Re: [R-sig-eco] [EXTERNAL] Error running an R code
It sounds like one of your columns is all zeros. Look at the input data to make sure all observations have positive values. -Original Message- From: R-sig-ecology On Behalf Of SANDILE N KHANYILE Sent: Saturday, March 16, 2024 2:32 PM To: r-sig-ecology@r-project.org Subject: [EXTERNAL] [R-sig-eco] Error running an R code This email has been received from outside of DOI - Use caution before clicking on links, opening attachments, or responding. Fellow Scientists, Please help me. I have environmental data (73 observations and 8 variables) and species data (73 observations and 24 variables). After running code, get the following error: Error in cca.default(d$X, d$Y, d$Z) : all row sums must be >0 in the community data matrix However the code run just fine when use another species data with more variables (73 observations and 169 variables) Thank You In advance.S. Khanyile [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] extracting variance components from lm
Hi all- I have a fairly simple model: m1 <- lm(Catch ~ Year + Station + Year*Station, data = data) I would like to extract the among years and year*station variance components and need assistance. I'm aware of the 'varComp' package, but I believe that only applies to nlme and requires a random effect. Any help is greatly appreciated. Thanks! Cheers, Laura Laura M. Lee Senior Stock Assessment Scientist Division of Marine Fisheries Department of Environmental Quality 252 808 8094 office 252 726 6062 fax mailto:laura@ncdenr.gov 3441 Arendell Street P.O. Box 769 Morehead City, NC 28557-0769 Email correspondence to and from this address is subject to the North Carolina Public Records Law and may be disclosed to third parties. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] lognormal gamlss with censored data
Hello all! I am fitting censored data with the 'gamlss' and 'survival' packages and assuming a lognormal distribution. Do I need to transform or back-transform the fitted values? cy - with(data, ifelse(NUMBERS=Limit, Limit, NUMBERS)) ci - with(data, ifelse(NUMBERS=Limit, 0, 1)) data - data.frame(data, cy, ci) rm(cy,ci) gen.cens(LOGNO,type=right) cfit - gamlss(Surv(cy, ci) ~ fyear + newWater, data=data, family=LOGNOrc) Thanks for your help, Laura ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] help with censored regression model
Hello all! I am trying to model censored catch-per-unit-effort (CPUE) data. The data are censored by trip limits that vary by year. I am using the 'gamlss' and 'survival' packages. My model covariates are Year and newWater. I need to get annual trends in CPUE by waterbody (newWater). After running the model and computing the index, I find the trends are the same among all water bodies--the magnitude is slightly different. I would not expect the trends to be the same among the different areas. I would appreciate any assistance. Code is below. cy - with(data, ifelse(NUMBERS=Limit, Limit, NUMBERS)) ci - with(data, ifelse(NUMBERS=Limit, 0, 1)) data - data.frame(data, cy, ci) rm(cy,ci) gen.cens(LOGNO,type=right) cfit - gamlss(Surv(cy, ci) ~ YEAR + newWater, data=data, family=LOGNOrc) data$y - exp(fitted(cfit)) out - with(data, tapply(y, list(YEAR,newWater), mean)) Thanks again for your help, Laura ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] Prediction intervals for hurdle model
All- I'm fitting a hurdle model using the 'pscl' package and would like to calculate standard errors and confidence intervals for the predicted values. I tried to apply the code found in the following thread: https://stat.ethz.ch/pipermail/r-help/2008-December/182806.html and was unsuccessful. I would appreciate any help. Thanks, Laura ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] seeking guidance on mixture models
Hi all! I'm interested in developing a mixture model that is a mixture of a negative binomial and a k-truncated negative binomial. I think this can be accomplished through one of the 'gamlss' packages, but I am seeking guidance and advice from someone who is experienced with doing this in R. Thanks in advance for any and all help! Cheers, Laura ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] k-truncated negative binomial
Hi all! Is there a package or function to model data using a k-truncated negative binomial distribution? I know the truncated function in the 'aster' package can be used to simulate data, but I need to model. Thanks! Laura ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] compare zero-inflated zero-altered
Is there a test to compare zero-inflated to zero-altered models or is it not appropriate to compare in this way? Thanks. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] convergence problems for zero-inflated model
Hi all! I'm using a zero-inflated model using the function 'zeroinfl' and running into convergence problems (system is computationally singular). How can I modify the code so it does not calculate a Hessian matrix? Thanks, Laura E-mail correspondence to and from this address is subject to the North Carolina Public Records Law and may be disclosed to third parties unless the context is exempt by statute or other regulation. [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] zeroinfl package - Year effect and precision
Hello. I originally posted this to the main R-help mailing list, but I'm afraid it got lost in the fray. I am using the zeroinfl package to fit a zero-inflated negative binomial. The explanatory variables are Year and Depth x STemp (interaction). I am in need of guidance for extracting the year effect and the associated precision. Thank you for your time. Cheers, Laura ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
