> On Jun 17, 2018, at 10:19 AM, Hannah van Noort <hannahvno...@gmail.com> wrote: > > Hi again, > > My apologies for the incomplete script last time. Hereby the updated dataset, > phylogenetic tree information and R-script. This time the errors I mentioned > should pop up. > Once again thank you in advance for any help/tips.
> row.names(d) <- c("Diomedea_exulans", "Diomedea_epomophora", > "Thalassarche_chrysostoma", "Thalassarche_melanophrys", > "Phoebetria_palpebrata", "Macronectes_giganteus", "Fulmarus_glacialis", + "Procellaria_aequinoctialis", "Puffinus_tenuirostris", "Puffinus_puffinus", "Oceanites_oceanicus", "Oceanodroma_leucorhoa", "Phaethon_rubricauda", + "Pelecanus_occidentalis", "Fregata_magnificens", "Morus_bassanus", + "Sula_dactylatra", "Sula_leucogaster", "Sula_sula", "Phalacrocorax_carbo", "Phalacrocorax_aristotelis", "Larus_dominicanus", "Larus_occidentalis", "Larus_argentatus", "Rissa_tridactyla", "Sterna_bergii", + "Sterna_sandvicensis", "Sterna_dougallii", "Sterna_hirundo", "Sterna_paradisaea", "Sterna_fuscata", "Anous_stolidus", "Anous_minutus", "Cepphus_columba", "Cepphus_grylle", "Uria_lomvia", "Alca_torda") Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length Needed to remove the extraneous "+" signs that persisted after copying from the console, but still no progress: length( c("Diomedea_exulans", "Diomedea_epomophora", "Thalassarche_chrysostoma", "Thalassarche_melanophrys", "Phoebetria_palpebrata", "Macronectes_giganteus", "Fulmarus_glacialis", + "Procellaria_aequinoctialis", "Puffinus_tenuirostris", "Puffinus_puffinus", "Oceanites_oceanicus", "Oceanodroma_leucorhoa", "Phaethon_rubricauda", + "Pelecanus_occidentalis", "Fregata_magnificens", "Morus_bassanus", + "Sula_dactylatra", "Sula_leucogaster", "Sula_sula", "Phalacrocorax_carbo", "Phalacrocorax_aristotelis", "Larus_dominicanus", "Larus_occidentalis", "Larus_argentatus", "Rissa_tridactyla", "Sterna_bergii", + "Sterna_sandvicensis", "Sterna_dougallii", "Sterna_hirundo", "Sterna_paradisaea", "Sterna_fuscata", "Anous_stolidus", "Anous_minutus", "Cepphus_columba", "Cepphus_grylle", "Uria_lomvia", "Alca_torda") + ) [1] 37 > nrow(d) [1] 40 So yet another error that prevents further progress. PLEASE PLEASE PLEASE Run your code in a clean session and try to recognize and correct the syntactic and other errors that I have already identified. I think it's time for you to adopt a strategy of creating asource file that is then submitted by your editor. (Such a facility is supplied by Rstudio.) > Kind regards, > > Hannah van Noort > > 2018-06-17 7:27 GMT+02:00 David Winsemius <dwinsem...@comcast.net>: > > > On Jun 16, 2018, at 1:37 PM, Hannah van Noort <hannahvno...@gmail.com> > > wrote: > > > > Hi everyone, > > > > I'm having trouble running a PGLS model with the package "AICmodavg". > > Did you mean "AICmodavg"? > > > > I > > continuously get the error of false convergence with certain Lambda > > values (even > > when trying to run the model with different Lambda values) and for other La > > mbda values I run into "error in eigen(val) : infinite or missing values in > > 'X' ". I've tried several optimizers and removing some outlier values but > > the same errors keep on popping up.. Does anyone know how to solve this > > problem? > > Below a part of my script with the specific dependent and independent varia > > bles and I've also attached files with the relevant data and phylogenetic > > tree information. > > d <- read.table("~/Seabirddat_growth.txt", head=TRUE) > library(AICmodavg) > Error in library(AICmodavg) : there is no package called ‘AICmodavg’ > library(AICcmodavg) > > > > Cand.models = list() > > niter = 100 > > for (i in 1:niter) { > > Cand.models[[i]] = gls(Maxgrowthrate ~ log.Forrang+log.Weight_av), > > A syntax error is thrown here -------------------------------------^ > #removed paren > > data = > > d, method= "ML", na.action=na.omit > > And here ---------------------------^ > > correlation = corPagel(value=0.4, trees[[i]])) > > And after fixing these errors I get the error that `gls` is not found (even > after adding `library(AICcmodavg)` > > could not find function "gls" > > ?corPagel > No documentation for ‘corPagel’ in specified packages and libraries: > you could try ‘??corPagel’ > > ??gls > > library(nlme) > > Attaching package: ‘nlme’ > > The following object is masked from ‘package:dplyr’: > > collapse > > > Cand.models = list() > > niter = 100 > > for (i in 1:niter) { > + Cand.models[[i]] = gls(Maxgrowthrate ~ log.Forrang+log.Weight_av, data = > + d, method= "ML", na.action=na.omit, > + correlation = corPagel(value=0.4, trees[[i]]) ) > + } > Error in corPagel(value = 0.4, trees[[i]]) : > could not find function "corPagel" > > ??corPagel > > library(ape) > > Attaching package: ‘ape’ > > The following object is masked from ‘package:Hmisc’: > > zoom > > > Cand.models = list() > > niter = 100 > > for (i in 1:niter) { > + Cand.models[[i]] = gls(Maxgrowthrate ~ log.Forrang+log.Weight_av, data = > + d, method= "ML", na.action=na.omit, > + correlation = corPagel(value=0.4, trees[[i]]) ) > + } > Error in corPagel(value = 0.4, trees[[i]]) : > object "phy" is not of class "phylo" > > > > Perhaps you have yet another unnamed package with a corPagel that doesn't > require a second argument of class "phylo"? I've reached "the end of my rope". > > > > > > } > > > > Thank you in advance for any help, it's much appreciated! > > Please submit code that will run in a clean session. Close R. Do not save > anything except your history. Delete or rename your `.Rdata` file and staart > a fresh session. then include everything needed to get the behavior you are > reporting. > > > > > Kind regards, > > > > Hannah van Noort > > <Seabirddat_growth.txt>______________________________________________ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > David Winsemius > Alameda, CA, USA > > 'Any technology distinguishable from magic is insufficiently advanced.' > -Gehm's Corollary to Clarke's Third Law > > > > > > > <Seabirddat_growth.txt><output.nex><Scripts_Growthrate.R> David Winsemius Alameda, CA, USA 'Any technology distinguishable from magic is insufficiently advanced.' -Gehm's Corollary to Clarke's Third Law ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.