Hi,
I'm using gl1ce with family=binomial like so:
>yy
succ fail
[1,] 76 23
[2,] 32 67
[3,] 56 43
...
[24,] 81 18
>xx
c1219 c643
X1 0.04545455 0.64274145
X2 0.17723669 0.90392792
...
X24 0.80629054 0.12239320
>test.gl1ce <- gl1ce(yy ~ xx, family = binomial(link=logit), bound =
0.5 )
or
>omit <- c(2,3)
>test.gl1ce <- gl1ce(yy[-omit,] ~ xx[-omit,], family =
binomial(link=logit), bound = 1 )
this seems to work fine and as i change the shrinkage parameter
everything behaves as expected.
if i try to get the fitted values (y-hat) using predict i have no
problems:
> predict.gl1ce(test.gl1ce)
[1] 0.38129977 0.16513661 0.47666779 0.45348757 0.09916513 0.18167674
[7] 0.11047684 0.15786664 0.14765670 0.40657031 0.19072570 0.80259477
[13] 0.36317090 0.35930557 0.23700520 0.17579282 0.18835043 0.52306049
[19] 0.28388953 0.41262864 0.29933710 0.43556139 0.15276727 0.73017401
***
I have problems, however, when i try to use predict.gl1ce() with
newdata.
so, the following tries all give errors:
> predict.gl1ce(test.gl1ce, xx, family=binomial(link-logit))
> predict.gl1ce(test.gl1ce, xx)
> predict.gl1ce(test.gl1ce, xx[omit,], family=binomial(link-logit))
Error in predict.l1ce(test.gl1ce, xx, family = binomial(link - logit)) :
Argument `newdata' is not a data frame, and cannot be coerced
to an appropriate model matrix
the following weak try also bombs:
> predict.gl1ce(test.gl1ce, data.frame(xx), family=binomial(link-logit))
Error in eval(expr, envir, enclos) : attempt to apply non-function
I've tried quite a few variations. It seems I'm missing something, but
if glm or gl1ce take a certain
data format then the corresponding predict me,thods should (what am i
missing).
thanks,
Rico
Richard Bonneau
Institute for Systems Biology
Seattle, WA
206-732-1463
206-732-1299 (fax)
Richard Bonneau <rbonneau at systemsbiology.org> writes:> Hi, > > I'm using gl1ce with family=binomial like so: > >yy > succ fail > [1,] 76 23 > [2,] 32 67 > [3,] 56 43 > ... > [24,] 81 18 > > >xx > c1219 c643 > X1 0.04545455 0.64274145 > X2 0.17723669 0.90392792 > ... > X24 0.80629054 0.12239320 > > >test.gl1ce <- gl1ce(yy ~ xx, family = binomial(link=logit), bound > 0.5 ) > or > >omit <- c(2,3) > >test.gl1ce <- gl1ce(yy[-omit,] ~ xx[-omit,], family > binomial(link=logit), bound = 1 ) > > this seems to work fine and as i change the shrinkage parameter > everything behaves as expected. > > if i try to get the fitted values (y-hat) using predict i have no > problems: > > predict.gl1ce(test.gl1ce) > [1] 0.38129977 0.16513661 0.47666779 0.45348757 0.09916513 0.18167674 > [7] 0.11047684 0.15786664 0.14765670 0.40657031 0.19072570 0.80259477 > [13] 0.36317090 0.35930557 0.23700520 0.17579282 0.18835043 0.52306049 > [19] 0.28388953 0.41262864 0.29933710 0.43556139 0.15276727 0.73017401 > > *** > I have problems, however, when i try to use predict.gl1ce() with > newdata. > > so, the following tries all give errors: > > predict.gl1ce(test.gl1ce, xx, family=binomial(link-logit)) > > predict.gl1ce(test.gl1ce, xx) > > predict.gl1ce(test.gl1ce, xx[omit,], family=binomial(link-logit)) > Error in predict.l1ce(test.gl1ce, xx, family = binomial(link - logit)) : > Argument `newdata' is not a data frame, and cannot be coerced > to an appropriate model matrix > > the following weak try also bombs: > > predict.gl1ce(test.gl1ce, data.frame(xx), family=binomial(link-logit)) > Error in eval(expr, envir, enclos) : attempt to apply non-function > > > I've tried quite a few variations. It seems I'm missing something, but > if glm or gl1ce take a certain > data format then the corresponding predict me,thods should (what am i > missing).1. try link=logit, as opposed to what you typed 2. xx is probably not a data frame (or yy~xx would unlikely work), so as.data.frame might do the trick. 3. what is gl1ce? I you're having trouble with an add-on package, you might have the courtesy to tell us which one. Not everyone uses lasso2 on a daily basis, you know. -- O__ ---- Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
On 3 Dec 2003 at 16:07, Richard Bonneau wrote: Could you tell us where you found gl1ec ? Kjetil Halvorsen> Hi, > > I'm using gl1ce with family=binomial like so: > >yy > succ fail > [1,] 76 23 > [2,] 32 67 > [3,] 56 43 > ... > [24,] 81 18 > > >xx > c1219 c643 > X1 0.04545455 0.64274145 > X2 0.17723669 0.90392792 > ... > X24 0.80629054 0.12239320 > > >test.gl1ce <- gl1ce(yy ~ xx, family = binomial(link=logit), bound > 0.5 ) or > >omit <- c(2,3) > >test.gl1ce <- gl1ce(yy[-omit,] ~ xx[-omit,], family = > binomial(link=logit), bound = 1 ) > > this seems to work fine and as i change the shrinkage parameter > everything behaves as expected. > > if i try to get the fitted values (y-hat) using predict i have no > problems: > > predict.gl1ce(test.gl1ce) > [1] 0.38129977 0.16513661 0.47666779 0.45348757 0.09916513 > 0.18167674 [7] 0.11047684 0.15786664 0.14765670 0.40657031 > 0.19072570 0.80259477 > [13] 0.36317090 0.35930557 0.23700520 0.17579282 0.18835043 0.52306049 > [19] 0.28388953 0.41262864 0.29933710 0.43556139 0.15276727 0.73017401 > > *** > I have problems, however, when i try to use predict.gl1ce() with > newdata. > > so, the following tries all give errors: > > predict.gl1ce(test.gl1ce, xx, family=binomial(link-logit)) > > predict.gl1ce(test.gl1ce, xx) > > predict.gl1ce(test.gl1ce, xx[omit,], family=binomial(link-logit)) > Error in predict.l1ce(test.gl1ce, xx, family = binomial(link - logit)) > : > Argument `newdata' is not a data frame, and cannot be coerced > > to an appropriate model matrix > > the following weak try also bombs: > > predict.gl1ce(test.gl1ce, data.frame(xx), > family=binomial(link-logit)) > Error in eval(expr, envir, enclos) : attempt to apply non-function > > > I've tried quite a few variations. It seems I'm missing something, but > if glm or gl1ce take a certain data format then the corresponding > predict me,thods should (what am i missing). > > thanks, > Rico > > > Richard Bonneau > Institute for Systems Biology > Seattle, WA > 206-732-1463 > 206-732-1299 (fax) > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help