search for: reef

I'm trying out a basic plot, but something about the way I subset my data leads to problems with the plot. Here is the first bit of my data set year,date,location,quadrat_juvenile,photo_location,photo_exists,genus,count,divers 2005,2005-04-30, 1 Fringing Reef,1, 1 Fringing Reef Coral Transect Pole 1-2 Quadrat 1,t,Acanthastrea,0,HP+MEM 2005,2005-04-30, 1 Fringing Reef,1, 1 Fringing Reef Coral Transect Pole 1-2 Quadrat 1,t,Acropora,0,HP+MEM 2005,2005-04-30, 1 Fringing Reef,1, 1 Fringing Reef Coral Transect Pole 1-2 Quadrat 1,t,Astreopora,0,HP+MEM 2005,200...

How can I print a data.frame to a PDF with pdf()...dev.off() ____________ Paulo E. Cardoso [[alternative HTML version deleted]]

...references? (I haven't found anything relevant in Pinheiro and Bates, but I may not have looked in the right place ...) thanks Ben Bolker self-contained but unnecessarily complicated simulation code/demonstration: --------------- library(lme4) library(lattice) simfun <- function(reefeff,ntreat=2,nreef=12, nreefpertreat=3, t.eff=10, totvar=25,seed=NA) { if (!is.na(seed)) set.seed(seed) ntot = nreef*nreefpertreat npertreat=ntot/ntreat reef = gl(nreef,nreefpertreat) treat = gl(ntreat,npertreat) r.sd = sqrt(totvar...

...-distributed. An example might be the test proposed in Kallioras et al, 2006, Communications in Statistics--Theory and Methods 35: 527-540. Thanks in advance. Regards, Sean ******************************************** Sean R. Connolly, PhD Associate Professor ARC Centre of Excellence for Coral Reef Studies, and School of Marine and Tropical Biology James Cook University Townsville, QLD 4811 AUSTRALIA Ph: 61 7 4781 4242 Fax: 61 7 4725 1570 http://www.coralcoe.org.au/research/seanconnolly.html http://www.jcu.edu.au/school/mbiolaq/staff/sconnolly.html ECOLOGICAL MODELLING LAB: http://www.jcu.ed...

Hello! I'm a PhD student working with coral reef fish diversity in Mexico. I want to do species accumulation curves but I have differential sampling effort for each "sample". Do you know or have developed an R script that consider the differential effort of each sample? PRIMER and other programs use each pack of species as a replica wit...

Hi there, I have been having trouble running negative binomial regression (glm.nb) using library MASS in R v2.15.0 on Mac OSX. I am running multiple models on the variables influencing the group size of damselfish in coral reefs (count data). For total group size and two of my species, glm.nb is working great to deal with overdispersion in my count data. For two of my species, I am getting a mixture of warning and error messages. These species are different from the others in that they have slightly smaller group sampl...

...assification to assess classification accuracy? (BTW, commands I used to generate predictions appended below.) Many thanks Mat Vanderklift > library(MASS) > Sep04 <- read.table("Sep04 dataframe2.txt", header=TRUE) > trainSep04 <- Sep04[1:125,] > Sep04.lda <- lda(Reef ~ ., trainSep04) > Sep04.lda > predict.Sep04 <- predict(Sep04.lda, Sep04) $class [[alternative HTML version deleted]]

Dear David, you asked this question a while ago on the R mailing list and got no answer. I have the same problem and was wondering if you had found a solution Cheers Loic Loic Thibaut, PhD candidate, ARC Centre of Excellence for Coral Reef Studies, School of Marine Biology, James Cook University, Townsville, Qld, 4811, Australia. Tel + 61 747 815 735, Fax: + 61 747 251 570, email: Loic.Thibaut at jcu.edu.au

...this error: .Random.seed is not an integer vector but of type 'double' I can't coerce the random seed and it's recommended not to alter it anyway. Can anybody help me? Thanks and kind regards, Piero Visconti, PhD candidate Australian Research Council Centre of Excellence for Coral Reef Studies James Cook University Townsville QLD 4811 Australia Phone +61 7 47816024 piero.visconti@jcu.edu.au http://www.coralcoe.org.au/ [[alternative HTML version deleted]]

...g 579 years, and has been successfully converted from zoo to matrix. Data plotting fine, jsut want to change axis - CaribMatrix<-as.matrix(ts4Ex) stackpoly(CaribMatrix, stack=TRUE, xlab="Year",ylab="Catch in tons", xaxlab=(1250:2008), main="Historical Florida reef fisheries catch by sector", axis4="FALSE") Any assistance appreciated! Thanks very much, Benjamin P Neal, Scripps Inst. of Oceanogrpahy

...icecast server is, everything is fine. But when The source is on other machine (even on the same LAN with server) we got buffer every 2-3 minutes. We have to user shoutcast to broadcast because of that. Did anyone experienced anything like that? Sorry for shool english, I am from Poland. regards Reef ---------------------------------------------------------------------- Nudzisz sie? Zagraj sobie! >>> http://link.interia.pl/f183d

...es) which works fine - ABUNDTMRT <- mvpart(abundance ~ .,factors,margin=0.08,cp=0,xv="1se",xval=nrow(abundance),xvmult=100,which=4) where abundance is 4th root transformed fish abundance (103 species x 168 samples), and factors is the relief (high, medium, low profile, sand inundated reef, flat), benthos (coral, sessile inverts, kelp, macroalgae, seagrass, sand), depth (continuous in meters), latitude, and longitude of each sample. To try and incorporate spatial autocorrelation (as a covariate) into this I have been trying the command - ABUNDTMRT <- mvpart(abundance ~ environ +...

Dear list, I am modelling fish distributions using the glm-function followed by the step-function, and then want to cross-validate the model via the cv.glm-function from the {boot} package. I am working on fish distributions on coral reefs. The code I have works for one fish species. Since I have 227 fishes, I wrote a loop. Now the cv.glm-function comes up with an error message: "Error in model.frame(formula, rownames, variables, varnames, extras, extranames, : variable lengths differ" and I cannot work out what the prob...

...antime somebody could enlighten me. Thanks, Stephen Ban *p. 226. Cooper, H., Hedges, L., and Valentine, J. The handbook of research synthesis and metaanalysis. Russell Sage Foundation, 2009. Stephen Ban, M.Sc. Ph.D. Candidate Australian Research Council Centre of Excellence for Coral Reef Studies James Cook University Townsville, Queensland 4811 Australia Phone: +61 7 4781 6063 Fax: +61 7 4781 6722 <mailto:stephen.ban@jcu.edu.au> stephen.ban@my.jcu.edu.au [[alternative HTML version deleted]]

...******************************************** Sean R. Connolly, PhD Senior Lecturer Department of Marine Biology James Cook University Townsville, QLD 4811 AUSTRALIA Ph: 61 7 4781 4242 Fax: 61 7 4725 1570 http://www.jcu.edu.au/school/mbiolaq/mbiol/staff/sconnolly.html VISIT THE NEW CENTRE FOR CORAL REEF BIODIVERSITY at http://www.jcu.edu.au/school/mbiolaq/ccrbio/ ********************************************* "We are raised to honor all the wrong explorers and discoverers-- thieves planting flags, murderers carrying crosses. Let us at last praise the colonizers of dreams." -- Peter Be...

...ommands follow). Could anybody suggest what is happening here? (I can attach files with plots separately if requested). Regards Mat Vanderklift > library(MASS) > Sep04 <- read.table("Sep04 dataframe.txt", header=TRUE) > trainSep04 <- Sep04[1:125,] > Sep04.lda <- lda(Reef ~ ., trainSep04, prior=c(1,1,1,1,1,1,1)/7) > plot(Sep04.lda, dimen=2) > predict.Sep04 <- predict(Sep04.lda, Sep04) > plot(predict.Sep04$x[1:125,], main="September 2004", xlab="first linear discriminant", ylab="second linear discriminant")

...nn to distinguish distances between the training data mediods and the validation data, but I have seen similar statements produced on the R help before. All suggestions welcomed and thank you in advance for your time. Kind Regards Steph O__ ---- Stephanie Januchowski ARC COE for Coral Reef Studies c/ /'_ --- James Cook University Townsville Queensland 4811 (*) \(*) -- P: 0747816024 E: stephanie.januchowski@jcu.edu.au ~~~~~~~~~~ [[alternative HTML version deleted]]

...ameters be specified (i.e., not estimated from data), and that the test statistic depends on sample size. Am I missing something? Thanks again. Sean ******************************************** >>Sean R. Connolly, PhD >>Associate Professor >>ARC Centre of Excellence for Coral Reef Studies, and >>School of Marine and Tropical Biology >>James Cook University >>Townsville, QLD 4811 >>AUSTRALIA >>______________________________________________ >>R-help at stat.math.ethz.ch mailing list >>https://stat.ethz.ch/mailman/listinfo/r-help >&g...

...ixed models but I can't get it to work with the following. Is there an obvious reason why it shouldn't work with a model of this structure ? *brief summary of objective: I want to test the effect of no-fishing marine reserves on the abundance of a target species. I have samples at coral reef sites inside and outside of reserves, from visits before and after the establishment of the reserves. Samples are counts of the target species. I plan to test this by looking at the interaction between reserve zone (green/blue, green means no-fishing allowed) and the change in abundance between th...

...ict the classification onto the new data using that matrix, however R keeps telling me there is no predict application for the code I have written. Any suggestions would be more than appreciated. Thank you all for your time. Stephanie -- Stephanie Januchowski ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville QLD 4810 P: 0747816024 E: stephanie.januchowski@jcu.edu.au Skype: stephierenee Web: www.coralcoe.org.au [[alternative HTML version deleted]]