Sorry I jumped the gun. That does not provide you with the same plot as gg2
that you are aiming for.
-T
On Wed, Apr 16, 2014 at 7:37 PM, Tim Marcella <timmarce...@gmail.com> wrote:
> I think all you have to do is add type="response" to your call for the
> predictions.
>
> Does this work for you
>
> # get fitted values on the logit scale
> pred <- data.frame(Arthritis,
> predict(arth.logistic, se.fit=TRUE,type="response"))
>
> library(ggplot2)
> library(scales)
> # plot on logit scale
> gg <- ggplot(pred, aes(x=Age, y=fit)) +
> geom_line(size = 2) + theme_bw() +
> geom_ribbon(aes(ymin = fit - 1.96 * se.fit,
> ymax = fit + 1.96 * se.fit,), alpha = 0.2, color =
> "transparent") +
> labs(x = "Age", y = "Log odds (Better)")
> gg
>
> -Tim
>
>
> On Wed, Apr 16, 2014 at 7:03 PM, Michael Friendly <frien...@yorku.ca>wrote:
>
>> I'm trying to see if & how I can use coord_trans() with ggplot2 to
>> transform the
>> Y axis of a plot on the logit scale to the probability scale, as opposed
>> to recalculating
>> everything "manually" and constructing a new plot.
>> Here is a simple example of the 'base' plot I'd like to transform:
>>
>> data(Arthritis, package="vcdExtra")
>> Arthritis$Better <- as.numeric(Arthritis$Improved > "None")
>> arth.logistic <- glm(Better ~ Age, data=Arthritis, family=binomial)
>>
>> # get fitted values on the logit scale
>> pred <- data.frame(Arthritis,
>> predict(arth.logistic, se.fit=TRUE))
>> library(ggplot2)
>> library(scales)
>> # plot on logit scale
>> gg <- ggplot(pred, aes(x=Age, y=fit)) +
>> geom_line(size = 2) + theme_bw() +
>> geom_ribbon(aes(ymin = fit - 1.96 * se.fit,
>> ymax = fit + 1.96 * se.fit,), alpha = 0.2, color =
>> "transparent") +
>> labs(x = "Age", y = "Log odds (Better)")
>> gg
>>
>> Things I've tried that don't work:
>>
>> > gg + coord_trans(ytrans="logis")
>> Error in get(as.character(FUN), mode = "function", envir = envir) :
>> object 'logis_trans' of mode 'function' was not found
>> >
>> > gg + coord_trans(ytrans=probability_trans("logis"))
>> Error in if (zero_range(range)) { : missing value where TRUE/FALSE needed
>> In addition: Warning message:
>> In qfun(x, ...) : NaNs produced
>> >
>>
>> Doing what I want "manually":
>>
>> # doing it manually
>> pred2 <- within(pred, {
>> prob <- plogis(fit)
>> lower <- plogis(fit - 1.96 * se.fit)
>> upper <- plogis(fit + 1.96 * se.fit)
>> })
>>
>>
>> gg2 <- ggplot(pred2, aes(x=Age, y=prob)) +
>> geom_line(size = 2) + theme_bw() +
>> geom_ribbon(aes(ymin = lower,
>> ymax = upper), alpha = 0.2, color = "transparent") +
>> labs(x = "Age", y = "Probability (Better)")
>> gg2
>>
>>
>>
>> --
>> Michael Friendly Email: friendly AT yorku DOT ca
>> Professor, Psychology Dept. & Chair, Quantitative Methods
>> York University Voice: 416 736-2100 x66249 Fax: 416 736-5814
>> 4700 Keele Street Web: http://www.datavis.ca
>> Toronto, ONT M3J 1P3 CANADA
>>
>> ______________________________________________
>> R-help@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.
>>
>
>
>
> --
> Tim Marcella
> 508.498.2989
> timmarce...@gmail.com
>
--
Tim Marcella
508.498.2989
timmarce...@gmail.com
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