[R] Nested variables
Hello Im am working with a biological data including variables called Habitat and Site, example: Habitat Site Forest Low Forest Low Forest High Forest High I want to tell R that the Site variable is nested within the Forest variable (that it is not a new variable). Does anyone know how to do this? Thanks alot Daniel W. Carstensen Denmark -- View this message in context: http://www.nabble.com/Nested-variables-tp23779402p23779402.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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.
Re: [R] Nested variables
Hi. Yes I am trying to model such data, and i need R to know that Site is nested within Habitat. Do I use some kind of command before running the model (like factor() and so on) or do i write it in the model formula. If so, how? Thanks Douglas Bates-2 wrote: > > On Fri, May 29, 2009 at 7:50 AM, DanielWC > wrote: > >> Hello >> I am working with a biological data including variables called Habitat >> and >> Site, example: > >> Habitat Site > >> Forest Low >> Forest Low >> Forest High >> Forest High > >> I want to tell R that the Site variable is nested within the Forest >> variable >> (that it is not a new variable). >> Does anyone know how to do this? > > If you could explain what you mean by "tell R", it would help. Are > you trying to model such data and you want to know how to express the > relationship between such factors in a model formula? > > __ > R-help@r-project.org mailing list > 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. > > -- View this message in context: http://www.nabble.com/Nested-variables-tp23779402p23813261.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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.
Re: [R] Nested variables
Hi again I read the chapter and it says that I can nest B in A by writing A/B. But it doesnt seem to work properly. The package I use is pscl, I am trying to model zero inflated data. Here is the full model: zip1<-zeroinfl(Visitation ~ Habitat/Site + Sps + TP + Resource + Sps*Habitat/Site + Sps*Resource + Sps*TP + TP*Resource + TP*Habitat/Site | TP + Sps + Resource + Habitat/Site + TP*Sps + Sps*Resource + TP*Resource + TP*Habitat/Site, data = data1) where as you can see I have tried to include Habitat/Site. But it doesnt seem like its possible to create interaction links that way. I would like create the interaction link between say Sps and Habitat/Site. If I write Sps*Habitat/Site R somehow thinks that its a 3-way interaction link and still includes habitat as a single variable. Here is the summary just so you can see: Count model coefficients (poisson with log link): Estimate Std. Error z value Pr(>|z|) (Intercept) 3.8643338 0.3450539 11.199 < 2e-16 *** Habitat -3.2757473 0.4871726 -6.724 1.77e-11 *** Sps -0.3332371 0.1117680 -2.982 0.00287 ** TP -0.3857513 0.0975556 -3.954 7.68e-05 *** Resource 0.0130935 0.0009545 13.717 < 2e-16 *** Habitat:Site 0.2487012 0.0415908 5.980 2.24e-09 *** Habitat:Sps 0.5432845 0.1230434 4.415 1.01e-05 *** Sps:Resource -0.0041420 0.0002632 -15.738 < 2e-16 *** Sps:TP0.0438085 0.0189411 2.313 0.02073 * TP:Resource -0.0009413 0.0002887 -3.260 0.00111 ** Habitat:TP0.1549435 0.1205884 1.285 0.19883 Habitat:Site:Sps -0.0305628 0.0107794 -2.835 0.00458 ** Habitat:Site:TP -0.0096408 0.0098497 -0.979 0.32768 Zero-inflation model coefficients (binomial with logit link): Estimate Std. Error z value Pr(>|z|) (Intercept) -1.3160850 0.8200631 -1.605 0.1085 TP 0.2808474 0.2657544 1.057 0.2906 Sps 0.8023648 0.1281520 6.261 3.82e-10 *** Resource-0.0075967 0.0035817 -2.121 0.0339 * Habitat -1.3122811 1.1348922 -1.156 0.2476 Habitat:Site 0.1390498 0.0984716 1.412 0.1579 TP:Sps -0.0189088 0.0406299 -0.465 0.6417 Sps:Resource-0.0005548 0.0006843 -0.811 0.4175 TP:Resource 0.0007100 0.0008454 0.840 0.4010 TP:Habitat 0.7195254 0.3666809 1.962 0.0497 * TP:Habitat:Site -0.0782610 0.0314229 -2.491 0.0128 * Thanks again Mark Difford wrote: > > Daniel, > >>> Yes I am trying to model such data, and i need R to know that Site is >>> nested within Habitat. >>> Do I use some kind of command before running the model (like factor() >>> and so on) or do i >>> write it in the model formula. If so, how? > > You still are not telling the list enough, since nesting specifications > are sometimes package/program specific. You could help yourself by reading > some of R's basic documentation about how to specify a nested model. Then > "it" will tell you what to do. > > ?formula > > Or read §11.1 of "An Introduction to R" (one of R's manuals). > > Regards, Mark. > > > DanielWC wrote: >> >> Hi. >> Yes I am trying to model such data, and i need R to know that Site is >> nested within Habitat. Do I use some kind of command before running the >> model (like factor() and so on) or do i write it in the model formula. If >> so, how? >> >> Thanks >> >> >> >> Douglas Bates-2 wrote: >>> >>> On Fri, May 29, 2009 at 7:50 AM, DanielWC >>> wrote: >>> >>>> Hello >>>> I am working with a biological data including variables called Habitat >>>> and >>>> Site, example: >>> >>>> Habitat Site >>> >>>> Forest Low >>>> Forest Low >>>> Forest High >>>> Forest High >>> >>>> I want to tell R that the Site variable is nested within the Forest >>>> variable >>>> (that it is not a new variable). >>>> Does anyone know how to do this? >>> >>> If you could explain what you mean by "tell R", it would help. Are >>> you trying to model such data and you want to know how to express the >>> relationship between such factors in a model formula? >>> >>> __ >>> R-help@r-project.org mailing list >>> 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. >>> >>> >> >> > > -- View this message in context: http://www.nabble.com/Nested-variables-tp23779402p23830019.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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.
Re: [R] Nested variables
>>What happens if you do something like the following? >>zeroinfl(Visitation ~ Sps*Habitat/Site - Sps:Habitat:Site, data = data1) >>zeroinfl(Visitation ~ Sps*Habitat/Site - Sps - Sps:Habitat:Site, data = data1) It seems to be working. Heres the model: nes3<-zeroinfl(Visitation ~ Sps + TP + Resource + Habitat/Site + Sps*Habitat/Site - Sps:Habitat:Site - Habitat*Site + Sps*Resource + Sps*TP + TP*Resource + TP*Habitat/Site - TP:Habitat:Site | TP + Sps + Resource + Habitat/Site + TP*Resource + TP*Habitat/Site - TP:Habitat:Site - Habitat*Site, data = data1) and the summary(nes3): Count model coefficients (poisson with log link): Estimate Std. Error z value Pr(>|z|) (Intercept) 2.4589163 0.2145054 11.463 < 2e-16 *** Sps -0.2404691 0.0749488 -3.208 0.001335 ** TP -0.3191130 0.0764331 -4.175 2.98e-05 *** Resource 0.0114463 0.0008878 12.892 < 2e-16 *** Habitat -0.4589395 0.0709937 -6.465 1.02e-10 *** Sps:Habitat 0.2213486 0.0214113 10.338 < 2e-16 *** Sps:Resource -0.0040594 0.0002697 -15.049 < 2e-16 *** Sps:TP0.0448839 0.0177702 2.526 0.011544 * TP:Resource -0.0009182 0.0002574 -3.567 0.000361 *** TP:Habitat0.0531861 0.0188101 2.828 0.004691 ** Zero-inflation model coefficients (binomial with logit link): Estimate Std. Error z value Pr(>|z|) (Intercept) -1.2634867 0.2990362 -4.225 2.39e-05 *** TP 0.5649008 0.1101841 5.127 2.95e-07 *** Sps 0.6861959 0.0553519 12.397 < 2e-16 *** Resource-0.0111935 0.0025538 -4.383 1.17e-05 *** TP:Resource 0.0015815 0.0008029 1.970 0.0489 * TP:Habitat -0.1064294 0.0269142 -3.954 7.67e-05 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Number of iterations in BFGS optimization: 29 Log-likelihood: -1237 on 16 Df It now only displays Habitat and not Site which it take is because Site has been nested within Habitat (?). Thanks for the help. Mark Difford wrote: > > Hi Daniel, > >>> I read the chapter and it says that I can nest B in A by writing A/B. >>> But it doesnt seem to >>> work properly. > > Then you need to read it again, and you need to play with some simple > models, so that you learn how to specify a model properly, using the > formula interface. (Achim Zeileis wrote the pscl function, which uses the > formula interface, so it almost certainly works as it should.) > > It also is not at all clear what model you are trying to fit, since I only > have an R-specified model to go on, and your concept of what that means is > different from mine (and R's). > >>> If I write Sps*Habitat/Site R somehow thinks that its a 3-way >>> interaction link and still >>> includes habitat as a single variable. > > It will, because that is what you are specifying. > > Reread this (from §11.1): > y ~ A*B > y ~ A + B + A:B > y ~ B %in% A > y ~ A/B > Two factor non-additive model of y on A and B. The first two specify the > same crossed classification and the second two specify the same nested > classification. In abstract terms all four specify the same model > subspace. > > And this (from §11.1): > y ~ (A + B + C)^2 > y ~ A*B*C - A:B:C > Three factor experiment but with a model containing main effects and two > factor interactions only. Both formulae specify the same model. > > What happens if you do something like the following? > > zeroinfl(Visitation ~ Sps*Habitat/Site - Sps:Habitat:Site, data = data1) > zeroinfl(Visitation ~ Sps*Habitat/Site - Sps - Sps:Habitat:Site, data = > data1) > > Regards, > Mark. > > > DanielWC wrote: >> >> Hi again >> I read the chapter and it says that I can nest B in A by writing A/B. But >> it doesnt seem to work properly. The package I use is pscl, I am trying >> to model zero inflated data. Here is the full model: >> >> zip1<-zeroinfl(Visitation ~ Habitat/Site + Sps + TP + Resource + >> Sps*Habitat/Site + Sps*Resource + Sps*TP + TP*Resource + TP*Habitat/Site >> | TP + Sps + Resource + Habitat/Site + TP*Sps + Sps*Resource + >> TP*Resource + TP*Habitat/Site, data = data1) >> >> where as you can see I have tried to include Habitat/Site. But it doesnt >> seem like its possible to create interaction links that way. I would like >> create the interaction link between say Sps and Habitat/Site. If I write >> Sps*Habitat/Site R somehow thinks that its a 3-way interaction link and >> still includes habitat as a single variable. Here is the summary just so >> you can see: >> >> Count model coefficients (poisson with log link): >>Estimate St
[R] RDA Triplot
Hi Im using the VEGAN package to do an RDA ordination. In my plot I get my environmental scores as arrows/vectors, but my species scores as points. I would like to get the species scores as arrows as well. I tried the envfit function, and this creates arrows, but the lenght is not proportionate to the strengh of the correlation and the point is still there (so I both have point and arrow). fit <- envfit(rdawal, dat.one, perm = 999, display = "wa") ordiplot(rdawal, type = "p") plot(fit, col = "red", add = TRUE, scaling = 2) Is there not a way I can tell R to plot both environmental and species scores as arrows/vectors? Thanks -- View this message in context: http://r.789695.n4.nabble.com/RDA-Triplot-tp3055474p3055474.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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.
Re: [R] RDA Triplot
Since I am doing an RDA with contraints I get this error message when trying to use biplot.rda: 'biplot.rda' not suitable for models with constraints Daniel 2010/11/26 Jari Oksanen [via R] < ml-node+3060660-1324000642-57...@n4.nabble.com > > Danielwc gmail.com> writes: > > > Im using the VEGAN package to do an RDA ordination. In my plot I get my > > environmental scores as arrows/vectors, but my species scores as points. > I > > would like to get the species scores as arrows as well. > > > > Is there not a way I can tell R to plot both environmental and species > > scores as arrows/vectors? > > See ?biplot.rda in vegan. > > Cheers, Jari Oksanen > > __ > [hidden email] <http://user/SendEmail.jtp?type=node&node=3060660&i=0>mailing > list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html> > and provide commented, minimal, self-contained, reproducible code. > > > -- > View message @ > http://r.789695.n4.nabble.com/RDA-Triplot-tp3055474p3060660.html > To unsubscribe from RDA Triplot, click > here<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=3055474&code=ZGFuaWVsLmNhcnN0ZW5zZW5AZ21haWwuY29tfDMwNTU0NzR8LTM3Mjc5OTMzMA==>. > > -- View this message in context: http://r.789695.n4.nabble.com/RDA-Triplot-tp3055474p3063712.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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.
