Dear R-helpers,
I need to show a linear fit through a subset of the data within each
combination of levels of two factors. So I prepared an xyplot with
different panels for each level of one of the factors, and different
symbols within each panel for the levels of the second factor. My problem
is selecting the subset of each combination through which the line should
be fit for subsequent plotting. This hopefully shows the idea:
---<---------------cut here---------------start-------------->---
toydf <- expand.grid(1:100, c("A", "B"),
c("pop1", "pop2", "pop3",
"pop4", "pop5"))
toydf <- data.frame(facA = toydf[[3]], facB = toydf[[2]],
x = toydf[[1]], y = rnorm(1000))
xyplot(y ~ x | facA, groups = facB, data = toydf,
panel.groups = function(x, y, subscripts, ...) {
panel.xyplot(x, y, ...)
lindx <- which(y[subscripts] == max(y[subscripts], na.rm = TRUE))
xleft <- mean(x[lindx], na.rm = TRUE)
fit <- lm(y[x >= xleft] ~ x[x >= xleft])
panel.abline(fit)
})
---<---------------cut here---------------end---------------->---
i.e. the left limit for fitting the line is defined by the mean of x
values where y is equal to the maximum y values, *within* each combination
of levels of both factors. The above is giving me:
Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) :
0 (non-NA) cases
In addition: Warning message:
no finite arguments to max; returning -Inf
which shows I'm not understanding how the 'subscripts' argument
works.
I'd appreciate some pointers on what I'm doing wrong, as I haven't
been
able to find help in the help pages and List archives.
Thanks,
--
Sebastian P. Luque
Based on your two first sentences I think the solution is to use
xyplot(y ~ x | facA, groups = facB, data =
toydf,type=c("p","r"))
Try it and see if this is what you want.
Best regards
Frede Aakmann T??gersen
Scientist
Danish Institute of Agricultural Sciences
Research Centre Foulum
Dept. of Genetics and Biotechnology
Blichers All?? 20, P.O. BOX 50
DK-8830 Tjele
Phone: +45 8999 1900
Direct: +45 8999 1878
E-mail: FredeA.Togersen at agrsci.dk
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> -----Oprindelig meddelelse-----
> Fra: r-help-bounces at stat.math.ethz.ch
> [mailto:r-help-bounces at stat.math.ethz.ch] P?? vegne af Sebastian Luque
> Sendt: 21. februar 2006 08:20
> Til: r-help at stat.math.ethz.ch
> Emne: [R] indexing within panels in xyplot
>
> Dear R-helpers,
>
> I need to show a linear fit through a subset of the data
> within each combination of levels of two factors. So I
> prepared an xyplot with different panels for each level of
> one of the factors, and different symbols within each panel
> for the levels of the second factor. My problem is selecting
> the subset of each combination through which the line should
> be fit for subsequent plotting. This hopefully shows the idea:
>
>
> ---<---------------cut here---------------start-------------->---
> toydf <- expand.grid(1:100, c("A", "B"),
> c("pop1", "pop2",
"pop3", "pop4",
> "pop5")) toydf <- data.frame(facA = toydf[[3]], facB =
toydf[[2]],
> x = toydf[[1]], y = rnorm(1000))
>
> xyplot(y ~ x | facA, groups = facB, data = toydf,
> panel.groups = function(x, y, subscripts, ...) {
> panel.xyplot(x, y, ...)
> lindx <- which(y[subscripts] == max(y[subscripts],
> na.rm = TRUE))
> xleft <- mean(x[lindx], na.rm = TRUE)
> fit <- lm(y[x >= xleft] ~ x[x >= xleft])
> panel.abline(fit)
> })
> ---<---------------cut here---------------end---------------->---
>
> i.e. the left limit for fitting the line is defined by the
> mean of x values where y is equal to the maximum y values,
> *within* each combination of levels of both factors. The
> above is giving me:
>
> Error in lm.fit(x, y, offset = offset, singular.ok =
> singular.ok, ...) :
> 0 (non-NA) cases
> In addition: Warning message:
> no finite arguments to max; returning -Inf
>
> which shows I'm not understanding how the 'subscripts' argument
works.
> I'd appreciate some pointers on what I'm doing wrong, as I
> haven't been able to find help in the help pages and List archives.
>
> Thanks,
>
> --
> Sebastian P. Luque
>
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> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
>
>
On 2/21/06, Sebastian Luque <spluque at gmail.com> wrote:> Dear R-helpers, > > I need to show a linear fit through a subset of the data within each > combination of levels of two factors. So I prepared an xyplot with > different panels for each level of one of the factors, and different > symbols within each panel for the levels of the second factor. My problem > is selecting the subset of each combination through which the line should > be fit for subsequent plotting. This hopefully shows the idea: > > > ---<---------------cut here---------------start-------------->--- > toydf <- expand.grid(1:100, c("A", "B"), > c("pop1", "pop2", "pop3", "pop4", "pop5")) > toydf <- data.frame(facA = toydf[[3]], facB = toydf[[2]], > x = toydf[[1]], y = rnorm(1000)) > > xyplot(y ~ x | facA, groups = facB, data = toydf, > panel.groups = function(x, y, subscripts, ...) { > panel.xyplot(x, y, ...) > lindx <- which(y[subscripts] == max(y[subscripts], na.rm = TRUE)) > xleft <- mean(x[lindx], na.rm = TRUE) > fit <- lm(y[x >= xleft] ~ x[x >= xleft]) > panel.abline(fit) > }) > ---<---------------cut here---------------end---------------->--- > > i.e. the left limit for fitting the line is defined by the mean of x > values where y is equal to the maximum y values, *within* each combination > of levels of both factors. The above is giving me: > > Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : > 0 (non-NA) cases > In addition: Warning message: > no finite arguments to max; returning -Inf > > which shows I'm not understanding how the 'subscripts' argument works. > I'd appreciate some pointers on what I'm doing wrong, as I haven't been > able to find help in the help pages and List archives.Well, there are exceptions to this rule, but generally x and y, when they are passed on to the panel function, are _already_ subsetted, so x[subscripts] makes absolutely no sense. Note how your panel function calls panel.xyplot(x, y, ...) without referring to subscripts at all. The subscripts argument is there for other variables (e.g. if you were drawing confidence intervals, and had a separate vector in your data specifying the interval lengths). In your case, there are no other variables involved, so just get rid of the subscripts. Deepayan