similar to: how todefine an variable/column in a dataframe as numeric mode

Dear R-listers, I do clustering on tens of individuals by thousands of traits. I have known the assignment of each individual. I want to classify the individuals by randomly resampling different subsets of the traits, for example, randomly resampling 100 traits for 100 times, then 200 traits for 100 times, then 300 traits for 100 times, ,,,,,,. By each subset of traits, I do clustering of the

Dear R-helpers I want to express my respect and thankfulness to all of you. I just switch from windows xp to Ubuntu linux platform. I am facing two problems when I run R in Ubuntu. I need your helps and advice, thanks in advance. ----------------------------------------------------------------------------------------------------------------------------------------------------------- 1. JGR()

Dear R-listers, I want to reperfrom a poisson distribution test that presented in a recent-published biological research paper (Plant Physiology 2008, vol 148, pp. 1189-1200). That test is about the occurrence number of a kind of gene in separate chromosomes. For instance: The observed gene number in chromosome A is 36. The expected gene number in chromosome A is 30. Then, the authors got a

Hi, R-listers, Failed, when I tried to merge df1 and df2 by "codetot" in df1 and "codetoto" in df2. I want to know the reason and how to merge them together. Data frames and codes I have used were listed as followed. Thanks a lot in advance. df1: popcode codetot p3need BCPy01-01 BCPy01-01-1 100.0000 BCPy01-01 BCPy01-01-2 100.0000 BCPy01-01 BCPy01-01-3 100.0000 BCPy01-02

Dear Ruser's I ask for helps on how to substitute missing values (NAs) by mean of the group it is belonging to. my dummy dataframe is: > df group traits 1 BSPy01-10 NA 2 BSPy01-10 7.3 3 BSPy01-10 7.3 4 BSPy01-11 5.3 5 BSPy01-11 5.4 6 BSPy01-11 5.6 7 BSPy01-11 NA 8 BSPy01-11 NA 9 BSPy01-11 4.8 10 BSPy01-12 8.1 11 BSPy01-12 6.0 12

Dear Mao Jianfeng, "r-help-owner" is not the place for help, but: r-help at r-project.org (CC-ed here) In any case, strsplit() does the job, i.e.: > unlist(strsplit("BCPy01-01", "-")) [1] "BCPy01" "01" You can work with the whole variable, like: splitpop <- strsplit(df1$popcode, "-") then access the first part with >

Dear R-help listers, I am new. I just want to get helps on how to plot two histograms overlapped in the same plane coordinate. What I did is very ugly. Could you please help me to improve it? I want to got a plot with semi- transparent overlapping region. And, I want to know how to specify the filled colors of the different histograms. I also prefer other solutions other than ggplot2. Many

Dear all, This is a simple probability problem. I want to know, How to generate a normal distribution with mean=1, min=0.2 and max=0.8? I know how the generate a normal distribution of mean = 1 and sd = 1 and with 500 data point. rnorm(n=500, m=1, sd=1) But, I am confusing with how to generate a normal distribution with expected min and max. I expect to hear your directions. Thanks in

Dear R-listers, There is my data and my codes to create a plot. I want to know why there are two small circles in the upper right and lower left of the plot respectively. Could you please share your experience or advice with me? # dummy data factor<-rep(c("Alice","Jone","Mike"),each=100) factor<-factor(factor) traits<-c(rnorm(100, mean=1, sd=1), rnorm(100,

Dear R-listers, I have created a plot to display the density lines for the same variable by different entities. Now, I want to fill the area under the density lines with semitransparent colors. Though I have checked that in web-searching and book-reading, I still do not perform that. Could anyone please give me any helps or advice? Thank you in advance. The data and code I used listed below: #

Dear R-listers, I am new to R in linux. And, I am now confused by updating R in Ubuntu 9.10 linux system. I would like to seek some advice on that problem. I have done what are listed in CRAN linux installation guide: 1. add an entry like "deb http://cran.cnr.berkeley.edu/bin/linux/ubuntu karmic/" in /etc/apt/sources.list file in my computer. 2. To install the complete R system, use

Dear Ruser's I want to substitute each "NA" by the group mean of which the "NA" is belonging to. For example, substitute the first record of traits "NA" by the mean of "BSPy01-10" in the dummy dataframe. I have ever tried to solve this problem by using doBy package. But, I failed. I ask for the advice on how to use "lapplyBy" function of

Dear R-helpers and Klaus, I would like to know how to write out a tree file with bootstrap from phangorn package. That tree file could be in newick format or others. I am new for phylogenetic operation in R. Could you please give me any directions on that? Thanks in advance. Best wishes, Jian-Feng, ######## # as a example # I accomplished 1000 bootstrap simulation on a fit object (a maximum

Dear all, I have data.frame object in R. I want to export it in tab-delimited file with several lines of header initiated with comment sign (#). I do not know how to do that in R. Could you please give helps on this problem? Thanks in advance. Best, Jian-Feng, ################################################################## The lines I want to write in the header lines look like, with words

Dear R-helpers, I intend to upgrade R in Mac OS with updated R version and updated Mac OS version. I think my Mac notebook is produced with Mac x86_64, darwin9.8.0. I have updated my Mac OS to Mac OS X version 10.6.5. But, when I installed R 2.12.1, the "version" function still gave me information that R is based on old Mac OS. I need to know how can I update R to let it to fit for

Hi R-listers, I am new to R and programming. I have a large dataframe composed of two grouping variables (species, population, with populations nested in species) and tens of continuously numeric variables. For each numeric variable, I want to make a boxplot with population as the X axis and the boxes filled according to which species it is belonging to. But, that is a definitely tedious work. I

Dear R-helpers I want to express my respect and thankfulness to all of you. I have ever ask this question about one hour ago. Following Mr. Henrik Bengtsson's advice I re-submit this query here. I just switch from windows xp to Ubuntu linux platform. I am facingtwo problems when I run R in Ubuntu. I need your helps and advice, thanks in advance. 1. R session info

Dear R-helpers, Very small amount of outliers can greatly affect the mean and many other statistic of a numeric variable. So, usually we must deal with the outliers properly in the process of data analysis. Here, I want to replace outliers with the group median of the variable. But, I can not construct a good way to do that efficiently, because of I am a newbie to R and programming. Can anybody

Dear R-listers, Here, I would like to hearing helps from you. I have GPS data (multiple points in the geographic scale) in longitude/latitude. I intend to calculate distance (in kilometer) among such points and output the distance matrix in dist class. I have gotten some progress, but I still can not get final goal. Could please give me any directions/advice? This email cc. to Mr. Pierre, the

Dear R-help listers, I am now asking for helps on how to draw stacked ellipses to illustrate the shared and specific of multiple objects using R. My problem comes from my population genetics study. Now, I genotyped three species, and I get known about the amount of shared and specific haplotypes in each of the species and their combinations. I want to illustrate this result in three stack