search for: traits

URLS http://rubyforge.org/projects/codeforpeople/ http://codeforpeople.com/lib/ruby/traits INSTALL yes|sudo gem install traits ABOUT traits.rb is set of attr_* like methods on steroids, caffeine, and botox. it encourages better living through meta-programming and uniform access priciples. traits.rb supports smart inheritence of class attributes and a fistful of hooks f...

URLS http://rubyforge.org/projects/codeforpeople/ http://codeforpeople.com/lib/ruby/traits ABOUT traits.rb is set of attr_* like methods on steroids, caffeine, and botox. it encourages better living through meta-programming and uniform access priciples. traits.rb supports smart inheritence of class attributes and a fistful of hooks for veryifying and munging attr values....

...hat 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: # dummy data factor<-rep(c("Alice","Jone","Mike"),each=100) factor<-factor(factor) traits<-c(rnorm(100, mean=1, sd=1), rnorm(100, mean=3, sd=3), rnorm(100, mean=6, sd=6)) myda<-data.frame(factor,traits) # my plot plot(c(min(myda$traits),max(myda$traits)),c(-0.03,0.5), xlab='State', ylab='ylab') lines(density(myda$traits[factor==c("Alice")]), lwd=2,col=2)...

...species_matrix.jpg> 2. A species trait score matrix: <http://r.789695.n4.nabble.com/file/n4643979/2trait_matrix.jpg> The trait matrix lists trait scores for each species as listed in the species abundance matrix. I would like to create a script that would effectively count the unique traits (trait richness) for each site and produce an output like this: <http://r.789695.n4.nabble.com/file/n4643979/trait_richness.jpg> Firstly, is this possible in R? Secondly, if so, how would you go about writing a script to achieve my aim? Many thanks in advance, please let me know if you ne...

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 BSPy01-12 6.0 13 BSPy01-13 6.1 I want to substitute each "NA&qu...

Following is a function that I wrote (It is working well). It's a simple one, nothing complicated. The only question that I have is a qutation mark issue, I guess. ############################################# funcname <- function(trait.file){ #line1 setwd('/root/subroot') # line 2 load('imge.RData')

Is there a package that will allow me to fit Brownian motion and Ornstein?Uhlenbeck models of evolution for discrete traits? I know that geiger and ouch have commands for fitting these models for continuous traits, but these aren't suitable for discrete trait evolution, correct? -- View this message in context: http://r.789695.n4.nabble.com/Discrete-trait-Ornstein-Uhlenbeck-in-R-tp4649356.html Sent from the R...

...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, mean=3, sd=3), rnorm(100, mean=6, sd=6)) myda<-data.frame(factor,traits) # my plot plot(c(min(myda$traits),max(myda$traits)),c(-0.03,0.5), xlab='State', ylab='ylab') lines(density(myda$traits[factor==c("Alice")]), lwd=2,col=2)...

I have a question for users of MCMCglmm that have experience implementing the zero-inflated poisson model. I find that the documentation, and previous questions, do not offer a lot of clear guidance on specifying and interpreting the zipoisson model. In particular, I see a lot of zero-inflated poisson examples that use the at.level(trait, x):variableName syntax. Specifically, the MCMCglmm

...ute [9] must be the same length as the vector [0] I checked the code for read.cross function in the package read.map.qtlcart("mapfile.txt") works fine... The problem was in the following function: read.cro.qtlcart("crofile.txt") I tried to debug and find the problem: debug: traits <- t(f[-(1:(2 + nmarkers)), ]) debug: traits = as.data.frame(traits) debug: if (nrow(traits) == 1) traits <- as.data.frame(t(traits)) ******************data frame with 0 columns and 102 rows**************** --- This is the problem portion ---It should read my 9 trait values for all the 102 in...

...----------- An HTML attachment was scrubbed... URL: <http://lists.llvm.org/pipermail/llvm-dev/attachments/20090116/18390546/attachment.html> -------------- next part -------------- /usr/local/llvm/src/include/llvm/ADT/ilist.h: In static member function 'static NodeTy* llvm::ilist_nextprev_traits<NodeTy>::getPrev(NodeTy*) [with NodeTy = llvm::Instruction*]': /usr/local/llvm/src/include/llvm/ADT/ilist.h:268: instantiated from 'NodeTy* llvm::iplist<NodeTy, Traits>::getTail() [with NodeTy = llvm::Instruction*, Traits = llvm::ilist_traits<llvm::Instruction*>]' /u...

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 "doBy" package. The commands used and the output I got are as fol...

...with associations, but the tricky part is that the association shouldn''t always be loaded. This is similar to putting a condition on a has_many association in a model, but the condition is dynamic rather than predefined. The situation I had is @entity = Entity.find(params[:id]) @traits = Trait.find :all, :include => [:trait_values => [:key_factors]] but I only want the key_factors that connect to the given entity to be loaded. E.g. I have entities Jane and Marco, and traits Height (with values Short, Medium, and Tall) and HairColor (with values Re...

Dear MCMCglmm users, I am currently struggling with the specification of a proper prior and model formula for a multi-response MCMCglmm with two of the three response variables being Gaussian and the third being za-poisson. The model includes several fixed effects and three nested random effects. In general, I would prefer to fit a model with a fixed effect of trait and suppressed intercept for

...'); Yori <- read.table("c:\\Trait.txt", sep=','); Y=as.matrix(Yori); X=t(as.matrix(Xori)); fit1=glmnet(X, Y, family="binomial"); in the above, X is a matrix with values 1, 0, and -1; Y is a one column matrix with values 1 and 0. I know how to analysis continuous traits using glmnet, but I have no idea about how to do it for binary dependent variables. I will appreciate it if you would give me any suggestion about this error or provide an example code for handling binary trait using glmnet. Looking forward for your kindly help. Thanks! Noah -- View this messa...

Hi, First I should note I am relatively new to R so I would appreciate answers that take this into account. I am trying to perform an MDS ordination using the function ?metaMDS? of the ?vegan? package. I want to ordinate species according to a set of functional traits. ?Species? here refers to ?sites? in traditional vegetation analyses while ?traits? here correspond to ?species? in such analyses. My data looks like this: Trait1 Trait2 Trait3 Trait4 Trait5 Trait? Species1 228.44 16.56 1.66 13.22 1 short Species2 150.55 28.07...

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...

Good afternoon, I REALLY try to answer to my question as an autonomous student searching in the huge pile of papers on my desk and on the Internet but I can't find out the solution. Would you mind giving me some help? Please. ######################################### I'm trying to use glm with factors: > Pyr.1.glm<-glm(Pyrale~Trait,DataRav,family=poisson) If I have correctly

Hello I have a data set summarized like this: File name= Height Group Ind Age Trait 1 1 1 20 1 1 2 21 1 2 1 22 1 2 2 21 1 3 1 24 1 3 2 45 1 4 1 23 1 4 2 26 2 1 1 45 2 1 2 12 2 2 1 25 2 2 2 26 2 3 1 45 2 3 2 43 2 4 1 23 2 4 2 47 . . . I would like to plot Trait ~ Age but a different plot for each Group. I tried: > plot(Height$Trait ~ Height$Age | Group) But does not work. Any

...his is required for subsquent operations work. example : rubyforge login rubyforge login --username zaphod --password 42 create_package(group_id, package_name) creates the named package under the specified group. example : rubyforge create_package 1024 traits rubyforge login && rubyforge create_package codeforpeople.com traits notes : in order to use group_ids by name, rather than number, you must edit the rubyforge[group_ids] translation table in your config.yml. add_release(group_id, package_id, release_name, use...