search for: m1

Hello, All! How might one accomplish this using the by() function? m1 is a data frame. # populate column "m1$major_allele" for ( i in 1:length(m1$major_allele)) { if ( m1$Freq1[i] == m1$MAF[i]){ m1$major_allele[i] = m1$Al1[i] } else{ m1$major_allele[i] = m1$Al2[i] } } Jim [[alternative HTML version deleted]]

Hi, final<-data.frame() ?? for (m1 in 4:10) { ?????? for (n1 in 4:10){? ?????????? for (x1 in 0: m1) { ????????????? for (y1 in 0: n1) { final<- rbind(final,c(m1,n1,x1,y1)) res}}}} ?final1<-within(final,{flag<-ifelse(x1/m1>y1/n1, 1,0)}) ?head(final1) #? m1 n1 x1 y1 flag #1? 4? 4? 0? 0??? 0 #2? 4? 4? 0? 1??? 0 #3? 4? 4?...

Hi, I''m trying to get a handle on hfsc. Here is my configuration: root@jmnrouter:/jmn# tc class show dev vlan1 class hfsc 1: root class hfsc 1:1 parent 1: ls m1 0bit d 0us m2 225000bit ul m1 0bit d 0us m2 225000bit class hfsc 1:10 parent 1:1 rt m1 191000bit d 25.0ms m2 135000bit ls m1 0bit d 0us m2 135000bit ul m1 0bit d 0us m2 225000bit class hfsc 1:20 parent 1:1 rt m1 22008bit d 25.0ms m2 56008bit ls m1 0bit d 0us m2 56008bit ul m1 0bit d 0us m2 225000bi...

Dear list, I have the following problem. I have a data frame like this CLUSTER YEAR variable Delta R_pivot M1 2005 EC01 NA NA M1 2006 EC01 2 NA M1 2007 EC01 4 5 M2 2005 EC01 NA...

...result is not quite what I would like. Here's sample code for you or anyone else who may be interested: Al1 = c('A','C','C','C') Al2 = c('G','G','G','T') Freq1 = c(0.0078,0.0567,0.9434,0.9908) MAF = c(0.0078,0.0567,0.0566,0.0092) m1 = data.frame(Al1=Al1, Al2=Al2,Freq1=Freq1,MAF=MAF,major_allele='') m1 Al1 Al2 Freq1 MAF major_allele 1 A G 0.0078 0.0078 2 C G 0.0567 0.0567 3 C G 0.9434 0.0566 4 C T 0.9908 0.0092 Using the suggestion involving "...

Hi, Does anyone know what the distribution for the product of two correlated normal? Say I have X~N(a, \sigma1^2) and Y~N(b, \sigma2^2), and the \rou(X,Y) is not equal to 0, I want to know the pdf or cdf of XY. Thanks a lot in advance. yu [[alternative HTML version deleted]]

I have problem with integer overflow that I cannot understand. I have a character vector curr.lemmas with the following properties: length(curr.lemmas) # 61224 length(unique(curr.lemmas)) # 2652 That vector is the input to the following function: yules.k1 <- function(input) { m1 <- length(input); temp <- table(table(input)) m2 <- sum("*"(temp, as.numeric(names(temp))^2)) return(10000*(m2-m1) / (m1*m1)) } When I run this, I get the following output: [1] NA Warning message: In m1 * m1 : NAs produced by integer overflow But when I change the functi...

HI, Using c11<- 0.01 c12<- 0.01 c1<- 0.10 c2<- 0.10 One possible problem is that: dim(res5) #[1] 513? 20 res6<-aggregate(.~m1+n1+m+n,data=res5[,c(1:6,9:12,21:24)] ,max) #Error in `[.data.frame`(res5, , c(1:6, 9:12, 21:24)) : ?# undefined columns selected A.K. ________________________________ From: Joanna Zhang <zjoanna2013 at gmail.com> To: arun <smartpink111 at yahoo.com> Sent: Saturday, March 9, 2013...

...a sparse Matrix via M[X]<-..., where X is a 2-column matrix, appears to drop user-assigned attributes. I dug around in the R code for Matrix trying to find the relevant machinery but my brain started to hurt too badly ... ?? Will submit this as a bug if it seems warranted. library(Matrix) m1 <- matrix(1:9,3,3) m1 <- Matrix(m1) attr(m1,"junk") <- 12 stopifnot(isTRUE(attr(m1,"junk")==12))? ## OK m1[cbind(1:2,2:3)] <- 1 stopifnot(isTRUE(attr(m1,"junk")==12)) ## not OK attr(m1,"junk") ## NULL ## note I have to use the ugly stopifnot(isT...

Dear list, I'll try to be more clear in explaining my problem. I have a data frame like this called X: CLUSTER YEAR variable value1 value2 M1 2005 EC01 NA NA M1 2006 EC01 2 5 M1 2007 EC01 4 5 M2 2005 EC01 NA...

...error massage. Error in split.default(x = seq_len(nrow(x)), f = f, drop = drop, ...) : Group length is 0 but data length > 0 On Thu, Jan 31, 2013 at 12:21 PM, arun kirshna [via R] < ml-node+s789695n4657196h87@n4.nabble.com> wrote: > Hi, > Try this: > colnames(d)<-c("m1","n1","x1","y1","p11","p12") > library(zoo) > res1<- do.call(rbind,lapply(lapply(split(d,list(d$m1,d$n1)),function(x) > {x$cp11[x$x1>1]<- cumsum(x$p11[x$x1>1]);x$cp12[x$y1>1]<- > cumsum(x$p12[x$y1>1]);x}),functi...

Dear R users, I'm trying to fit a gamma-frailty model on a simulated dataset, with 6 covariates, and I'm running into some results I do not understand. I constructed an example from my simulation code, where I fit a coxph model without frailty (M1) and with frailty (M2) on a number of data samples with a varying degree of heterogeneity (I'm running R 2.3.1, running takes ~1 min). library(survival); set.seed(10000) lambda <- 0.01 # Exp. hazard rate # Beta coefficients for Age,TC,HDLC,SBP,Diab,Smok beta <- c(0.0483,0.0064,-0.0270...

Dear R-helpers, I have a huge data-set so need to avoid for loops as much as possible. Can someone think how I can compute the result in the following example (that uses a for-loop) using some version of apply instead (or any other similarly super-efficient function)? example: #Suppose a matrix: m1=cbind(1:5,1:5,1:5) #The aim is to create a new matrix with every column containing the cumulative sum of all previous columns. m2=m1 for(i in 2:ncol(m1)){ m2[,i]=apply(m1[,1:i],1,sum) } m2 Many thanks in advance Eleni Rapsomaniki Research Associate Strangeways Research Laboratory Department...

Hello Currently, I plot some coefficients with some intervals using function "plotCI()" (package "gplots") using the following code: (m1 <- matrix(0:5, nrow=2, byrow=T, dimnames=list(c("v1", "v2"), c("lo", "m", "hi")))) m2 <- m1 + 1 library(gplots) plotCI( x=1:length(m1[, 1]), pch="", xlab="v1/v2", xlim=c(1-.2, length(m1[, 1])+.2), ylim=c(-...

Hello there This is the first time I have used r-help message board so I hope I have got the right address. I am trying to check the residuals of a GLMM model(run using the package lme4). I have been able to check the residiuals of REMLs in lme4 using the following: m1<-lmer(vTotal~Week+fCollar+ (1|fCat), collars) res<-resid(m1) plot(res) qqnorm(res) library(MASS) par(mfrow=c(2,3)) res<-residuals(m1) truehist(res,main="Histogram of Residuals") curve(dnorm(x,mean=mean(res),sd=sd(res)),add=TRUE) qqnorm(fitted(m1),resid(m1), ylim=range(fitted(m1)...

Hi, everyone I am trying to estimate 3 parameters for my survival function. It's very complicated. The negative loglikelihood function is: l<- function(m1,m2,b) -sum( d*( log(m1) + log(m2) + log(1- exp(-(b + m2)*t)) ) + (m1/b - d)*log(m2 + b*exp(-(b + m2)*t) ) + m1*t - m1/b*log(b+m2) ) here d and t are given, "sum" means sum over these two vairables. the parameters are assumed small, m1, m2 in thousandth, m2 in millionth. I use...

...t.ecodist will not accept data with NA values, returning a "matrix is not square error. is it possible to perform this test in ecodist? many thanks Nevil Amos > library(ecodist) > library(ncf) > x<-sample(1:1000,20) > y<-sample(1:1000,20) > z<-sample(1:1000,20) > M1<-as.matrix( distance(x)) > M2 <-as.matrix( distance(y )) > M3<-as.matrix( distance(z )) > D1<-(lower(M1)) > D2<-(lower(M2)) > D3<-(lower(M3)) > mantel(D1 ~ D2+D3, nperm=1000) mantelr pval1 pval2 pval3 llim.2.5% ulim.97.5% 0.09014696 0.10300000...

...overflow that I cannot understand. > >I have a character vector curr.lemmas with the following properties: > >length(curr.lemmas) # 61224 >length(unique(curr.lemmas)) # 2652 > >That vector is the input to the following function: > >yules.k1 <- function(input) { > m1 <- length(input); temp <- table(table(input)) > m2 <- sum("*"(temp, as.numeric(names(temp))^2)) > return(10000*(m2-m1) / (m1*m1)) >} > >When I run this, I get the following output: > >[1] NA >Warning message: >In m1 * m1 : NAs produced by integer ov...

Hi, I stumbled upon a strange thing regarding types and module linking, which I don't quite get, so maybe someone around here can enlighten me. Consider the following code, which will create 2 modules m1 and m2, and a named structured type %T = { i32 }; m1 contains only a function definition f(%T), m2 contains a function declaration f(%T) and a function definition h(%T), where h will call f in its body. Note that all functions in m1 and m2 are based upon the same structured type %T: LLVMConte...

Today's R 1.9.0 beta: > m1 [,1] [,2] [,3] [,4] [1,] NA NA NA NA [2,] NA NA NA NA [3,] NA NA NA NA [4,] NA NA NA NA > class(m1[1,1]) [1] "list" > cbind(m1,m1) Error in cbind(...) : cannot create a matrix from these types > rbind(m1,m1) Error in rbind(...) : cannot create...