Re: [R] question about capscale (vegan)
Hi Gavin, I have been analyzing real data (sorry but I am not allowed to post these data here) and what I got was this, mydistmat_f.cap - capscale(distmat_f ~ F + L + F:L, mfactors_frame) Warning messages: 1: some of the first 30 eigenvalues are 0 in: cmdscale(X, k = k, eig = TRUE, add = add) 2: Se han producido NaNs in: sqrt(ev) mydistmat_f.cap Call: capscale(formula = distmat_f ~ F + L + F:L, data = mfactors_frame) Inertia Rank Total 0.3758 Constrained0.21104 Unconstrained 0.16484 Inertia is squared distance Some constraints were aliased because they were collinear (redundant) Eigenvalues for constrained axes: CAP1 CAP2 CAP3 CAP4 1.679e-01 2.954e-02 1.349e-02 1.233e-05 Eigenvalues for unconstrained axes: MDS1 MDS2 MDS3 MDS4 1.388e-01 2.601e-02 4.076e-05 2.064e-07 So, by these results I can tell that there are 4 axes that explain 0.1648 of the total variance and another 4 axes that explain 0.2110 of the total variance. But I don't understand the difference between constrained and unconstrained. anova(mydistmat_f.cap) Permutation test for capscale under direct model Model: capscale(formula = distmat_f ~ F + L + F:L, data = mfactors_frame) DfVar F N.Perm Pr(F) Model 4 0.21 1.2798 400.00 0.0875 . Residual 4 0.16 --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 summary(anova(mydistmat_f.cap)) Df Var F N.PermPr(F) Min. :4 Min. :0.1648 Min. :1.280 Min. :200 Min. :0.12 1st Qu.:4 1st Qu.:0.1764 1st Qu.:1.280 1st Qu.:200 1st Qu.:0.12 Median :4 Median :0.1879 Median :1.280 Median :200 Median :0.12 Mean :4 Mean :0.1879 Mean :1.280 Mean :200 Mean :0.12 3rd Qu.:4 3rd Qu.:0.1994 3rd Qu.:1.280 3rd Qu.:200 3rd Qu.:0.12 Max. :4 Max. :0.2110 Max. :1.280 Max. :200 Max. :0.12 NA's :1.000 NA's : 1 NA's :1.00 Then, I want to know the sum of squares of anova to check with other analysis that we performed but I can't see them by the output of anova. Besides, I am wondering if there is any manner to identify the main effects, factor effects and interaction in this anova analysis. I would be very grateful if you could help me to understand these results. Thank you very much, Alicia __ R-help@stat.math.ethz.ch 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] question about capscale (vegan)
Hello, Thank you for your help. I have tried to perform the analysis I wanted with data of example, I mean not real data because I can't provide it here. So, what I have tried is this, matrix [,1] [,2] [,3] [1,] 0.00 0.13 0.59 [2,] 0.13 0.00 0.55 [3,] 0.59 0.55 0.00 dist_mat 12 2 0.13 3 0.59 0.55 # here, distance matrix is calculated from percentaje of different nucleic acids between two sequences and R is not used to perform it. The original data would be like this: n1 n2 n3 n4 n5 n6 n7 n8 n9 n10 n11 n12 m1 A C G T A G C T A C T A m2 G C T A T G C T A C T A m3 G A G T A G C T A C T A factors_frame time regioncity 1 2006 europe london 2 2005 africa nairobi 3 2005 europe paris my.cap - capscale(dist_mat ~ time + region + time:region + region:city + time:region:city, factors_frame) my.cap Call: capscale(formula = dist_mat ~ time + region + time:region + region:city + time:region:city, data = factors_frame) Inertia Rank Total 0.445 Constrained 0.4452 Inertia is squared distance Some constraints were aliased because they were collinear (redundant) Eigenvalues for constrained axes: CAP1CAP2 0.42978 0.01522 anova(my.cap) Erro en `names-.default`(`*tmp*`, value = Residual) : se intenta especificar un atributo en un NULL Then, I am still concerned about 'comm' argument since I don't understand how important could it be for my type of data and I don't understand to what it referes in my data. Another thing, is that what I am really interested in is to perform a factorial anova with another factor nested (the model I have provided above), and as you can see R gives an error that I don't understand either. Thank you for your help in advance. Regards, Alicia On Thu, 2006-11-16 at 17:25 +0100, Alicia Amadoz wrote: Hello, I am interested in using the capscale function of vegan package of R. I already have a dissimilarity matrix and I am intended to use it as 'distance' argument. But then, I don't know what kind of data must be in 'comm' argument. I don't understand what type of data must be referred as 'species scores' and 'community data frame' since my data refer to nucleic distances between different sequences. No, that is all wrong. Read ?capscale more closely! It says that you need to use the formula to describe the model. distance is used to tell capscale which distance coefficient to use if the LHS of the model formula is a community matrix. Argument comm is used to tell capscale where to find the species matrix that will be used to determine species scores in the analysis, *if* the LHS of the formula is a distance matrix. comm isn't used if the LHS is a data frame, and distance is ignored if the LHS is a distance matrix. As you don't provide a reproducible example of your problem, I will use the inbuilt example from ?capscale ## load some data data(varespec) data(varechem) Now if you want to fit a capscale model using the raw species data, then you would describe the model as so: vare.cap - capscale(varespec ~ N + P + K + Condition(Al), data = varechem, distance = bray) vare.cap In the above, LHS of formula is a data frame so capscale looks to argument distance for the name of the coefficient to turn it into a distance matrix. The terms on the RHS of the formula are variables looked up in the object assigned to the data argument. Now lets alter this to start with a dissimilarity/distance matrix instead. The exact complement of the above would be: dist.mat - vegdist(varespec, method = bray) vare.cap2 - capscale(dist.mat ~ N + P + K + Condition(Al), data = varechem, comm = varespec) vare.cap2 To explain the above example; first create the Bray Curtis distance matrix (dist.mat). Then use this on the LHS of the formula. When capscale now wants to calculate the species scores of the analysis it will look to argument comm to use in the calculation; which in this case we specify is the original species matrix varespec. As for what are species scores, well this is a throw back to the origins of the package and the methods included - all of this is related to ecology and mainly vegetation analysis (hence vegan). For species scores, read variable scores. The distance matrix (however calculated) describes how similar your individual sites (read samples) are to one another. You can also display information about the variables used to determine those distances/similarities, and this is what is meant by species scores. Whatever you used to generate the distance matrix, the columns represent
Re: [R] question about capscale (vegan)
Hello Gavin, Thank you very much for your help. I'm sorry I forgot to include all commands that I used but next time I will try to write all of them. I will try with my real data and see how it goes. I think I finally have understood how capscale works with this kind of data. Thank you. Regards, Alicia On Fri, 2006-11-17 at 12:18 +0100, Alicia Amadoz wrote: Hello, Thank you for your help. I have tried to perform the analysis I wanted with data of example, I mean not real data because I can't provide it here. So, what I have tried is this, Hi Alicia, It would have been more helpful if you'd included the actual commands to generate each object, but thanks for including an example. dat - matrix(c(0.00,0.13,0.59,0.13,0.00,0.55,0.59,0.55,0.00), ncol = 3) dist.mat - as.dist(dat) dist.mat 12 2 0.13 3 0.59 0.55 time - as.factor(c(2006, 2005, 2005)) region - as.factor(c(europe, africa, europe)) city - as.factor(c(london, nairobi, paris)) factors.frame - data.frame(time, region, city) my.cap - capscale(dist.mat ~ time + region + time:region + region:city + time:region:city, factors.frame) my.cap So, stop here. Look at the output. You can extract 2 constrained axes that explain 100% of the variance in your data. This causes my.cap$CA to be NULL, which is why when you do: anova(my.cap) You get this error message: Error in `names-.default`(`*tmp*`, value = Residual) : attempt to set an attribute on NULL The error has nothing to do with providing comm or not (I think) as I don't see how this would alter my.cap$CA, and anyway, comm is used to generate species scores and if you look at summary(my.cap) you will see that you have species scores (though their meaning may be hard to understand if no comm provided - see ?capscale) I hesitate to call this a bug in capscale() or permutest.cca() (this is where the error comes from by the way: traceback() 5: `names-.default`(`*tmp*`, value = Residual) 4: `names-`(`*tmp*`, value = Residual) 3: permutest.cca(object, step, ...) 2: anova.cca(my.cap) 1: anova(my.cap) ), but anova.cca doesn't seem to handle situations where there isn't an unconstrained component. I've CC'd Jari Oksanen, the author of vegan to insure he sees this. This error is related to the specific dummy problem you sent - do you get this error when you run the analysis on your full data set? If so, you might want to consider removing some constraints as your model isn't really constrained anymore. As number constraints approaches number sites the constraint on the ordination drops away and you are back to a Principal Coordinates Analysis (IIRC) of your dissimilarity matrix. anova(my.cap) Erro en `names-.default`(`*tmp*`, value = Residual) : se intenta especificar un atributo en un NULL Then, I am still concerned about 'comm' argument since I don't understand how important could it be for my type of data and I don't understand to what it referes in my data. Another thing, is that what I am really interested in is to perform a factorial anova with another factor nested (the model I have provided above), and as you can see R gives an error that I don't understand either. As for your original data - by the looks of it, you wouldn't be able to use that as the argument to comm. It would need to be numeric and recoded etc. before you could use it, and how to do that in the best way I'm not sure. But in this instance, if you are interested in the samples and how they relate to one another, constrained by your factors_frame, then you don't need comm and you can proceed without it, and not bother displaying species scores. If you are interested in how the samples relate to one another and how the nucleic acids relate to one another and the samples, constrained by your factors_frame, then you will need to recode that example matrix into something numeric, and even then it may not be possible with the way capscale is written. Hope this helps, G Thank you for your help in advance. Regards, Alicia On Thu, 2006-11-16 at 17:25 +0100, Alicia Amadoz wrote: Hello, I am interested in using the capscale function of vegan package of R. I already have a dissimilarity matrix and I am intended to use it as 'distance' argument. But then, I don't know what kind of data must be in 'comm' argument. I don't understand what type of data must be referred as 'species scores' and 'community data frame' since my data refer to nucleic distances between different sequences. No, that is all wrong. Read ?capscale more closely! It says that you need to use the formula to describe the model. distance is used to tell capscale which distance coefficient to use if the LHS of the model formula is a community matrix. Argument comm is used to tell capscale where to find the species matrix that will be used to determine
[R] question about capscale (vegan)
Hello, I am interested in using the capscale function of vegan package of R. I already have a dissimilarity matrix and I am intended to use it as 'distance' argument. But then, I don't know what kind of data must be in 'comm' argument. I don't understand what type of data must be referred as 'species scores' and 'community data frame' since my data refer to nucleic distances between different sequences. I would be very grateful if you could help me with this fact in any manner. Thank you in advance for your help. Regards, Alicia __ R-help@stat.math.ethz.ch 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.
[R] question about amova (ade4)
Hello, I am interested in using the amova function of ade4 package of R. I would like to know if there is any possibility to perform an amova with a specific anova model, as a factorial anova with some factors nested, or, if this could not be done, how could I perform an anova with my specific model but with molecular distance data? I would be very grateful if you could help me with this fact in any manner. Thank you in advance for your help. Regards, Alicia __ R-help@stat.math.ethz.ch 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.
[R] RSPerl problem with testing
Hi, I'm trying to install de RSPerl module and i have some problems trying to test it. I've tried to contact with the author but the e-mail address seems not to exist. Hope that anyone in this list could explain me a little about this problem. I have a bash shell and what i do is the following: #PERLLIB=/usr/lib/R/library/RSPerl/share/blib/arch:/usr/lib/R/library/RSPerl/share/blib/lib # export PERLLIB # LD_LIBRARY_PATH=/usr/lib/R/bin:/usr/lib/R/library/RSPerl/libs # export LD_LIBRARY_PATH # perl test.pl 1..1 Can't load '/usr/lib/R/library/RSPerl/share/blib/arch/auto/R/R.so' for module R: /usr/lib/R/library/RSPerl/libs/libPerlConverter.so: undefined symbol: R_GlobalEnv at /usr/lib/perl5/5.8.3/i386-linux-thread-multi/DynaLoader.pm line 229. at test.pl line 11 Compilation failed in require at test.pl line 11. BEGIN failed--compilation aborted at test.pl line 11. not ok 1 I move to the /usr/local/src to test again and i get the same error. Any help would be much appreciated. Thanks. Regards, Alicia *** Alicia Amadoz Evolutionary Genetics Unit Cavanilles Institute for Biodiversity and Evolutionary Biology University of Valencia Apartado Oficial 22085 E-46071 Valencia SPAIN Phone: (+34) 96 354 3687 FAX: (+34) 96 354 3670 e-mail: [EMAIL PROTECTED] http://www.uv.es/~amadoz *** NOTE! For shipments by EXPRESS COURIER use Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Polígono de la Coma s/n, 46980 Paterna (Valencia), Spain instead of P.O. Box no. and Post Code/City above. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] problem with installation on Linux (beginners)
Hello, I'm new to the installation R on Linux and I've followed the instructions on the R Installation and Administration Manual and on the FAQs. I also have changed the path at the .bash_profile file but when I try to type R at the shell prompt, it says: Fatal error: R home directory is not defined I've tried many things but all the time it says the same. Any help would be appreciated. Regards, Alicia __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
