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Sorkin, John

2019-Dec-16 18:12 UTC

[R] How does one pass arguments to a function, such as coxph, that itself is inside a function?

Question summary: How does one pass arguments to a function, such as coxph, that
itself is inside a function.

I am trying to write a function that will allow me to call coxph using different
outcome and time variables. The coxph works when the coxph is NOT contained in a
larger function (which passes the outcome and time variable to? use), but does
not work when coxph is contained in a? larger funciton.

My code:

fit0 <-
coxph(Surv(FUtime,Death)~Age_in_years_at_A1_max+factor(Diabetes)+factor(CKD_stage)+
                                                      
factor(Phase1_first),data=mydata)
summary(fit0)

this works:?

Call:
coxph(formula = Surv(FUtime, Death) ~ Age_in_years_at_A1_max + 
? ?                         factor(Diabetes) + factor(CKD_stage) +
factor(Phase1_first),
? ? data = mydata)

? n= 350, number of events= 56 

? ? ? ? ? ? ? ? ? ? ? ? ? ?coef exp(coef) se(coef) ? ? ?z Pr(>|z|) ? ?
Age_in_years_at_A1_max ?0.04618 ? 1.04727 ?0.01384 ?3.338 0.000845 ***
factor(Diabetes)1 ? ? ? 0.12247 ? 1.13029 ?0.28282 ?0.433 0.664991 ? ?
factor(CKD_stage)3 ? ? -0.28418 ? 0.75263 ?0.38744 -0.733 0.463261 ? ?
factor(CKD_stage)4 ? ? ?0.33938 ? 1.40407 ?0.36583 ?0.928 0.353572 ? ?
factor(CKD_stage)5 ? ? ?0.97121 ? 2.64115 ?0.40171 ?2.418 0.015618 * ?
factor(Phase1_first)1 ? 0.02204 ? 1.02229 ?0.29713 ?0.074 0.940868 

other output deleted.

But this code does not work:

doit <- function(time,outcome,data){
? fit0 <-
coxph(Surv(time,outcome)~Age_in_years_at_A1_max+factor(Diabetes)+factor(CKD_stage)+factor(Phase1_first),data=data)
? print(summary(fit0))
}
doit(FUtime,Death,mydata)

 Error in Surv(time, outcome) : object 'FUtime' not found 

I am certain I have a scoping problem, but I don't know how to solve it. 

John David Sorkin M.D., Ph.D.

Professor of Medicine

Chief, Biostatistics and Informatics

University of Maryland School of Medicine Division of?Gerontology and Geriatric
Medicine

Baltimore VA Medical Center

10 North Greene Street

GRECC (BT/18/GR)

Baltimore, MD 21201-1524

(Phone) 410-605-7119

(Fax) 410-605-7913 (Please call phone number above prior to faxing)

Rui Barradas

2019-Dec-16 18:45 UTC

head link

[R] How does one pass arguments to a function, such as coxph, that itself is inside a function?

Hello,

You can assemble the formula with deparse/substitute and paste.
This is the example 2 from ?coxph. I have changed list(...) to 
data.frame(...)


doit <- function(s1, s2, data){
   s1 <- deparse(substitute(s1))
   s2 <- deparse(substitute(s2))
   fmla <- paste("Surv(", s1, ",", s2, ",
event)")
   fmla <- paste(fmla, "x", sep = "~")

   coxph(as.formula(fmla), data = data)
}

doit(start, stop, test2)


It works.

Hope this helps,

Rui Barradas

?s 18:12 de 16/12/19, Sorkin, John escreveu:> Question summary: How does one pass arguments to a function, such as coxph,
that itself is inside a function.
> 
> I am trying to write a function that will allow me to call coxph using
different outcome and time variables. The coxph works when the coxph is NOT
contained in a larger function (which passes the outcome and time variable to?
use), but does not work when coxph is contained in a? larger funciton.
> 
> My code:
> 
> fit0 <-
coxph(Surv(FUtime,Death)~Age_in_years_at_A1_max+factor(Diabetes)+factor(CKD_stage)+
>                                                        
factor(Phase1_first),data=mydata)
> summary(fit0)
> 
> this works:
> 
> Call:
> coxph(formula = Surv(FUtime, Death) ~ Age_in_years_at_A1_max +
>  ? ?                         factor(Diabetes) + factor(CKD_stage) +
factor(Phase1_first),
>  ? ? data = mydata)
> 
>  ? n= 350, number of events= 56
> 
>  ? ? ? ? ? ? ? ? ? ? ? ? ? ?coef exp(coef) se(coef) ? ? ?z Pr(>|z|)
> Age_in_years_at_A1_max ?0.04618 ? 1.04727 ?0.01384 ?3.338 0.000845 ***
> factor(Diabetes)1 ? ? ? 0.12247 ? 1.13029 ?0.28282 ?0.433 0.664991
> factor(CKD_stage)3 ? ? -0.28418 ? 0.75263 ?0.38744 -0.733 0.463261
> factor(CKD_stage)4 ? ? ?0.33938 ? 1.40407 ?0.36583 ?0.928 0.353572
> factor(CKD_stage)5 ? ? ?0.97121 ? 2.64115 ?0.40171 ?2.418 0.015618 *
> factor(Phase1_first)1 ? 0.02204 ? 1.02229 ?0.29713 ?0.074 0.940868
> 
> other output deleted.
> 
> But this code does not work:
> 
> doit <- function(time,outcome,data){
>  ? fit0 <-
>
coxph(Surv(time,outcome)~Age_in_years_at_A1_max+factor(Diabetes)+factor(CKD_stage)+factor(Phase1_first),data=data)
>  ? print(summary(fit0))
> }
> doit(FUtime,Death,mydata)
> 
>   Error in Surv(time, outcome) : object 'FUtime' not found
> 
> I am certain I have a scoping problem, but I don't know how to solve
it.
> 
> John David Sorkin M.D., Ph.D.
> 
> Professor of Medicine
> 
> Chief, Biostatistics and Informatics
> 
> University of Maryland School of Medicine Division of?Gerontology and
Geriatric Medicine
> 
> Baltimore VA Medical Center
> 
> 10 North Greene Street
> 
> GRECC (BT/18/GR)
> 
> Baltimore, MD 21201-1524
> 
> (Phone) 410-605-7119
> 
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
> 
> 
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

William Dunlap

2019-Dec-16 18:58 UTC

head link

[R] How does one pass arguments to a function, such as coxph, that itself is inside a function?

You can use substitute() to fiddle with the formula.  The following shows
how to do it using lm() instead of coxph(), but the manipulations are the
same.  It also has an 'envir' argument in case the formula depends on
anything in the callers enviroment.  The 'substitute(data)' is make the
printouts prettier.

f <- function (response, data, envir = parent.frame())
{
    formula <- eval(substitute(response ~ X), envir = envir)
    eval(as.call(list(quote(lm), formula, data = substitute(data))),
        envir = envir)
}
> d <- data.frame(check.names=FALSE, "Y-one"=1:10,
"Y-two"=sqrt(1:10),
X=log(1:10))> lm(`Y-one` ~ X, data=d)
Call:
lm(formula = `Y-one` ~ X, data = d)

Coefficients:
(Intercept)            X
    -0.4371       3.9307
> f(`Y-one`, data=d)
Call:
lm(formula = `Y-one` ~ X, data = d)

Coefficients:
(Intercept)            X
    -0.4371       3.9307> g <- function() {+     Y3 <- 1/(1:10)
+     f(Y3, data=d)
+ }> g()
Call:
lm(formula = Y3 ~ X, data = d)

Coefficients:
(Intercept)            X
     0.8338      -0.3581



E.g.,
Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Mon, Dec 16, 2019 at 10:12 AM Sorkin, John <jsorkin at
som.umaryland.edu>
wrote:
> Question summary: How does one pass arguments to a function, such as
> coxph, that itself is inside a function.
>
> I am trying to write a function that will allow me to call coxph using
> different outcome and time variables. The coxph works when the coxph is NOT
> contained in a larger function (which passes the outcome and time variable
> to  use), but does not work when coxph is contained in a  larger funciton.
>
> My code:
>
> fit0 <-
>
coxph(Surv(FUtime,Death)~Age_in_years_at_A1_max+factor(Diabetes)+factor(CKD_stage)+
>
>  factor(Phase1_first),data=mydata)
> summary(fit0)
>
> this works:
>
> Call:
> coxph(formula = Surv(FUtime, Death) ~ Age_in_years_at_A1_max +
>                             factor(Diabetes) + factor(CKD_stage) +
> factor(Phase1_first),
>     data = mydata)
>
>   n= 350, number of events= 56
>
>                            coef exp(coef) se(coef)      z Pr(>|z|)
> Age_in_years_at_A1_max  0.04618   1.04727  0.01384  3.338 0.000845 ***
> factor(Diabetes)1       0.12247   1.13029  0.28282  0.433 0.664991
> factor(CKD_stage)3     -0.28418   0.75263  0.38744 -0.733 0.463261
> factor(CKD_stage)4      0.33938   1.40407  0.36583  0.928 0.353572
> factor(CKD_stage)5      0.97121   2.64115  0.40171  2.418 0.015618 *
> factor(Phase1_first)1   0.02204   1.02229  0.29713  0.074 0.940868
>
> other output deleted.
>
> But this code does not work:
>
> doit <- function(time,outcome,data){
>   fit0 <-
>
>
coxph(Surv(time,outcome)~Age_in_years_at_A1_max+factor(Diabetes)+factor(CKD_stage)+factor(Phase1_first),data=data)
>   print(summary(fit0))
> }
> doit(FUtime,Death,mydata)
>
>  Error in Surv(time, outcome) : object 'FUtime' not found
>
> I am certain I have a scoping problem, but I don't know how to solve
it.
>
> John David Sorkin M.D., Ph.D.
>
> Professor of Medicine
>
> Chief, Biostatistics and Informatics
>
> University of Maryland School of Medicine Division of Gerontology and
> Geriatric Medicine
>
> Baltimore VA Medical Center
>
> 10 North Greene Street
>
> GRECC (BT/18/GR)
>
> Baltimore, MD 21201-1524
>
> (Phone) 410-605-7119
>
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
>
>
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
	[[alternative HTML version deleted]]

R help - Dec 2019 - How does one pass arguments to a function, such as coxph, that itself is inside a function?

[R] How does one pass arguments to a function, such as coxph, that itself is inside a function?

[R] How does one pass arguments to a function, such as coxph, that itself is inside a function?

[R] How does one pass arguments to a function, such as coxph, that itself is inside a function?