search for: genus

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I have a list of scientific names in a data set. I would like to split the names into genus, species and subspecies. Not all names include a subspecies. Could someone show me how to do this? My example code is: a <- matrix(c('genusA speciesA', 10, 'genusB speciesAA', 20, 'genusC speciesAAA subspeciesA', 15, &...

Hi all, Given a data frame as... > head(veg) genus species trophia type geo zone importance 1 Sphagnum subsecundum M A En 100 2 Sphagnum denticulatum M A En 200 3 Molinia caerulea M A En 300 4 Sphagnum flexuosum M A En 400 5 Juncus squarrosus...

...r $ SUBPHYLUM : chr $ SUPERCLASS : chr $ CLASS : chr $ SUBCLASS : chr $ INFRACLASS : chr $ SUPERORDER : chr $ ORDER : chr $ SUBORDER : chr $ INFRAORDER : chr $ SUPERFAMILY: chr $ FAMILY : chr $ SUBFAMILY : chr $ TRIBE : chr $ SUBTRIBE : chr $ GENUS : chr $ TAXON : chr One command (all on one line) is: itis.ttable <- rbind(itis.ttable, data.frame(PHYLUM = "ARTHROPODA", SUBPHYLUM = "MANDIBULATA", SUPERCLASS = NA, CLASS = "INSECTA", SUBCLASS = "DICONDYLIA", INFRACLASS = "PTERYGOTA&...

...T version. I then converted a file from Stata 6.0 to R format by using the stataread library. The file converts perfectly and I was able to use the VR function lda on the dataframe without difficulty. I then tried to use the same dataframe with RPART. The model statement: test.rp<-rpart(genus~x+y+z+a+b+c, data=mydata) fails with the following error: Error in model.frame(formula, rownames, variables, varnames, extras, extranames, : invalid variable type (the identical model statement works perfectly in lda) I've traced the error to how RPART (or R) deals with the depend...

...steps provided by Grueber et al (2011) Multimodel inference in ecology and evolution: challenges and solutions in JEB. I created a global model to see if malaria prevalence (binomial distribution) is related to any life history traits of 14 different birds species, while controling for Family and genus in a GLMM: global.model.Para<-lmer(cbind(Parahaemoproteus,FailPh)~factor(SS)+factor(NT)+NH+W+IT+factor(MS)+(1|Family/Genus),family=binomial,data=malaria) I than standardize the input variables using the function standardize form the arm package: stdz.model.Para<-standardize(global.model.Pa...

To account for likely differences between families in naturalization rates, we fitted a generalized linear mixed model, using PROC NLMIXED in SAS10, with the naturalization rate per genus (that is, the number of naturalized species in a genus as a proportion of the total number of introduced species in a genus) as the response variable, a variable coding genera as containing at least one native species or not as a fixed-effect predictor, and a variable coding for family as a random...

Dear List, I am looking to calculate two things from my data frame and was after some advice. For the example below i want to know. 1. How many unique Orders/Families and Genera there are per eco-name 2. How many incidences are there for each Order/Family and Genus there are per eco-region I have 650 econame. I.e for Biak-Numfoor rain forests there are 2 orders, 2 families and two genera. Also, Alismatales are represented once, Asparagales once etc etc. Thanks for any advice. Chris ECO_NAME Order Family Genus Biak-Numfoor rain forests Alis...

Hello, I have an Lacie NAS disk attached to an Gigabit network. Since it only exports samba I mounted on one of my gigabit Linux boxes with smbmount //lacie/terabyte /TERABYTE -o defaults,username=genuser,password=genuser Now I need to export that to all my linux boxes not on the Gigabit network using nfs. When I try to mount I get: mount: old:/TERABYTE failed, reason given by server: Permission denied Is it possible to export an smbmounted filesystem? I saw another theread about this on the...

Dear R users, in the example below the name of the genus will be displayed in the main titles using the variable predictor[i] and paste. I would like to have the genus name in italic. However all my attempts using expression and substitute failed. Does anybody know a solution? Thanks a lot in advance. bernd Acrobeles <-c(65.1,0.0,0.0,0.0,0.0...

I am making a barplot using barplot2 from gplots where each bar represents a specific tree species. I have formatted the species names on the x-axis so that the genus name is above the species name and have then rotated the labels 45 degrees to save room. This is my code: >columncolor<-c("grey20", "grey20", "grey20", "grey70", "grey70", "grey70", "grey70", "grey70", &quot...

...represent counts of species, recorded with a particular coding system. The abundance column is not needed for this particular operation, but is present in the data files. I am interested in counting entries (rows) in the sppcode component of dat. The sppcode takes a particular format: Order Family Genus Species, with 2 alphanumeric digits allocated for each level of the hierarchy. I want to know how many species there are in each site (the id factor), but I should only count a higher level entry if there are no lower levels present. For example, for the above data excerpt (just the headed rows),...

I am making a barplot using barplot2 from gplots and would like to format the names of my categorical variables (tree species) on the x- axis so that the genus name is above the species name (to save room). My code so far is: speciesnames<-c("Dialium guianensis", "Inga alba", "Tachigali versicolor", "Brosimum utile", "Caryocar costaricense", "Castilla tunu", "Otoba novagranatensis&...

...nc --verions rsync: unknown option -- verions Segmentation fault (core dumped) $ ./rsync --version $ ./rsync --help Segmentation fault (core dumped) The above error (about ==) does not appear in google, so any help you could offer a novice would be greatly appreciated. $ uname -a CYGWIN_NT-5.1 GENUS 1.3.15(0.63/3/2) 2002-11-06 22:41 i686 unknown Thanks, Dan.

...kage ade4 to obtain classification from a .txt file. I use the following commands: cronquist <- read.table("cronquist.txt", h = T, row.names = 8) cronquist <- as.taxo(cronquist[7:1]) cro.phy <- taxo2phylog(cronquist) in which cronquist.txt is a file with a classification of 218 genus of tree species from french Guiana. We I try to use the function taxo2phylog, I obtain the following error message (in French) : Erreur dans newick2phylog.addtools(res) : la longueur de 'dimnames' [2] n'est pas ??gale ?? l'??tendue du tableau Error in newick2phylog.addtools(res)...

...ng in R or should I restrict myself to specific image analysis software (e.g. ImageJ)?. The reason I consider R would be a good choice is because then It would probably be possible to use R statistical power to do pattern recognition on each bug's image to try to identify each bug (Family, genus or species). Is anybody working in this direction? Thanks, Angel

...read a list of TXT files, calculate the values and write the results in an iterative manner to avoid manually reading each file individually Suggestions? Tnx, Bruce* * *# This works* *#read in a data file * *>Corbre_2 <- read.table("E:/Acoustic Parameters/~Emballonuridae/Data by genus/~Corbre/Corbre_2.txt",header=T,sep="\t",quote="")* *# create and calculate a new variable for time between call pusles * *Corbre_2 [c("TBC")] <- recode.variables(Corbre_2[c("TBC")] , "0 -> NA;")* *# Create new BW variable for band widt...

...utshell, I embrace the PHP Markdown Extra syntax, with one change: I would like to see the colon replaced with a tilde (for backwards compatibility, both should be supported). That means that a simple definition list would look like this: > Apple: > ~ Pomaceous fruit of plants of the genus Malus in the family > Rosaceae. > ~ An american computer company. > > Orange: > ~ The fruit of an evergreen tree of the genus Citrus. And a more complicated one would look like this: > Term 1: > > ~ This is a definition with two paragraphs. Lorem ipsum > dol...

...Here is a small example that produces the desired boxplots and labels them horizontally with "GO", "HO", "PA", "PO" as I want: attach(hominoid) #contains raw data groups<-c("GO", "HO", "PA", "PO") boxplot(latsupri~genus, main = "latsupri", horizontal=T, las=1, names=groups) This example produces the needed boxplot, but fails to put the "GO" anywhere on the plot attach(hominoid) groups<-"GO" # groups<-c("GO") doesn't do any better boxplot(latsupri~g...

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 Pol...