similar to: lme nesting/interaction advice

My previous question put in a simpler way: How would I pass a value of a variable to a function such as lm(Effect1~Trt*Dose, data = x, contrasts = list(Trt = contr.sum, Dose = contr.sum))? Here, 'Effect' is a column name in my data matrix, and I want "Effect1" to be replaced by "Effect2" and so on (my other column names in the data frame) for successive anova

Dear All, I would like to ask you to help me with my memeory. I remember using some function that would list all the possible methods I could apply to an object. Say, if I had an object of class=lme, it would tell me that that I could do stuff like qqnorm(myobjct), or VarCorr(myobject). In general, a very complete list. I though this list of all possible methods would pop out by typing

Here are two effects (with a common base) that perform a stage left/right effect. The effect is named after the Hanna Barbara character Snagglepuss. :) It shakes the contents briefly and then jets off (stage) to the left or right. I used the Shake effect as a guide to this one. The StageBase accepts the element and an "amount" to initially shake the element by. So in

Hi All, I have a list of matrices: > x [,1] [,2] [1,] 1 4 [2,] 2 5 [3,] 3 6 > y [,1] [,2] [,3] [,4] [,5] [,6] [1,] 18 21 24 27 30 33 [2,] 19 22 25 28 31 34 [3,] 20 23 26 29 32 35 > z =list(x,y) I want to create a second list that is has a subset each matrix in the list subsetting so I get the 2nd and 3rd row of each (and

Dear All, I saved by mistake the environment I was working in after typing q(), and now I get the annoying message: [Previously saved workspace restored] I have already deleted all the objects in the environment, saving it as an empty environment, so it's just a matter of nitpicking I suppose. The message does not appear if I start R from any other place in the directory tree. I am

I wrote a simple toggle function similar to Element.toggle that will toggle a section between being up and down using the Blind effect. I''m relatively new to the code, so I''m not sure if it''s implemented 100% correctly or if it can be done better. I am using it though and it seems to be working fine. Anyway, here''s the code and if you think it''s

Hi All, I have a vector of data, a vector of bin breakpoints and I want to put my data in the bins and then extract fanciful informations like the mean value of each bin. I know I can write my own function, but I would have thought that R should have somewhere a function that took as arguments something like (data, breaks, what to do with the data in the bins). I surey could not find it

Hi All, a colleague wants to calculate the Fisher information matrix for a model he wrote (not in R). He can easily get the neg-log-likelihood and the best fit parameters at the minimum. He can also get negLLs for other parameter values too. Given these data, is there a way in R to calculate the Fisher information matrix? Best, Federico -- Federico C. F. Calboli Department of Epidemiology

Hi All, I have the following problem: x = c(1,2) x [1] 1 2 as.matrix(x) [,1] [1,] 1 [2,] 2 BUT, if I add: y = c(3,4) as.matrix(rbind(x,y)) [,1] [,2] x 1 2 y 3 4 It does not transpose. Since I will need as.matrix() for a list of data that is in one or more lines, I need as.matrix to behave in a consisten fashions, so I get as.matrix(x, whatever) [,1] [,2] x 1

Hi All, is there an equivalent of the Unix command 'less' (or 'more'), so I can look at what's inside a data.frame or a matrix without having it printed out on console? I am using R on Debian Linux and Mac OS 10.4.5 Cheers, F -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44

HI All, I have a data frame such as: > test x y p d [1,] 1 0 10 21 0 [2,] 2 3 11 12 0 [3,] 3 4 12 23 0 [4,] 3 5 13 24 0 and I want to perfor some operations on the first two coulums, conditional on the uneqaulity values on the 3rd and 4th columns. For instance: j = 3 test[test[,1] == j, 5] = test[test[,1] == j,2] + test[test[,2] == j,1] gives me the result: test: x y p d

Hi All, I am using plot(x, type = 'l') for some plotting, but I would like rounded edges rather than jagged edges in the plot (purely for aestetic reasons). How could I achieve that? Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020

Hi You could try to find an equivalent representation as a string and try to match those. > (A <- cbind(sample(1:2, 10, rep=TRUE), sample(1:2, 10, rep=TRUE))) [,1] [,2] [1,] 1 2 [2,] 1 2 [3,] 1 2 [4,] 2 2 [5,] 1 1 [6,] 1 2 [7,] 1 2 [8,] 1 1 [9,] 1 2 [10,] 1 1 > (B <- unique(A)) [,1] [,2] [1,] 1 2

Hi All, I am looking for references on R as a programming language (apart form the standard R-lang.pdf and the other manuals), reference that would cover _in_depth_ things like loops, code optimisation, debugging tools etc... and is as up-to-date as possible. Can anyone suggest any book or other reference apart from the "green book" and the V&R "S-programming"? Cheers,

Hi All, I am (almost) successfully using apply() to apply a function recursively on a data matrix. The function is question is as.genotype() from the library 'genetics' apply(subset(chr1, names$breed == 'lab'),2,as.genotype,sep ="") Unfortuantely apply puts it's results into a matrix object rather than a data frame, tranforming my factors into numerics and

Glad to see this list get going! I have a custom effect ''Pulse'' that basically does an opacity fade in/ out. I want to execute this effect with a custom duration. I''m looking for a consistent approach that is inline with script.alicio.us and Prototype. Is there a way to do something like this (pseudo code): Effect2.Pulse = function(element) { new

Hi I have data from 12 subjects. The measurement is log(expression) of a particular gene and can be assumed to be normally distributed. The 12 subjects are divided into the following groups: Infected, Vaccinated, Lesions - 3 measurements Infected, Vaccintaed, No Lesions - 2 measurements Infected, Not Vaccinated, Lesions - 4 measurements Uninfected, Not Vaccinated, No Lesions - 3 measurements

Dear All, I am trying to calculate the Hardy-Weinberg Equilibrium p-value for 42 SNPs. I am using the function HWE.exact from the package "genetics". In order not to do a lot of coding "by hand", I have a for loop that goes through each column (each column is one SNP) and gives me the p.value for HWE.exact. Unfortunately some SNP have reached fixation and HWE.exact requires a

Hi All, is there any chance of vectorising the two ifelse() statements in the following code: for(i in gp){ new[i,1] = ifelse(srow[i]>0, new[srow[i],zippo[i]], sample(1:100, 1, prob =Y1, rep = T)) new[i,2] = ifelse(drow[i]>0, new[drow[i]>0,zappo[i]], sample(1:100, 1, prob =Y1, rep = T)) } Where I am forced to check if the value of drow and srow are >0 for each line... in

Good day, All, Is there any way to maintain the number of decimal places in the type of situation below? I would like to maintain the number of decimal places in 0.667, despite the fact that its column-mates have a fourth decimal place. Thank you for your time. Jim dat.txt contents: MARKER ALLELES FREQ1 RSQR EFFECT2 STDERR CHISQ PVALUE rs6599753 C,T