Re: [R-pkg-devel] import with except(ion)
No need to reinvent the wheel. Göran, you already use the "specials"
feature of terms.formula to find strata():
> specials: which functions in the formula should be marked as special in
> the 'terms' object? A character vector or 'NULL'.
I think you can do the same for frailty(), for example:
> formula <- Surv(time, status) ~ age + frailty(inst)
>
> Terms <- terms(formula, specials = "frailty")
> frailties <- attr(Terms, "specials")$frailty
> if (length(frailties)) warning("frailty() is not supported by coxreg")
Best regards,
Sebastian
Am 31.10.20 um 14:30 schrieb Gabor Grothendieck:
> coxreg could search for frailty and issue a warning or error if found. This
> returns TRUE if frailty is used in the formula argument as a function but
> not otherwise. That would allow implementation of a nicer message than
> if it were just reported as a missing function.
>
> find_frailty <- function(e) {
> if (is.logical(e)) return(e)
> if (length(e) > 1) {
> if (identical(e[[1]], as.name("frailty"))) return(TRUE)
> for (i in 1:length(e)) if (isTRUE(Recall(e[[i]]))) return(TRUE)
> }
> FALSE
> }
> find_frailty(frailty ~ frailty)
> ## [1] FALSE
> fo <- Surv(time, status) ~ age + frailty(inst)
> find_frailty(fo)
> ## [1] TRUE
>
> On Fri, Oct 30, 2020 at 2:46 PM Göran Broström wrote:
>>
>> My CRAN package eha depends on the survival package, and that creates
>> problems with innocent users: It is about the 'frailty' function
>> (mainly). While (after 'library(eha)')
>>
>> f1 <- coxph(Surv(time, status) ~ age + frailty(inst), data = lung)
>>
>> produces what you would expect (a frailty survival analysis), the use of
>> the coxreg function from eha
>>
>> f2 <- coxreg(Surv(time, status) ~ age + frailty(inst), data = lung)
>>
>> produces (almost) nonsense. That's because the survival::frailty
>> function essentially returns its input and coxreg is happy with that,
>> treats it as an ordinary numeric (or factor) covariate, and nonsense is
>> produced, but some users think otherwise. (Maybe it would be better to
>> introduce frailty in a separate argument?)
>>
>> I want to prevent this to happen, but I do not understand how to do it
>> in the best way. I tried to move survival from Depends: to Imports: and
>> adding import(survival, except = c(frailty, cluster)) to NAMESPACE. This
>> had the side effect that a user must qualify the Surv function by
>> survival::Surv, not satisfactory (similarly for other popular functions
>> in survival).
>>
>> Another option I thought of was to define my own Surv function as
>> Surv <- survival::Surv in my package, but it doesn't feel right.
>> It seems to work, though.
>>
>> As you may understand from this, I am not very familiar with these
>> issues. I have used Depends: survival for a long time and been happy
>> with that.
>>
>> Any help on this is highly appreciated.
>>
>> Göran
>>
>> __
>> R-package-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>
>
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Re: [R-pkg-devel] import with except(ion)
Thanks!
Göran
On 2020-11-02 11:09, Sebastian Meyer wrote:
No need to reinvent the wheel. Göran, you already use the "specials"
feature of terms.formula to find strata():
specials: which functions in the formula should be marked as special in
the 'terms' object? A character vector or 'NULL'.
I think you can do the same for frailty(), for example:
formula <- Surv(time, status) ~ age + frailty(inst)
Terms <- terms(formula, specials = "frailty")
frailties <- attr(Terms, "specials")$frailty
if (length(frailties)) warning("frailty() is not supported by coxreg")
Best regards,
Sebastian
Am 31.10.20 um 14:30 schrieb Gabor Grothendieck:
coxreg could search for frailty and issue a warning or error if found. This
returns TRUE if frailty is used in the formula argument as a function but
not otherwise. That would allow implementation of a nicer message than
if it were just reported as a missing function.
find_frailty <- function(e) {
if (is.logical(e)) return(e)
if (length(e) > 1) {
if (identical(e[[1]], as.name("frailty"))) return(TRUE)
for (i in 1:length(e)) if (isTRUE(Recall(e[[i]]))) return(TRUE)
}
FALSE
}
find_frailty(frailty ~ frailty)
## [1] FALSE
fo <- Surv(time, status) ~ age + frailty(inst)
find_frailty(fo)
## [1] TRUE
On Fri, Oct 30, 2020 at 2:46 PM Göran Broström wrote:
My CRAN package eha depends on the survival package, and that creates
problems with innocent users: It is about the 'frailty' function
(mainly). While (after 'library(eha)')
f1 <- coxph(Surv(time, status) ~ age + frailty(inst), data = lung)
produces what you would expect (a frailty survival analysis), the use of
the coxreg function from eha
f2 <- coxreg(Surv(time, status) ~ age + frailty(inst), data = lung)
produces (almost) nonsense. That's because the survival::frailty
function essentially returns its input and coxreg is happy with that,
treats it as an ordinary numeric (or factor) covariate, and nonsense is
produced, but some users think otherwise. (Maybe it would be better to
introduce frailty in a separate argument?)
I want to prevent this to happen, but I do not understand how to do it
in the best way. I tried to move survival from Depends: to Imports: and
adding import(survival, except = c(frailty, cluster)) to NAMESPACE. This
had the side effect that a user must qualify the Surv function by
survival::Surv, not satisfactory (similarly for other popular functions
in survival).
Another option I thought of was to define my own Surv function as
Surv <- survival::Surv in my package, but it doesn't feel right.
It seems to work, though.
As you may understand from this, I am not very familiar with these
issues. I have used Depends: survival for a long time and been happy
with that.
Any help on this is highly appreciated.
Göran
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Re: [R-pkg-devel] import with except(ion)
Just a final observation: This can happen to anybody
-
> lm(weight ~ feed, data = chickwts)
Call:
lm(formula = weight ~ feed, data = chickwts)
Coefficients:
(Intercept) feedhorsebeanfeedlinseed feedmeatmeal
feedsoybean feedsunflower
323.583 -163.383 -104.833-46.674
-77.155 5.333
> lm(weight ~ frailty(feed), data = chickwts)
Error in frailty(feed) : could not find function "frailty"
> library(survival)
> lm(weight ~ frailty(feed), data = chickwts)
Call:
lm(formula = weight ~ frailty(feed), data = chickwts)
Coefficients:
(Intercept) frailty(feed)
232.165 8.147
---
G,
On 2020-11-02 11:15, Göran Broström wrote:
Thanks!
Göran
On 2020-11-02 11:09, Sebastian Meyer wrote:
No need to reinvent the wheel. Göran, you already use the "specials"
feature of terms.formula to find strata():
specials: which functions in the formula should be marked as special in
the 'terms' object? A character vector or 'NULL'.
I think you can do the same for frailty(), for example:
formula <- Surv(time, status) ~ age + frailty(inst)
Terms <- terms(formula, specials = "frailty")
frailties <- attr(Terms, "specials")$frailty
if (length(frailties)) warning("frailty() is not supported by coxreg")
Best regards,
Sebastian
Am 31.10.20 um 14:30 schrieb Gabor Grothendieck:
coxreg could search for frailty and issue a warning or error if
found. This
returns TRUE if frailty is used in the formula argument as a function
but
not otherwise. That would allow implementation of a nicer message than
if it were just reported as a missing function.
find_frailty <- function(e) {
if (is.logical(e)) return(e)
if (length(e) > 1) {
if (identical(e[[1]], as.name("frailty"))) return(TRUE)
for (i in 1:length(e)) if (isTRUE(Recall(e[[i]]))) return(TRUE)
}
FALSE
}
find_frailty(frailty ~ frailty)
## [1] FALSE
fo <- Surv(time, status) ~ age + frailty(inst)
find_frailty(fo)
## [1] TRUE
On Fri, Oct 30, 2020 at 2:46 PM Göran Broström
wrote:
My CRAN package eha depends on the survival package, and that creates
problems with innocent users: It is about the 'frailty' function
(mainly). While (after 'library(eha)')
f1 <- coxph(Surv(time, status) ~ age + frailty(inst), data = lung)
produces what you would expect (a frailty survival analysis), the
use of
the coxreg function from eha
f2 <- coxreg(Surv(time, status) ~ age + frailty(inst), data = lung)
produces (almost) nonsense. That's because the survival::frailty
function essentially returns its input and coxreg is happy with that,
treats it as an ordinary numeric (or factor) covariate, and nonsense is
produced, but some users think otherwise. (Maybe it would be better to
introduce frailty in a separate argument?)
I want to prevent this to happen, but I do not understand how to do it
in the best way. I tried to move survival from Depends: to Imports: and
adding import(survival, except = c(frailty, cluster)) to NAMESPACE.
This
had the side effect that a user must qualify the Surv function by
survival::Surv, not satisfactory (similarly for other popular functions
in survival).
Another option I thought of was to define my own Surv function as
Surv <- survival::Surv in my package, but it doesn't feel right.
It seems to work, though.
As you may understand from this, I am not very familiar with these
issues. I have used Depends: survival for a long time and been happy
with that.
Any help on this is highly appreciated.
Göran
__
R-package-devel@r-project.org mailing list
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