similar to: help with converting a data frame into object of class "track"

Hi, I have used Vegan to construct an NMDS ordination plot. I plotted sites of three forest types with the site number in it. My reviewer has asked me to use different symbols for each of the forest types. Can anyone send me how I can do this in R in simple steps. I have used the options like ordiplot, sel and pl syntaxes that are not working for the question that I asked for. Best, Sinu --

Hi the list I am fighting with the twins setAs and setIs... Here are some questions and comments (comments to myself but that migth be wrong, it is why I am posting them) 1. Very surprising : using setIs define 'is', 'as<-' but not 'as' ??? 2. Using setAs define 'as', 'as<-' but not 'is'... What surprise me is that as<- can be define by

Andreas, As far as I can tell (/conjecture), this is because the list of classes a particular class inherits from directly is appended to as needed, and so the order that a class extends others isd refined by the order that those connections are defined. We can see this with two setClassUnion calls, rather than required setAs: > setClass("grandma", slots = c(a =

Dear R core team Please apologize for posting the same question twice on R-help and R-devel. Since I was not sure which list is appropriate I tried R-help (Tue Mar 22), but got no answer. Now I do not know if the formulation of my question was unclear or the question is not so easy to answer or to easy (what I do not hope). My problem: I create a new S4 class, containing one slot, data (of

First of all, let me confess that I am a newbie to R and don't know much about the language or the environment. We have a need for plugging in R in our production runtime and need the ability to pull data out of our existing services. I am trying to see if I can take advantage of SSOAP such that we can expose the data via webservices and use SSOAP to call into them. Our runtime is mostly

Dear R gurus I've a question concerning the transformation of a new S4 class (that I defined) and the existing class "POSIXlt". I did the following: ## Definition of the new class: setClass("dtime", representation(data = "POSIXlt"), prototype(data = as.POSIXlt("2004/06/01"))) ## Transformation between the new class "dtime"

I ran into a problem recently trying to update a package which uses S4 methods using a recent beta of R. I think I can reproduce it with a simple example. I have package called `testpkg' in directory testpkg/. In the R/ subdirectory of testpkg/ I have a file called testpkg.R which contains the following two lines: setClass("testpkg", representation(pts = "list"))

I'm trying to resolve a small problem that has arisen from introducing a NAMESPACE for the package SparseM. Prior to the namespace I had a class "matrix.diag.csr" that consisted of diagonal sparse matrices. It was defined to have the same attributes as the matrix.csr class and setAs was used to define how to coerce integers and vectors into this form:

Dear colleagues, there is a behaviour with S4 (virtual) classes that I find very hard to understand: Depending on the position of setAs(), the tree of inheritance changes. This is my baseline example that defines the classes "grandma", "mother", "daughter" and a virtual class "mr_x". For a new instance if "daughter", "mr_x" is betweeen

Dear list, I'd like to write coercion methods for some of my Reference Classes. However, using 'setAs()' is not a real option as its argument 'def' only allows for functions depending on one single argument. In some cases, that is simply too much of a limitation for me. And I don't really see why it needs to be this way, so I guess this question is also some sort of a

An example sent by Ross Ihaka points out a non-obvious step needed to export the results of setAs(). The as() mechanism can't use ordinary method dispatch because the second argument is the name of a class, not an object from the class. So it uses a "helper" function, coerce(), and sets methods for that function. Therefore, if you want to export the results of setAs(), at the

By reading the documentation for _setIs_ I noted that for the same object three different names are used. 1) the name of the first argument in the functions coerce and replace in setIs must be _obj_ (see example section or) setIs("MVCa","list",coerce=function(obj){obj@list},replace=function(obj,value){obj@list<-value}) 2) At the same time in the usage section:

Hi, While checking the package I am getting all the time the following complain about the function: Undocumented S4 methods: generic coerce and siglist matrix,Massvector I have not defined the function nowhere in the R files. My gues is that this has something to do with the following definition of the setAs function. setAs("matrix","Massvector" ,def=

Consider this: $ cat test.dat 1 a 2 b Now, we want to read the 2nd column as a factor and ignore the first (since it's just a sequential ID). We can't just put "factor" among the colClasses (would have been nice), so let's try this instead > setAs("character","factor",as.factor) Arguments in definition changed from (x) to (from) >

(I am not sure if this is a bug or a request for a more understandable warning, or possible something obvious I should be posting on r-help.) I am trying to coerce an new class object to be a DBIConnection and it does not work the way I think it should: R version 2.5.1 (2007-06-27) ... > require("RMySQL") # or require("RSQLite") Loading required package: RMySQL Loading

Hi, We've observed rather strange behavior related to as(). When as() is used to make a conversion to a super class, an invalid entry is inserted into the table of methods. > setClass("A", contains="list") > get(".MTable", environment(coerce))[["list#A"]] NULL > as(list(), "A") > get(".MTable",

Hi list, I've got a class B that contains a slot obj of class A. I'd like to be able to call all the methods of class A directly on objects of class B as if I had called the method on slot obj. This without overloading all methods of class A to work on class B. I don't define B as an extension of A, because I want class B to also work with objects of classes that inherit from

This seemed too advanced for r-help and is related to the recent discussion of character vectors in dataframes. Following Brian Ripley's most excellent advice, we are moving to a world in which character vectors in dataframes are always of class AsIs. The cool way of doing this seemed to be the following: > cat(c("x", "y", "z"), file = "test.txt",

Dear R Community, We am pleased to announce the release of the 'bcpa' package. The source code and binaries is now on CRAN (http://cran.r-project.org/web/packages/bpca/index.html). The bpca package implements biplot (2d and 3d) and diagnostic tools of the quality of the reduction. It depends R (>= 2.6.0), scatterplot3d, rgl and MASS packages. Regards, --

Hi! Concerning different behaviour between 1.9.1 patched and: R : Copyright 2004, The R Foundation for Statistical Computing Version 2.0.0 Under development (unstable) (2004-09-06), ISBN 3-900051-07-0 Subtitle: as(x,"vector"); x is of class "Massvector"; never enters setAs("Massvector","vector"... The same code: as(mvl[[1]],"vector") causes