search for: nestedness

Dear R-users, I set up an experiment where I put up bluebird boxes across an urbanization gradient. I monitored these boxes and at some point I pulled a feather from a chick and a friend used spectral properties (rtot, a continuous var) to index chick health. There is an effect of sex that I would like to include but how would I set up a regression and look at the effect of urbanization

...2hill.c -o data2hill.o gfortran -g -O2 -pipe -c decorana.f -o decorana.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c goffactor.c -o goffactor.o gfortran -g -O2 -pipe -c monoMDS.f -o monoMDS.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c nestedness.c -o nestedness.o gfortran -g -O2 -pipe -c ordering.f -o ordering.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c pnpoly.c -o pnpoly.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c stepacross.c -o stepacross.o gcc -I/usr/lib/R/include -DNDEBUG...

...na.omit) where rtot = total reflectance, box = nest box (i.e., birdhouse), julian = day of the year and purbank = the proportion of urban cover in a 1 km buffer around the nest box. I'm not interested in the box effect and I've seperated males and female chicks. I've asked about nestedness before and I was given code that included "|" to indicate nestedness but this indicates a grouping does it not? I suspect that there is something wrong. In the summary I get Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 2.880e-01 3.224e-03 89.3...

Dear list, I hope this is the right place to post a feature request. If there's exists a more formal channel (e.g. as for bug reports), I'd appreciate a pointer. I work a lot with named nested lists with arbitrary degrees of "nestedness". In order to retrieve the names and/or values of "bottom layer/bottom tier", I love the functionality of 'unlist()', or 'names(unlist(x))', respectively as it avoids traversing the nested lists via recursive loop constructs. I'm also aware that the general su...

...e null models created seem to be incredibly dependent on the 1) burnin and 2) thin values. These are the 1) Number of null communities discarded before proper analysis in sequential methods "swap" and "tswap" and 2) Number of discarded null communities between two evaluations of nestedness statistic in sequential methods "swap" and "tswap". What are the significance of these values? -- View this message in context: http://r.789695.n4.nabble.com/Null-models-of-species-co-occurrence-tp4325097p4325097.html Sent from the R help mailing list archive at Nabble.com.

I'm dealing with count data that's nested and has spatial dependence. I ran a glmm in lmer with a random factor for nestedness. Spatial dependence seems to have been accommodated by model. However I can't add a variance strcuture to this model (to accommodate heterogeneity). Is there a model that can have a poisson distribution *AND* a variance structure *AND* have AIC in output (for model comparison and selection)?...

Greetings, I have recently come into some confusion over weather or not AIC results for comparing among models requires that they be nested. Reading Burnham & Anderson (2002) they are explicit that nested models are not required, but other respected statisticians have suggested that nesting is a pre-requisite for comparison. Could anyone who feels strongly regarding either position

Dear R-users, I did some more research and I'm still not sure how to set up an ANCOVA with nestedness. Specifically I'm not sure how to express chicks nested within boxes. I will be getting Pinheiro & Bates (Mixed Effects Models in S and S-Plus) but it will not arrive for another two weeks from our interlibrary loan. The goal is to determine if there are urbanization (purban) effects on...

...sn't that small. I get the same error message ("Web is really too small...") even with larger webs. I also switched to a Mac recently. > Error in colSums(web) : 'x' must be an array of at least two dimensions In addition: Warning message: In networklevel(m, index = c("nestedness", "connectance", "links per species", : Web is really too small to calculate any reasonable index. You will get the values nonetheless, but I wouldn't put any faith in them! The web I used is: >m [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]...

Hello, Why does anova.lm sometimes return a p-value and at other times not ? Is it because it recognizes nested models from non-nested ones ? > x<-seq(1,100,1) > y<-3*x+rnorm(100) > anova(lm(y~x),lm(y~x+I(x^2)),test="F") Analysis of Variance Table Model 1: y ~ x Model 2: y ~ x + I(x^2) Res.Df RSS Df Sum of Sq F Pr(>F) 1 98 90.449 2 97 90.288 1

...ery unlikely to get implemented. R is not a clone of #S, and has the features it has because the workers had need of them. Well, this worker has need of this feature, which is why I wrote those workarounds! It does seem to me that, if a language allows one to use recursive structures of arbitrary nestedness, then there should be a simple mechanism for accessing and changing arbitrary elements of a recursive structure. For now, I will just submit my R code as a mini-library. My point about having a .Primitive was one of speed-- my R code seems to work OK, but it must slow things down. I doubt that I...

Hello, all. I've got what is probably a simple question about comparison of models using anova, specifically about the situations in which it's valid. I understand, I think, what's going on when the models are strictly nested (as most are in the demo(lm) examples). My question involves what happens when the models aren't strictly nested. In my particular case, I'm doing

Hi there, I have a data frame as listed below: > Ca.P.Biomass.A P Biomass 1 334.5567 0.2870000 2 737.5400 0.5713333 3 894.5300 0.6393333 4 782.3800 0.5836667 5 857.5900 0.6003333 6 829.2700 0.5883333 I have fit the data using logistic, Michaelis?Menten, and linear model, they all give significance. > fm1 <- nls(Biomass~SSlogis(P, phi1, phi2, phi3), data=Ca.P.Biomass.A)

Dear R-experts, I have a question on the formulas used in the gam function of the mgcv package. I am trying to understand the relationships between: y~s(x1)+s(x2)+s(x3)+s(x4) and y~s(x1,x2,x3,x4) Does the latter contain the former? what about the smoothers of all interaction terms? I have (tried to) read the manual pages of gam, formula.gam, smooth.terms, linear.functional.terms but

Dear R-experts, I have a question on the formulas used in the gam function of the mgcv package. I am trying to understand the relationships between: y~s(x1)+s(x2)+s(x3)+s(x4) and y~s(x1,x2,x3,x4) Does the latter contain the former? what about the smoothers of all interaction terms? I have (tried to) read the manual pages of gam, formula.gam, smooth.terms, linear.functional.terms but

...; list at the beginning. sphinx > will generate that itself (albeit without the snippets, but your titles > should be descriptive enough) with the following directive > .. contents:: > :local: > > the :local: prevents the document itself from appearing as an extra level > of nestedness in the table of contents (it's just the title, which you > "already know" when reading). > > 3. the convention in reStructuredText is 3-space indent. don't ask me why, > I have no clue. > > 4. I'm not sure exactly how to markup the questions. The sphinx FAQ (...

...mini "table of contents" list at the beginning. sphinx will generate that itself (albeit without the snippets, but your titles should be descriptive enough) with the following directive .. contents:: :local: the :local: prevents the document itself from appearing as an extra level of nestedness in the table of contents (it's just the title, which you "already know" when reading). 3. the convention in reStructuredText is 3-space indent. don't ask me why, I have no clue. 4. I'm not sure exactly how to markup the questions. The sphinx FAQ ( http://sphinx.pocoo.org/faq...

I just finished up the first draft of the FAQ translated verbatim from HTML to Sphinx. Sphinx did puzzle me a few times but I got used to its approximate error messages and figured out what the problems were. Perhaps you could take a quick glance at this file and tell me if I am doing something wrong? Otherwise I'll send it off to llvm-commits and see what they say. Thanks, Mikael

> 8. A Technical Writer FAQ (should include the Sphinx documentation from the lld docs). I'm working on the Sphinx stuff; if you have any questions about writing Sphinx docs feel free to ask. --Sean Silva On Wed, Jun 13, 2012 at 4:37 PM, Mikael Lyngvig <mikael at lyngvig.org> wrote: > I think the best way that I can currently contribute to the project is > through technical