Note that neither call to glm in your myglm function really works - the first one is using the 'weights' object from the global environment, not the weights argument. E.g., in the fresh R session, where I avoid making unneeded assignments and use fixed x and y for repeatability,
> n <- 16 > data <- data.frame(x = log2(1:n), y = 1:n) > myglm2 <- function(formula, data, weights) { glm(formula, data=data, family=gaussian(), weights=weights) } > myglm2(y~., data=data, weights=1/(1:n)) Error in model.frame.default(formula = formula, data = data, weights = weights, : invalid type (closure) for variable '(weights)' The error arises because glm finds stats::weights, a function, not the argument called weights. glm(), lm() and their ilk evaluate their weights and subset arguments in the environment of the formula. In this case environment(y~.) is .GlobalEnv, not the function's environment. The following function gives one way to deal with this, by giving formula a new environment that inherits from its original environment and contains the extra variables. > myglm3 <- function(formula, data, weights) { envir <- list2env(list(weights=weights), parent=environment(formula)) environment(formula) <- envir glm(formula, data=data, family=gaussian(), weights=weights) } > myglm3(y~., data=data, weights=1/(1:n)) Call: glm(formula = formula, family = gaussian(), data = data, weights = weights) Coefficients: (Intercept) x -0.09553 2.93352 Degrees of Freedom: 15 Total (i.e. Null); 14 Residual Null Deviance: 60.28 Residual Deviance: 7.72 AIC: 70.42 This is the same result you get with a direct call to glm(y~., data=data, weights=1/(1:n)) This is a common problem and I don't know if there is a FAQ on it or a standard function to deal with it. Bill Dunlap TIBCO Software wdunlap tibco.com On Fri, Aug 28, 2020 at 8:33 AM John Smith <jsw...@gmail.com> wrote: > > Dear R-help: > > I am writing a function based on glm and would like some variations of > weights. In the code below, I couldn't understand why the second glm > function fails and don't know how to fix it: > > Error in eval(extras, data, env) : object 'newweights' not found > Calls: print ... eval -> <Anonymous> -> model.frame.default -> eval -> eval > Execution halted > > ### R code > y <- rnorm(100) > x <- rnorm(100) > data <- data.frame(cbind(x, y)) > weights <- rep(1, 100) > n <- 100 > myglm <- function(formula, data, weights){ > ## this works > print(glm(formula, data, family=gaussian(), weights)) > ## this is not working > newweights <- rep(1, n) > glm(formula, data, family=gaussian(), weights=newweights) > } > myglm(y~., data, weights) > > [[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. ______________________________________________ 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.