Murdoch, Gray Calhoun, and others. We are almost there. For whatever reason, I can't change the symbol from a circle to a triangle in the upright posture plots.
Any ideas? I have
included the problem in full.
# 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)
# Need upright in same plots (e.g., dashed line)
par(cex.lab=1.2,cex.axis=1.3)
par(mfrow=c(2,1))
plot(c(datasu$concsu, dataup$concup) ~ c(datasu$time, dataup$time),
xlab =
"Time (minutes)",
ylab = "3H-NE (dpm/ml)", main="3H-NE Post-infusion Plasma
Disappearance
Curves", ylim=c(0,1000),cex=1.25, pch=16,col=1)
lines(times, predictionssu(fit.wt.su, times))
I don't think this is a complete presentation. My system thinks "times" is a function from the chron package, so either you have a numeric object named "times" or you are putting in "times" when you meant "time". I did try dropping the "s" but still get the same error: lines(time, predictionssu(fit.wt.su, time)) Error in -a1 * time : non-numeric argument to binary operator
lines(times, predictionsup(fit.wt.up, times), lty = "dashed")
plot(c(datasu$concsu, dataup$concup) ~ c(datasu$time, dataup$time),
xlab =
"Time (minutes)",
ylab = "3H-NE (dpm/ml)", log = "y", ylim=c(1,1000),cex=1.25,
pch=16,col=1)
lines(times, predictionssu(fit.wt.su, times))
lines(times, predictionsup(fit.wt.up, times), lty = "dashed")
Deeply grateful in advance...
--
Oscar
Oscar A. Linares, MD
Translational Medicine Unit
LaPlaisance Bay, Bolles Harbor
Monroe, Michigan 48161
Department of Medicine,
University of Toledo College of Medicine
Toledo, OH 43606-3390
Department of Internal Medicine,
The Detroit Medical Center (DMC)
Harper University Hospital
Wayne State University School of Medicine
Detroit, Michigan 48201
[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD Heritage Laboratories West Hartford, CT
On Nov 29, 2009, at 8:51 AM, oscar linares wrote:
Dear Wiz[R]ds,
I am deeply grateful for the help from Duncan Murdoch, Gray Calhoun,
and
others. We are almost there. For whatever reason, I can't change the
symbol
from a circle to a triangle in the upright posture plots. Any ideas?
I have
included the problem in full.
# 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)
# Need upright in same plots (e.g., dashed line)
par(cex.lab=1.2,cex.axis=1.3)
par(mfrow=c(2,1))
plot(c(datasu$concsu, dataup$concup) ~ c(datasu$time, dataup$time),
xlab =
"Time (minutes)",
ylab = "3H-NE (dpm/ml)", main="3H-NE Post-infusion Plasma
Disappearance
Curves", ylim=c(0,1000),cex=1.25, pch=16,col=1)
Try: ..., pch=c(rep(2,length(datasu$concsu)), rep(17,length(datasu $concsu)) ), ... (open triangles and filled triangles)
lines(times, predictionssu(fit.wt.su, times))
lines(times, predictionsup(fit.wt.up, times), lty = "dashed")
plot(c(datasu$concsu, dataup$concup) ~ c(datasu$time, dataup$time),
xlab =
"Time (minutes)",
ylab = "3H-NE (dpm/ml)", log = "y", ylim=c(1,1000),cex=1.25,
pch=16,col=1)
lines(times, predictionssu(fit.wt.su, times))
lines(times, predictionsup(fit.wt.up, times), lty = "dashed")
Deeply grateful in advance...
--
Oscar
Oscar A. Linares, MD
Translational Medicine Unit
LaPlaisance Bay, Bolles Harbor
Monroe, Michigan 48161
Department of Medicine,
University of Toledo College of Medicine
Toledo, OH 43606-3390
Department of Internal Medicine,
The Detroit Medical Center (DMC)
Harper University Hospital
Wayne State University School of Medicine
Detroit, Michigan 48201
[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD Heritage Laboratories West Hartford, CT