similar to: Extracting a function from a R package

Dear R users: I am looking for the source code for the R function extractAIC. Type the function name doesn't help: > extractAIC function (fit, scale, k = 2, ...) UseMethod("extractAIC") <environment: namespace:stats> And when I search it in the R source code, the best I can find is in (R source root)/library/stats/R/add.R: extractAIC <- function(fit, scale, k = 2,

Hi All, I'm having trouble with the automatized model generation (dredge) function in the MuMIn package. I'm trying to use it to automatically generate subsets of models from a global cox proportional hazards model, and rank them based on AICc. These seems like it's possible, and the Mumin documentation says that coxph is supported. However, when I run the code (see below), it gives

tl;dr: S3 lookup no longer works in custom non-namespace environments as of R 3.6.1. Is this a bug? I am implementing S3 dispatch for generic methods in environments that are not packages. I am trying to emulate the R package namespace mechanism by having a ?namespace? environment that defines generics and methods, but only exposes the generics themselves, not the methods. To make S3 lookup work

I am using R 2.0.2 on a WinXP I am trying to get the code of the Kruskal-Wallis test but > kruskal.test function (x, ...) UseMethod("kruskal.test") <environment: namespace:stats> > ls(3) [1] "acf" "acf2AR" "add.scope" .............. [181] "kruskal.test" "ks.test"

Hi, I have a question about how to extract paramters from a fitted model. I can extract coefficients and std, but from some other statistics, I dont know how to extract. Can anyone help? Here it is an example: > coxout<-coxph(Surv(t,t.censor)~x) > coxout Call: coxph(formula = Surv(t, t.censor) ~ x) coef exp(coef) se(coef) z p x 0.349 1.42 0.257 1.36 0.17 Likelihood

Dear All, there seems to be some strange influence of the Design package on data.frame. If I build a data.frame containing a Surv object without loading the package Design, the data frame is usable to coxph. If instead I just load Design and build a data.frame afterwards, the naming of the Surv object is different and it does not work with coxph. (In my real application I loaded Design to use the

Dear all, how can I check the source code for a hidden function like cor.test()? At the moment I get ... > cor.test function (x, ...) UseMethod("cor.test") <environment: namespace:stats> Thanks in advance, Will

Dear List, How do I extract the approximate Wald test for the frailty (in the following example 17.89 value)? What about the P-values, other Chisq, DF, se(coef) and se2? How can they be extracted? ######################################################> kfitm1 Call: coxph(formula = Surv(time, status) ~ age + sex + disease + frailty(id, dist = "gauss"), data = kidney)

>na.contiguous function (object, ...) UseMethod("na.contiguous") <environment: namespace:stats> this is what I get when I look for the source code for some functions- Is there a way to look at the source code? -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like

In S-Plus, I can look at the structure of a function (for example, hist) simply by entering hist <RETURN> however, if I do this in R, I get the response function (x, ...) UseMethod("hist") <environment: namespace:graphics> How can I inspect the structure of a function in R? ------------------------------- Richard Dybowski 143 Village Way

Dear List, I have a question regarding "ipred" package. Under 10-fold cv, for different knn ( = 1,3,...25), I am getting same misclassification errors: ############################################# library(ipred) data(iris) cv.k = 10 ## 10-fold cross-validation bwpredict.knn <- function(object, newdata) predict.ipredknn(object, newdata, type="class") for (i in

Hello Pardon for the elementary question, I did try searching the archives with various terms, but to no avail. I am using R1.9.1 on a windows machine One of the great advantages of R (to me, anyway) is being able to see the code for a function , e.g. by typing sd one sees the code for getting a standard deviation. However, for many functions this only provides info. including UseMethod, eg.

On Sat, 18 May 2019 at 23:34, Pavel Krivitsky <pavel at uow.edu.au> wrote: > > > The issue here is that you are registering a non-standard name > > (.gen.formula) for that generic and then defining what would be the > > standard name (gen.formula) for... what purpose? IMHO, this is a bad > > practice and should be avoided. > > The situation initially arose

I am having a problem extracting from "mer" objects.    I have constructed my problem using existing datasets.   Using the following commands:   require(lme4) fm1 <- lmer(Yield ~ 1 + (1 | Batch), Dyestuff) fixef(fm1) I get the following error message: "Error in UseMethod("fixef") : no applicable method for "fixef""   I know that "fixef" is in

Hi, If I try to read the codes of functions in e1071 package, it gives me following error message. >library(e1071) > svm function (x, ...) UseMethod("svm") <environment: namespace:e1071> > predict.svm Error: Object "predict.svm" not found > Can someone help me on this how to read the codes of the functions in the e1071 package? Thanks. Raj

Dear List, After including cluster() option the coxreg (from eha package) produces results slightly different than that of coxph (from survival) in the following time-dependent treatment effect calculation (example is used just to make the point). Will appreciate any explaination / comment. cheers, Ehsan ############################ require(survival) require(eha) data(heart) # create weights

Hi all. If I run the simple regression when x is a categorical variable ( x <- factor(x) ): > MyFit <-coxph( Surv(start, stop, event) ~ x ) How can I get the overall p-value on x other than for each dummy variable? > anova(MyFit) does NOT provide that information as previously suggested on the list. All the best, Kare [[alternative HTML version deleted]]

Hello, I am using Dr. Harrell's rms package to make a nomogram. I was able to make a beautiful one. However, I want to change 5-year survival probability to 5-year failure probability. I couldn?t get hazard rate from Hazard(f1) because I used cph for the model. Here is my code: library(rms) f1 <- cph(Surv(retime,dfs) ~ age+her2+t_stage+n_stage+er+grade+cytcyt+Cyt_PCDK2 , data=data11,

Hello, I am trying to use the package "exams" to construct problem sets. I have constructed an exercise which generates a list of integers and asks the student to compute the median. rx is the vector of n numbers >str(rx) num [1:16] 21 9 8 18 4 12 17 2 9 7 ... I want to print out the entire vector as part of the problem. When I use \Sexpr(rx) only the first value (in this case

Dear List, Can anyone please explain the difference between cluster() and frailty() in a coxph? I am a bit puzzled about it. Would appreciate any useful reference or direction. cheers, Ehsan > marginal.model <- coxph(Surv(time, status) ~ rx + cluster(litter), rats) > frailty.model <- coxph(Surv(time, status) ~ rx + frailty(litter), rats) > marginal.model Call: coxph(formula =