search for: taxon

...rompt) : syntax error on line 1)" I have searched the "Creating R packages" manual but have been unable to determine how to solve my problem. Thank you in advance for any and all help. Niels Waller Vanderbilt University H:\R\rw2001\src\gnuwin32>rcmd build --binary --use-zip taxon * checking for file 'taxon/DESCRIPTION' ... OK installing R.css in h:/TEMP/Rbuild.1020 ---------- Making package taxon ------------ adding build stamp to DESCRIPTION installing R files installing inst files installing data files installing man source files installing indices E...

Getting the through items from a has_many :through :uniq relationship In a nutshell, I have been using the has_many :through :uniq relationship, and I want a DRY way to list the join model objects. Currently, my objects include taxon objects, toxin objects, data_object objects, and taxon_toxin_citation objects ("citation" is another word for data_object). A taxon has many data objects, has many taxon_toxin_citations, and has many toxins through taxon_toxin_citations. As well as a taxon causing many toxins, a toxin can...

...Perl and tools (from Ripley) installed Any help would be greatly appreciated Thanks, Niels Waller niels.waller@vanderbilt.edu ******* my bat file ********** set TMPDIR=h:\TEMP set path=d:\Latex\texmf\miktex\bin;h:\bin;h:\R\rw1081\bin;g:\Perl\bin; R\rw1081\bin; rcmd build --binary --use-zip taxon **** end of my bat file ***** ***my error messages ****** H:\R\rw1081\src\gnuwin32>rcmd build --binary --use-zip taxon * checking for file 'taxon/DESCRIPTION' ... OK make: *** H:/R/rw1081/src/src/gnuwin32: No such file or directory. Stop. *** Installation of taxon failed *** *...

Dear R experts I am running a negative-binomial GLM (glm.nb) to test the null hypotheses that species 1 and 2 are equally abundant between site 1 and site2, and between each other. So, I have a 2x2 factorial design with factors Site (1,2) and Taxon (1,2). Since the Site:Taxon interaction is significant, I need to do the equivalent to a "post-hoc test" for ANOVA, however, the same tests (e.g. Tukey HSD) do not seem to be applicable for the GLM. I tried specifying orthogonal contrasts, but could not figure out what the interaction con...

...em that was discussed previously (see quoted discussion below). I am trying to do the same thing, using a string to indicate a column with the same name. I am making "foo" a string taken from a list of names. It matches the row where "item" = 5, and picks the corresponding "taxon" > foo <- list$taxon[match(5,list$item)] Let's say this returns foo as "Aulacoseira_islandica". I have another matrix "counts" with column headers corresponding to the taxon list. But, when I try to access the data in the Aulacoseira_islandica column, it instead...

...r $ 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", SUPERORDER = &...

...e 'data=' argument seems to be necessary in the gls case- if I don't, there is a further problem: 'Row names in dataframe do not match tree tip names. data taken to be in the same order as in tree. in: Initialize.corPhyl(X[[1]], ...)') This seems to go away if I remove the root taxon (A1): tree2<-drop.tip(tree, "A1") x2<-c(B1=47,D1=43,C1=45,B2=50,B3=47,B4=48) y2<-c(B1=2.9,D1=5.4,C1=2.8,B2=3.5,B3=3.2,B4=3.5) dat2<-as.data.frame(cbind(x2,y2)) model2<-gls(y2~x2,data=dat2, correlation=corBrownian(phy=tree2)) This raises various questions: 1) Was I mislead...

Hi This question is far less simple than the title suggests, please read carefully, thanks. I have 2 sets of data, both read into R >data1<-read.table ("1.txt", header=T, sep="\t") >data2<-read.table ("2.txt", header=T, sep="\t") >data1 Taxon stage1 stage2 stage3 stage4 T1 0 0 1 1 T2 0 1 1 0 T3 0 0 0 1 T4 1 0 0 0 >data2 # this is a library file, it contains all possible values of st...

Dear all, I was wondering if you could help me with the following. I want to do calculate this equation: Ps(t)= (?_(r=1)^N Xtr* 1/?drs)/(?_(r=1)^N 1/?drs) Ps(t) ? Probability that taxon t will occur at site s (300 sites s) N ? Number of sites = from 1 to 49 Xtr ? Value for taxon t at site r (I have this information in a table, 40 taxa (columns) t, 49 sites r) drs ? Distance from site r to site s (this information is on a table, s sites (columns)) I thought that R would be the so...

Dear List, I can'f figure how to add point labels in the next plot (example from ?taxondive help page): library(vegan) data(dune) data(dune.taxon) taxdis <- taxa2dist(dune.taxon, varstep=TRUE) mod <- taxondive(dune, taxdis) plot(mod) The points in this plot are diversity values of single sites, and I'd like to add a label to each one. The plot command don't accept a &q...

Dear List, I can'f figure how to add point labels in the next plot (example from ?taxondive help page, from vegan package): library(vegan) data(dune) data(dune.taxon) taxdis <- taxa2dist(dune.taxon, varstep=TRUE) mod <- taxondive(dune, taxdis) plot(mod) The points in this plot are diversity values of single sites, and I'd like to add a label to each one. The plot command d...

...ode to solve a problem. I've searched the list, combed Crawley's 'R book' and several others, but can't quite find what i want. I want to generate permutations of various 'blocks' of 14 numbers. Each number within a block is a character state for a particular biological taxon. In the example below, for 'character 1' (i.e., block 1) there are thus 4 'states' (0, 1, 2, and 3), BUT there are differing quantities of each state (e.g., five of state 0, two of state 1, four of state 2, etc.). I'd like to 'shuffle' these states across the 14 taxon la...

...doing a comparative analysis of mammal brain and body size data. I'm following Charlie Nunn and Natalie Cooper's instructions for "Running PGLS in R using caper". I run into the following error when I create my comparative dataset, combining my phylogenetic tree (mammaltree) and taxon measures (mammaldata): "Error in phy$node.label[which(newNb > 0) - Ntip] : only 0's may be mixed with negative subscripts" My full script is provided at the bottom. I have looked at the caper manual by David Orme to understand how comparative.data() constructs the dataset, but s...

...at efficiently converts it to a site-by-taxa matrix or data frame that looks like this: LMA LCY SCO PNT Forest 1 1 1 0 Meadow 2 1 0 3 With no repeating taxa names and zeros where a taxon is not listed for a site. Any help would be greatly appreciated. Regards, Drew Garey Aquatic Ecoloy Lab Manager Virginia Commonwealth University [[alternative HTML version deleted]]

Hello: I need to take a species-sample matrix and transpose it to the format used by PC-ORD for analysis. Unfortunately, the number of species is very large (>5000), and so this operation cannot be performed simply in an application like Excel, which has a 255 column limit. So, I wrote relatively simple code in R that I hoped would do this (appended below). But there are glitches. The

...1 1 1 0 0 0 0 1 1 0 0 0 1 0 0 1 1 1 1 0 0 0 0 0 0 1 0 0 1 0 0 1 1 1 1 0 0 0 0 ...but the number of possible communities increases exponentially with each added taxon. n<-11 #number of taxa sum(for (i in 0:n) choose(i, k = 0:i)) #number of combos So all possible combinations of 11 taxa taken 1:11 at a time is 2048, all combos of 12 taken 1:12 is 4096, 13 taken 1:13 = 8192...etc etc such that when I reach about 25 taken 1:25 the number of combos is 3355...

...disturbed "D" or undisturbed "U" by soldier crab burrowing activity. The abundances of each of *p *= 56 species were recorded from each core (variables 1 to 39 in the file are nematode worms and variables 40-56 in the file are copepods, as identified by the column headed "Taxon"). Note that the *rows *are the species and the *columns *are the scores (sample units) in the raw data file. When i want to do ANOSIM i get an NaN error message. What is wrong? R output is here under > tasmania.df=read.table(file.choose(),header=T) > attach=(tasmania.df) > tasmania.d...

Hi Derek, I was getting this too, with three tables, called taxa, databases and references I found I could add an irregular pluralisation for taxa: Inflector.inflections do |inflect| inflect.irregular ''taxon'', ''taxa'' end to the environment.rb, but no amount of modification there would allow databases and references to work - I ended up renaming them to edatabases and ereferences and all is well. I don''t know if you found a solution, b...

...m all the NA values Error in Math.data.frame(strain.data) : non-numeric variable in data frame: NA..1NA..2NA..3NA..4NA..5NA..6NA..7NA..8NA..9 You have only 6 observations. In strain.data, since each column has a single 1 and the other 5 rows are 0's. Assuming that the columns are taxa, each taxon is found at only one site. I suspect there is a problem with your data or with the way you have coded the data. David L Carlson -----Original Message----- From: Sanjay Kumar Jaiswal [mailto:JaiswalSK at tut.ac.za] Sent: Tuesday, July 18, 2017 4:27 PM To: David L Carlson <dcarlson at tamu.edu...