search for: popbio

Hello, I'm in need of running a PVA and want to load {popbio}. However, I can't find it. I can't see where or how to load it. I have added repositories and changed the CRAN mirror site. I see {polynom} and {popgen} but no {popbio} between. What am I doing wrong? Thanks, Michelle [[alternative HTML version deleted]]

Hello R users, I am trying to calculate the stochastic lambda for a published matrix population model using the popbio package. Unfortunately, I have been unable to match the published results. Can anyone tell me whether this is due to slightly different methods being used, or have I gone wrong somewhere in my code? Could the answer be as simple as comparing deterministic lambdas to stochastic lambdas? My stoc...

Hello All. I am using the image2 plot function in the popbio package to create 6 elasticity analyses. I am trying to reduce the number of significant digits that displays -- from 3 digits to 2. I tried rounding my original matrices, but one is comprised primarily of zeros, and the cut / breaks options returns an error message. (see code and error message bel...

Dear all, I am running matrix population models using package "popbio". In a deterministic model {i.e., transition matrix is defined as A <- matrix(c(0.70, 0.70,0.35,0.50), nrow=2,byrow=TRUE}, population growth rate can be estimated from the dominant eigenvalue {command "eigen.analysis"}. However, I cannot figure out the way to compute the asympto...

Hello, I am trying to use the projection.matrix( ) function and am following the example given. I have my data formatted very similar to the test.census example. > str(AsMi05mat) `data.frame': 1854 obs. of 6 variables: $ Tag : num 501 502 503 504 505 506 507 508 509 510 ... $ Year : int 1995 1995 1995 1995 1995 1995 1995 1995 1995 1995 ... $ Length : num 34

Hello, I am running the plot from countCDFxt (popbio). I would like to report the y-axis as a percent instead of the log scale (e^01...). I can add an axis with axis(2, 0:1, line =2) but I'm having trouble understanding how to assign the tic marks (with 'at ='). I'd like to tell it to make tics with the percent value (or decimal if th...

I am using the function logi.hist.plot in package popbio. I want to change the colour of the probability line from the default red to black. I have not been able to find out how to do that. [[alternative HTML version deleted]]

...late elasticities and sensitivities of each parameters involved in the following transition matrix: A <- matrix(c( sigma*s0*f1, sigma*s0*f2, s, v ), nrow=2, byrow=TRUE,dimnames=list(stage,stage)) The command "eigen.analysis" avaliable in package "popbio" provides sensibility matrix and elasticity matrix (same dimension than A). I would like to know if there is a way to calculate separetely the elasticity of sigma, s0, f1, f2, s and v ? Thanks and regards, privalan -- View this message in context: http://www.nabble.com/Elasticity-in-Leslie-...

Dear R users I want change the entries in a matrix. I did a matrix A=0 1 5 .3 0 0 0 .5 0 A1<-A A2<-A*0.90 A2 1 2 3 1 0.00 0.90 4.5 2 0.27 0.00 0.0 3 0.00 0.45 0.0 I need replace elements one by one in a loop I tried the following using package POPBIO, total <-matrix(0, nrow=5, ncol=60) for(i in 1:10){ A1<-A A1[1,2] <- A2[1,2] A1[1,3]<-A2[1,3] A1[2,1]<-A2[2,1] A1[3,2]<-A2[3,2] n <-runif(3) n <- n/sum(n) p1<-pop.projection(A1,n,60) total[i,] <- p1$pop.sizes} matplot2(total, legend=NA,xlab=c(years)) but...

...e code below) I am not able to add a second plane with good results. I tried with par(new=TRUE) but the output was very poor. I have found some previous discussions about this point but (apparently) without a clear solution. Any advice would be appreciated. Simone Tenan ################## library(popbio) fec<-seq(0.1,2,0.1) delta <- seq(0,0.6,0.05) lambda<-matrix(0,length(fec), length(delta)) S0=0.7 S1=0.8 S2=0.85 S3=S2 for (j in 1:length(delta)){ for (i in 1:length(fec)){ F1=0 F2=fec[i]*0.05 F3=fec[i]*0.3 M<-matrix(0,3,3) M[1,]<-c(F1,F2*S...

....08 0.00 [33] 0.33 0.08 1.00 0.00 16 Levels: 0 0.00 0.08 0.13 0.17 0.25 0.33 0.50 0.67 1.00 Dead Dormant Reproductive ... Vegetative with Herbivory I want to read all matrices into stoch.projection( ) {popbio} Thanks for any suggestions. I could enter them all in the .txt document if I can't read them from the Excel sheet. Michelle DePrenger-Levin [[alternative HTML version deleted]]

> On Nov 5, 2017, at 6:03 AM, G?ran Bergqvist <Goran.Bergqvist at jagareforbundet.se> wrote: > > I am using the function logi.hist.plot in package popbio. I want to change the colour of the probability line from the default red to black. I have not been able to find out how to do that. If you look at the code for that function you see this line: logi.curve <- function(independ, depend, mod = logi.mod, col.cur = "red", lwd.cur...

hello all, i'm trying to use QPmat, from the popbio package. it appears to be based on solve.QP and is intended for making a population projection matrix. QPmat asks for: nout, A time series of population vectors and C, C constraint matrix, (with two more vectors, b and nonzero). i believe the relevant code from QPmat is: function (nout, C, b, nonz...

useR's, I have several matrices of size 4x4 that I want to calculate means of their respective positions with. For example, consider I have 3 matrices given by the code: mat1 <- matrix(sample(1:20,16,replace=T),4,4) mat2 <- matrix(sample(-5:15,16,replace=T),4,4) mat3 <- matrix(sample(5:25,16,replace=T),4,4) The result I want is one matrix of size 4x4 in which position [1,1] is the