Re: [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 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@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@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.
Re: [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 Às 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@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. __ R-help@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.
[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) __ R-help@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.