[R] ggplot2: using coord_trans for logit -> probability

[ONKELINX, Thierry]

Dear Michael,

You can use geom_smooth directly.

ggplot(pred, aes(x = Age, y = Better)) + geom_smooth(method = "glm", family = binomial)

Best regards,

Thierry

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
+ 32 2 525 02 51
+ 32 54 43 61 85
Thierry.Onkelinx at inbo.be
www.inbo.be

To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

-----Oorspronkelijk bericht-----
Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] Namens Michael Friendly
Verzonden: donderdag 17 april 2014 4:03
Aan: R-help
Onderwerp: [R] ggplot2: using coord_trans for logit -> probability

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

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