search for: offspr

Hi all, I am reading a huge data set(12M rows) that contains family information, Offspring, Parent1 and Parent2 Parent1 and parent2 should be in the first column as an offspring before their offspring information. Their parent information (parent1 and parent2) should be set to zero, if unknown. Also the first column should be unique. Here is my sample data set and desired outpu...

...ame as year.hatch Second, I want the focal individual to be born by a mother that reproduces for the first time. So the /parents /of the focal individual should have year == year.1st.reprod. The problem for me, I think, is that in my data set with several generations, an individual can be both offspring and parent to other offspring at the same time (e.g. id=3 in test.data). In the 'offspring role', to select a individual from which I want the measurements, I would use year==year.hatch. However, for the /same/ individual in the 'parent role', to pass the 'parent test'...

...sions better. I have a share which is not behaving as I expect. [family] path = /home/shares/family create mask = 0664 directory mask = 0775 force group = parental guest ok = No valid users = @parental, @family writeable = Yes in Group parental are mum & dad; in group family are mum, dad and offspring. With file permissions of 0664 and force group parental, I would expect the offspring to be able to browse the share but not write to or delete from it. Unfortunately, they can both write and delete. How do I achieve this please? -- ---------------------------------------------------------...

...n the following dataset I would like to insert a new column that refers to the data of the previous row. My question is whether the probability of a female (Id) changes if she had given birth to a pup in the previous year. So my dataframe consists of the column Id, year (2003-2007 for each Id) and offspring (=of; 1-0): Id year of 1 2003 1 1 2004 0 1 2005 1 1 2006 1 1 2007 0 with 1= female (Id) gave birth to offspring (same year) 2 2003 0 and 0 = female didn't pup 2 2004 1 2 2005 1 2 2006 0 2 2007...

Dear R users, I encounter a problem regarding number of significant digits on y-axis. Below is my basic code: myplotkid<-xyplot(expected_offspringnumber~afr|decade,groups=SES,data1, auto.key=list(space="right"),layout=c(9,1),xlab="",ylab="Offspring number", aspect="fill",scales=list(x=list(draw=F)),strip=T) >From this code, you can see there are 9 small panels in a single row. Thus, there is only...

...ran it through oggenc. Originally the wav was 25 seconds, the ogg is 24 seconds. This happens at various quality levels, and I saved several copys of the file on a webserver at http://array26.rockefeller.edu/www/ogg/ If anyone wants to confirm my observations. The command lines were: oggenc -l offspring -a offspring -q 9 "01 - Time to Relax.wav" \ -o "01 - Time to Relax-q9.ogg" oggenc -l offspring -a offspring -q 4 "01 - Time to Relax.wav" \ -o "01 - Time to Relax-q4.ogg" This happened at other -q settings as well. c:\>oggenc -v OggEnc v1.0.1 (lib...

I am getting "Chi-squared approximation may be incorrect in: chisq.test(x)" with the data bleow. Frequency distribution of number of male offspring in families of size 5. Number of Male Offspring N 0 518 1 2245 2 4621 3 4753 4 2476 5 549 Total 15,162...

Is there a way I can have R automatically execute the commands in a source file without ever having to use R interactively? If so, what arguments should I pass to the UNIX call to R? I need to do this to run several R jobs in parallel. An alternative may be to have R and an R package behave as a stand-alone application that can be called from the UNIX command line. Is there any documentation on

R-Users, Hopefully someone can shed some light on these questions as I had little luck searching the archives (although I probably missed something in my search due to the search phrase). I estimated multinomial probabilities for some count data (number successful offspring) ranging from 0 to 8 (9 possible response categories). I constructed a barplot (using barplot2) and I want to "overlay" a normal distribution on the figure (using rnorm (1000, mean, sd)). My intent is to show that using a mean(and associated sd) estimated from discrete count data may...

Hi, I am sampling two random columns from females and two random columns from males to produce tetraploid offspring. For every female I am sampling a random male. In the end I want to write out a a matrix with all the offspring, but that does not work. I get always only the offspring from the last females. There must be a mistake in my script: moms<-read.delim("females.txt", stringsAsFacto...

Hi, I am trying to fit a curve to data. My command line is: model10=nls(offspring~((A*c^k)/gamma(k))*((degdays-alpha)^(k-1))*exp(-c*(degdays-alpha)), start=list(A=30,k=2,c=.018,alpha=131)) I get the error message: Error in numericDeriv(form[[3]], names(ind), env) : Missing value or an infinity produced when evaluating the model In addition: Warning message: full pr...

...'I.D' 'age' 'mothers I.D' 01 5 03 02 6 06 03 16 NA 04 8 06 05 3 NA 06 17 NA I need to create a new column for 'mothers age' which puts the age of the individual with 'mothers i.d' into the row for her offspring (so individual 01 would have 16 in the mothers age column, as thats the age of individual 03) Hope that makes sense, any help appreciated, Thanks Laura [[alternative HTML version deleted]]

...eprodictive process (i.e. meiosis, sexual reproduction). My code is someting like: off = function(sire, dam){ # simulation of reproduction, two inds sch.toll = round(runif(1, min = 1, max = 2)) dch.toll = round(runif(1, min = 1, max = 2)) s.gam = sire[,sch.toll] d.gam = dam[,dch.toll] offspring = cbind(s.gam,d.gam) # offspring } for (i in 1:dim(new)[1]){ if(ped[i,3] != 0 & ped[i,5] != 0){ zz = off(as.matrix(t(new[ped[i,3],])),as.matrix(t(new[ped[i,5],]))) new[i,1] = zz[1] new[i,2] = zz[2] } } I am also attribution a generation index to each row with a trivial calulation: for(i i...

...************* Estimate sire 1 BLUP "broad 2.2037 sire 1 BLUP "narrow" 2.1609 sire 1 BLUP with dam1 2.1002 Data details: The data is animal science data in which five sires were randomly sampled from the population and were randomly mated with two dams. Two offspring per sire dam combination were measured. Average daily gain was recorded. We are interested in breeding value of ith sire(means that which gives offsprings with higher gain NIL [[alternative HTML version deleted]]

...hat we did solve but I am not happy with the solution. I feel there should be a better way of doing this. Briefly, he is simulating births and deaths in a linear array of cells. Births and deaths are required to alternate. For a birth, one of the cells is selected at random to be the parent. The offspring cell is generated according to some rules based on the type of the parent then inserted into the array either to the left or to the right of the parent. The left/right choice is random. The part that took us the longest time was deciding how to insert the offspring cell into the array in a way...

Hi all, I try to generate sets of strategies that contain probability distributions for a defined number of elements, e.g. imagine an animal that can produce 5 different types of offspring and I want to figure out which percentage of each type it should produce in order to maximize its fitness. In order to do so, I need to calculate the fitness for all potential strategies. As an example, if I assume the probability levels to be 0, 0.2, 0.4, 0.6, 0.8, 1, I can generate all possibl...

Dear R users, I encounter a problem regarding space control in xyplot. Basically, I want to control spaces between label, tick and axis. I remember there is a function called mgp in general plot. Is there a similar function for xyplot or xYplot? Below is my basic code: myplotkid<-xyplot(expected_offspringnumber~afr|decade,groups=SES,data1, auto.key=list(space="right"),layout=c(9,1),xlab="",ylab="Offspring number", aspect="fill",scales=list(x=list(draw=F)),strip=T) By the way, since there is no x-axis, I just want to control space parameters in y-axis. Does...

...n record if its parents were not known. Missing parental (sire and/or dam) identifiers can occur. I need to export the data for use in another program that requires the pedigree to be coded as integers, increasing with date of birth (therefore sire and dam always have lower identifiers than their offspring) and with missing values coded as 0. How would I go about doing this? And a second, simpler related question, if I have a column with n different values (may be strings or non-sequential integers) identifying levels (possibly with repeated occurences), how can I recode them to be sequential fr...

...[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 practical terms, I am attributing haplotypes to a pedigree, so I have to give the haplotypes to the parents before I give them to the offspring. The vectors *zippo* and *zappo* are the chances of getting one or the other hap from the sire and dam respectively. *gp* is the vectors of non-ancestral animals. *new* is a two col matrix where the haps are stored. Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Pu...

...uot;matrix population models" and Rmetasim package,but I find it's very difficult to understand this model fully and can't find a good teacher.My question is that:Now I do some research about one marine shrimp: Penaeus chinensis, it's life cycle is one year. after it breed it's offsprings, it will died. This shrimp's life cycle is dicrete ,if i use project matrix or life cyle graph to express it,how can i do it? Best regards luan_sheng