similar to: differences between aov and lme

Hi, we noticed there was a error in the "arules" package. After reading the source code, we saw that the Dice similarity index was "miscalculated" in "dissimilarity" function : an copy-paste from Jaccard Index was not corrected (2* a_b_c, ie 2*(a+b+c) in the code instead of 2*a +b + c !!!). After our mail to R-help (21/11/2006), we thought the authors could do

Bonjour, we wanted to fit a manova as descripted in Marieta /et al./ 2003, "convergent habitat segregation of /Aedes aegyptii/ and /Aedes albopictus/ (Diptera: /Culicidae/) in Southern Brazil and Florida", /J. Med. Entomol./, *40* (6), 785-794. They did their analysis with SAS software. We have the same kind of data with two insect species and city, habitat and season factors. We

Hi, I misunderstand the definition of Canberra distance in R. On Internet and in function description pages of dist() from stats and Dist() from amap, Canberra distance between vectors x and y, d(x,y), is : d(x,y) = sum(abs(x-y)/(x+y)) But in use, through simple examples, we find that the formula is : d(x,y) = (NZ + 1)/NZ * sum(abs(x-y)/(x+y)) with NZ = nb of pairs of coordinates that are

Dear All user, Hello, I'm a student and I have some trouble with the experimental (columns-experiments) design of my project. I use a randomized block design with 4 treatments including a control. For each treatment, I use 3 replicates and 3 blocks. The treatments are: -T1 = COD (300 mg/Lit) COD=chemical oxygen demand -T2 = COD (200 mg/Lit) -T3 = COD (100 mg/Lit) -T4 = COD (0 mg/Lit) as

Hi, I have this: lme(y~x1+x2,random=~1|x1/x2) How to make this random effect using lmer? I try this: lmer(y~x1+x2+(1|x1/x2) But it dont work. Any idea? Thanks Ronaldo -- System halted! -- |> // | \\ [***********************************] | ( ?? ?? ) [Ronaldo Reis J??nior ] |> V [UFV/DBA-Entomologia ] | / \ [36570-000 Vi??osa -

---------- Forwarded message ---------- From: alis villiyam <aalisiyan at gmail.com> Date: Mon, Jul 27, 2009 at 9:47 AM Subject: randomized block design analysis in R To: bolker at zoology.ufl.edu Dear All user Hello, I'm a student and I have some trouble with the experimental (columns-experiments) design of my project. I use a randomized block design with 4 treatments including a

Does anyone know how to extract residuals in lmer? Here's the error I get: > crop.lme=lmer(response~variety*irrigation*pesticide+(1|rep)+(1|rep: pesticide)+(1|rep:pesticide:irrigation), crop.data) > qqnorm(crop.lme) Error in qqnorm.default(crop.lme) : y is empty or has only NAs > resid(crop.lme) NULL Thanks! --Jake

r-help at stat.math.ethz.ch on Wednesday, October 26, 2005 at 6:00 AM -0500 wrote: Ronaldo, Try Harold's suggestion. The df still won't agree, because lmer (at least in its current version) just puts an upper bound on the df. But that should be OK, because all those t tests are approximations anyways, and you can get better confidence intervals (credible intervals, whatever) by using the

Hi, I have a data frame with variables a, b, c (character vars) and t (time var, could be represented as POSIXct or character, depending on which is most useful. The format is "yyyy-mm-dd hh:mm:ss CET"). Now, I want to sort the data frame in ascending order by a, b, c and then in descending order by t. Here's what I've got, but I'm not sure how to put the

Hi,   I am making a mock user interface in tcltk and I would like to add a 'check menu button' such as shown here: http://zetcode.com/tutorials/pygtktutorial/images/checkmenuitem.png   Does anybody know how to do this? I am quite new to R. Cheers!! Albert-Jan ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ All right, but apart from the sanitation, the medicine,

Hi,   I'm reading 100s of excel files and many of them contain links to external files (I hate that, but that aside). Every time such a file is opened, a menu pops up asking if I want to update the links. I never want to update the links. I used the macro recorder to see what code would be needed to suppress that message, but to no avail (I tried more variations, but one attempt is shown

Hi! How to calculate the correct SE of mean in a nested or spliplot anova? Nested example: --------------------- m <- aov(Glycogen~Treatment+Error(Treatment/Rat/Liver)) > m Call: aov(formula = Glycogen ~ Treatment + Error(Treatment/Rat/Liver)) Grand Mean: 142.2222 Stratum 1: Treatment Terms: Treatment Sum of Squares 1557.556 Deg. of Freedom 2 Estimated

Hello, A simple question perhaps, but how do I, within each row, find the first occurence of the number 1 in the df below? I want to use this position to programmatically create the variable 'year'. I'v come up with a solution, but I find it downright ugly. Is there a simpler way? I was hoping for a useful built-in function that I don;t yet know about. df <-

Hello, How can I tell RODBC to scan all the records of an xls file to determine the data type? If the first n records happen to be empty Rodbc assumes a character, and any numbers are made <NA>. And if, for instance, the first n records contain numbers, and later they also contain characters, those characters become NA. Cheers!! Albert-Jan

Hi,   I would like to recursively loop through al subfolders of a directory and do stuff with certain file types in those dirs. Is there a package/function that could do this? So it's more than Sys.glob. I'm looking for equivalent of Python's os.walk *) and I don't want to reinvent the wheel.   Thank you. Cheers!! Albert-Jan   *)

Hi,   I'm new to R and S4 classes. I defined a class with two methods (myMethod1 and myMethod2). I want to call myMethod1 within myMethod2. Why does the code below not work? The name 'myMethod1' doesn't appear to have meaning inside myMethod2, even though the two methods belong to the same class.     setClass(Class="SomeClass",      representation=representation(      

Hi,   If I use sprintf and return inside a function, sprintf doesn't print anything anymore. See the non-sense example below.   > x <- function() { a <- 888 + sprintf("xxx %s", a) } > x() [1] "xxx 888" > x <- function() { a <- 888 + sprintf("xxx %s", a) + return(a) } > x() [1] 888 Is this a bug? Cheers!! Albert-Jan

Hi,   Is there a built in function that returns a character vector of all subclasses of a given superclass? showClass(Class = "SomeClass") contains the info that I want, but I don't know how to access it. getSubClasses <- function(superClass) return(setdiff(getClasses(.GlobalEnv), superClass)) wíll only work if the global enviroment isn;t filled with other class definitions.

Hi R experts,   The fix() function canbe used to edit normal functions. I would like to know whether it's also possible to use something similar to edit a method of an S4 class. In other words, is there a fix-like function that allows me to edit method definitions without having to go back to the source code?   setGeneric (name="doStuff",def =

Hello,   Does anybody know if the OOP module (Chambers & Temple Lang) is going to replace the the S4 (and the S3) class system? http://www.omegahat.org/OOP/oop.pdf Cheers!! Albert-Jan ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ All right, but apart from the sanitation, the medicine, education, wine, public order, irrigation, roads, a fresh water system, and public