[Rd] Web site for MacOSX R-devel precompiled version
From several years, I used this site http://r.research.att.com to get a precompiled version of macosx R-devol but the most recent version is frozen at the 18/8 build (r 71112). Is there an alternative (except than compile myself !) ? Thanks, Marc __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Suggestion for optim() in stats package
When optim() is used with method="BFGS", the name of parameters within
the vector are transmitted (see below, first example).
When method="Brent", the name of parameter (only one parameter can be
fitted with Brent method) is not transmitted. As there is only one, of
course, we know which parameter it is, but it makes things
non-consistent between methods.
It would be better that same convention is used for different method as
it will permit to make more general use of optim().
Marc
Tested in R-3.4.1
For example, here:
@@@
Method BFGS
@@@
# The names of values in par are transmitted
fitnorm_meansd<-function(par, val) {
print(par)
-sum(dnorm(x=val, mean=par["mean"], sd=par["sd"], log = TRUE))
}
val <- rnorm(100, mean=20, sd=2)
p<-c(mean=20, sd=2)
result<-optim(par=p, fn=fitnorm_meansd, val=val, method="BFGS")
The print(par) shows the named vector:
> result<-optim(par=p, fn=fitnorm_meansd, val=val, method="BFGS")
mean sd
202
mean sd
20.001 2.000
mean sd
19.999 2.000
mean sd
20.000 2.001
etc...
@@@
Method Brent
@@@
# The name of value in par is not transmitted
fitnorm_mean<-function(par, val) {
print(par)
-sum(dnorm(x=val, mean=par, sd=2, log = TRUE))
}
val <- rnorm(100, mean=20, sd=2)
p<-c(mean=20)
result<-optim(par=p, fn=fitnorm_mean, val=val, method="Brent", lower=10,
upper=30)
The print(par) does not show named vector:
> result<-optim(par=p, fn=fitnorm_mean, val=val, method="Brent",
lower=10, upper=30)
[1] 17.63932
[1] 22.36068
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] MASS:::dropterm.glm() and MASS:::addterm.glm() should use ... for extractAIC()
Here is a change required from MASS:::dropterm.glm() and MASS:::addterm.glm(). Thanks Marc The stepAIC() function from package MASS uses extractAIC() to get the AIC from a model. Several methods exist: extractAIC.glm() for example, some in MASS packages and some in stats package. The parameters for extractAIC() are: fit, scale, k = 2, ... The ... are not used in most of the extractAIC.xxx() methods, from example in stats:::extractAIC.glm() or MASS:::extractAIC.loglm() but its presence could be necessary if extractAIC() is changed to use for example to use AICc rather than AIC. Within stepAIC(), extractAIC() uses always the ... parameter. So all is ok for that. However, stepAIC() uses dropterm() or addterm(). Within MASS:::dropterm.glm() and MASS:::addterm.glm(), extractAIC() is also used but without the ... parameter. It prevents to use new version of extractAIC() that could use this parameter. The solution is simple: In MASS:::dropterm.glm(), line 60 and MASS:::addterm.glm(), line 84: aic <- aic + (extractAIC(object, k = k)[2L] - aic[1L]) must be changed to aic <- aic + (extractAIC(object, k = k, ...)[2L] - aic[1L]) Other dropterm.xxx() and addterm.xxx() do not suffer this problem. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] MASS:::dropterm.glm() and MASS:::addterm.glm() should use ... for extractAIC()
Hi, I have sent this message to this list the July, 7th. It was about a problem in MASS package. Until now there is no change in the devel version. As the problem occurs in a package and not in the R-core, I don't know if the message should have been sent here. Anyway, I have added a copy to Pr Ripley. I hope it could have been fixed. Sincerely Marc Le 09/07/2017 à 16:05, Marc Girondot via R-devel a écrit : Here is a change required from MASS:::dropterm.glm() and MASS:::addterm.glm(). Thanks Marc The stepAIC() function from package MASS uses extractAIC() to get the AIC from a model. Several methods exist: extractAIC.glm() for example, some in MASS packages and some in stats package. The parameters for extractAIC() are: fit, scale, k = 2, ... The ... are not used in most of the extractAIC.xxx() methods, from example in stats:::extractAIC.glm() or MASS:::extractAIC.loglm() but its presence could be necessary if extractAIC() is changed to use for example to use AICc rather than AIC. Within stepAIC(), extractAIC() uses always the ... parameter. So all is ok for that. However, stepAIC() uses dropterm() or addterm(). Within MASS:::dropterm.glm() and MASS:::addterm.glm(), extractAIC() is also used but without the ... parameter. It prevents to use new version of extractAIC() that could use this parameter. The solution is simple: In MASS:::dropterm.glm(), line 60 and MASS:::addterm.glm(), line 84: aic <- aic + (extractAIC(object, k = k)[2L] - aic[1L]) must be changed to aic <- aic + (extractAIC(object, k = k, ...)[2L] - aic[1L]) Other dropterm.xxx() and addterm.xxx() do not suffer this problem. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
