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Ben quant
Verzonden: woensdag 14 maart 2012 19:48
Aan: Patrick Breheny
CC: r-help@r-project.org
Onderwerp: Re: [R] gam - Y axis probability scale with confidence/error lines
Thank you. The binomial()$linkinv() is good to know.
Ben
On Wed
Hello,
How do I plot a gam fit object on probability (Y axis) vs raw values (X
axis) axis and include the confidence plot lines?
Details...
I'm using the gam function like this:
l_yx[,2] = log(l_yx[,2] + .0004)
fit - gam(y~s(x),data=as.data.frame(l_yx),family=binomial)
And I want to plot it so
The predict() function has an option 'se.fit' that returns what you are
asking for. If you set this equal to TRUE in your code:
pred - predict(fit,data.frame(x=xx),type=response,se.fit=TRUE)
will return a list with two elements, 'fit' and 'se.fit'. The pointwise
confidence intervals will
That was embarrassingly easy. Thanks again Patrick! Just correcting a
little typo to his reply. this is probably what he meant:
pred = predict(fit,data.frame(x=xx),type=response,se.fit=TRUE)
upper = pred$fit + 1.96 * pred$se.fit
lower = pred$fit - 1.96 * pred$se.fit
# For people who are
Actually, I responded a bit too quickly last time, without really
reading through your example carefully. You're fitting a logistic
regression model and plotting the results on the probability scale. The
better way to do what you propose is to obtain the confidence interval
on the scale of
Thank you. The binomial()$linkinv() is good to know.
Ben
On Wed, Mar 14, 2012 at 12:23 PM, Patrick Breheny
patrick.breh...@uky.eduwrote:
Actually, I responded a bit too quickly last time, without really reading
through your example carefully. You're fitting a logistic regression model
and
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