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Fabio Monteiro

2016-Feb-22 13:00 UTC

[R] FD package

Hi

thank you for your quick answer

I finally managed to insert everything correctly and dbFD is caltulated.

I'm now trying to plot the results.

My objects are matrices.

x is a functional trait and species matrice. a is the species and samples

Thank you

2016-02-22 12:19 GMT+00:00 PIKAL Petr <petr.pikal at precheza.cz>:
> Hi
>
> comments inline
>
> > -----Original Message-----
> > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of
Fabio
> > Monteiro
> > Sent: Monday, February 22, 2016 11:51 AM
> > To: r-help at r-project.org
> > Subject: [R] FD package
> >
> > Hi.
> >
> > First i would like to say that i'm really new in R. I recently
started
> > working with R and i'm using the FD package.
> >
> > I'm having some errors that doesn't make any sense.
> >
> > I have 2 matrix, one is the species with functional traits and the
> > second one is the species and abundances.
>
> Your objects are matrices or data frames? From docs dbFD expects various
> inputs byt they have to be properly formatted.
>
> >
> > When I try to run the dbFD to calculate the functional diversity, the
> > error is the number of species is different in x and a.
> >
> > I checked a lot of times and the number of species is the same and
> > there are no mistakes in their names like spaces or caps.
>
> How did you checked?
>
> dim(trait) and  dim(abund)
>
> shall give you the same number of rows in traits as columns in abund.
>
> If trait is vector, you need to use length instead of dim.
>
> >
> > Can you help me?
>
> Without better description of your objects and code you used you hardly
> get any answer. You can start by using examples from help page, which shall
> work and see how your data differ from those examples.
>
> Cheers
> Petr
>
>
> >
> > F?bio Monteiro
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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.
>
> ________________________________
> Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou
> ur?eny pouze jeho adres?t?m.
> Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav?
> neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie
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> Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email
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> Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi
> ?i zpo?d?n?m p?enosu e-mailu.
>
> V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?:
> - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en?
> smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu.
> - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout;
> Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany
> p??jemce s dodatkem ?i odchylkou.
> - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve
> v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech.
> - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za
> spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n
> nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto
> emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich
> existence je adres?tovi ?i osob? j?m zastoupen? zn?m?.
>
> This e-mail and any documents attached to it may be confidential and are
> intended only for its intended recipients.
> If you received this e-mail by mistake, please immediately inform its
> sender. Delete the contents of this e-mail with all attachments and its
> copies from your system.
> If you are not the intended recipient of this e-mail, you are not
> authorized to use, disseminate, copy or disclose this e-mail in any manner.
> The sender of this e-mail shall not be liable for any possible damage
> caused by modifications of the e-mail or by delay with transfer of the
> email.
>
> In case that this e-mail forms part of business dealings:
> - the sender reserves the right to end negotiations about entering into a
> contract in any time, for any reason, and without stating any reasoning.
> - if the e-mail contains an offer, the recipient is entitled to
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> - the sender insists on that the respective contract is concluded only
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> - the sender of this e-mail informs that he/she is not authorized to enter
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> represented by the recipient, or the existence of such authorization is
> known to the recipient of the person represented by the recipient.
>
	[[alternative HTML version deleted]]

stephen sefick

2016-Feb-22 13:58 UTC

head link

[R] FD package

If memory serves me, dbFD returns a lot of output. What do you want to
plot? Also, please provide reproducible examples, so that we can help you
solve your R related queries.
kindest regards,

Stephen

On Mon, Feb 22, 2016 at 7:00 AM, Fabio Monteiro <
fabio.monteiro1992 at gmail.com> wrote:
> Hi
>
> thank you for your quick answer
>
> I finally managed to insert everything correctly and dbFD is caltulated.
>
> I'm now trying to plot the results.
>
> My objects are matrices.
>
> x is a functional trait and species matrice. a is the species and samples
>
> Thank you
>
> 2016-02-22 12:19 GMT+00:00 PIKAL Petr <petr.pikal at precheza.cz>:
>
> > Hi
> >
> > comments inline
> >
> > > -----Original Message-----
> > > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf
Of Fabio
> > > Monteiro
> > > Sent: Monday, February 22, 2016 11:51 AM
> > > To: r-help at r-project.org
> > > Subject: [R] FD package
> > >
> > > Hi.
> > >
> > > First i would like to say that i'm really new in R. I
recently started
> > > working with R and i'm using the FD package.
> > >
> > > I'm having some errors that doesn't make any sense.
> > >
> > > I have 2 matrix, one is the species with functional traits and
the
> > > second one is the species and abundances.
> >
> > Your objects are matrices or data frames? From docs dbFD expects
various
> > inputs byt they have to be properly formatted.
> >
> > >
> > > When I try to run the dbFD to calculate the functional diversity,
the
> > > error is the number of species is different in x and a.
> > >
> > > I checked a lot of times and the number of species is the same
and
> > > there are no mistakes in their names like spaces or caps.
> >
> > How did you checked?
> >
> > dim(trait) and  dim(abund)
> >
> > shall give you the same number of rows in traits as columns in abund.
> >
> > If trait is vector, you need to use length instead of dim.
> >
> > >
> > > Can you help me?
> >
> > Without better description of your objects and code you used you
hardly
> > get any answer. You can start by using examples from help page, which
> shall
> > work and see how your data differ from those examples.
> >
> > Cheers
> > Petr
> >
> >
> > >
> > > F?bio Monteiro
> > >
> > >       [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more,
see
> > > 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.
> >
> > ________________________________
> > Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a
jsou
> > ur?eny pouze jeho adres?t?m.
> > Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav?
> > neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho
> kopie
> > vyma?te ze sv?ho syst?mu.
> > Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento
> email
> > jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat.
> > Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou
modifikacemi
> > ?i zpo?d?n?m p?enosu e-mailu.
> >
> > V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?:
> > - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en?
> > smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu.
> > - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn?
> p?ijmout;
> > Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany
> > p??jemce s dodatkem ?i odchylkou.
> > - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve
> > v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech.
> > - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za
> > spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn?
> zmocn?n
> > nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi
> tohoto
> > emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo
jejich
> > existence je adres?tovi ?i osob? j?m zastoupen? zn?m?.
> >
> > This e-mail and any documents attached to it may be confidential and
are
> > intended only for its intended recipients.
> > If you received this e-mail by mistake, please immediately inform its
> > sender. Delete the contents of this e-mail with all attachments and
its
> > copies from your system.
> > If you are not the intended recipient of this e-mail, you are not
> > authorized to use, disseminate, copy or disclose this e-mail in any
> manner.
> > The sender of this e-mail shall not be liable for any possible damage
> > caused by modifications of the e-mail or by delay with transfer of the
> > email.
> >
> > In case that this e-mail forms part of business dealings:
> > - the sender reserves the right to end negotiations about entering
into a
> > contract in any time, for any reason, and without stating any
reasoning.
> > - if the e-mail contains an offer, the recipient is entitled to
> > immediately accept such offer; The sender of this e-mail (offer)
excludes
> > any acceptance of the offer on the part of the recipient containing
any
> > amendment or variation.
> > - the sender insists on that the respective contract is concluded only
> > upon an express mutual agreement on all its aspects.
> > - the sender of this e-mail informs that he/she is not authorized to
> enter
> > into any contracts on behalf of the company except for cases in which
> > he/she is expressly authorized to do so in writing, and such
> authorization
> > or power of attorney is submitted to the recipient or the person
> > represented by the recipient, or the existence of such authorization
is
> > known to the recipient of the person represented by the recipient.
> >
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.



-- 
Stephen Sefick
**************************************************
Auburn University
Biological Sciences
331 Funchess Hall
Auburn, Alabama
36849
**************************************************
sas0025 at auburn.edu
http://www.auburn.edu/~sas0025
**************************************************

Let's not spend our time and resources thinking about things that are so
little or so large that all they really do for us is puff us up and make us
feel like gods.  We are mammals, and have not exhausted the annoying little
problems of being mammals.

                                -K. Mullis

"A big computer, a complex algorithm and a long time does not equal
science."

                              -Robert Gentleman

	[[alternative HTML version deleted]]

Fabio Monteiro

2016-Feb-22 14:03 UTC

head link

[R] FD package

This is the output.

I want to plot, for example FRic

$nbsp
 com1  com2  com3  com4  com5  com6  com7  com8  com9 com10 com11 com12
com13 com14 com15 com16
   17    21    18    12    15    20    16    12    18    15    18    16
 10    11    17    20
com17 com18 com19 com20 com21 com22 com23 com24 com25 com26 com27 com28
com29 com30 com31 com32
    9    13    11    10    11    15    12    16    18    18    11    19
 12    13    13    12
com33 com34 com35 com36 com37 com38 com39 com40 com41 com42 com43 com44
com45 com46 com47 com48
   15    11    15     8     7    12    10     9    12    15    13    13
 15    13    10    16
com49 com50 com51 com52 com53 com54 com55 com56 com57 com58 com59 com60
com61 com62 com63 com64
   14    12    14    13    14    13    15    13    11    12    16    13
9     8    11    15
com65 com66 com67 com68 com69 com70 com71 com72 com73 com74 com75 com76
com77 com78 com79 com80
   13    18    13    15    10    11    12    11    14     8    10    12
 11    12    14    13
com81 com82
    9    12

$sing.sp
 com1  com2  com3  com4  com5  com6  com7  com8  com9 com10 com11 com12
com13 com14 com15 com16
   17    21    18    12    15    20    16    12    18    15    18    16
 10    11    17    20
com17 com18 com19 com20 com21 com22 com23 com24 com25 com26 com27 com28
com29 com30 com31 com32
    9    13    11    10    11    15    12    16    18    18    11    19
 12    13    13    12
com33 com34 com35 com36 com37 com38 com39 com40 com41 com42 com43 com44
com45 com46 com47 com48
   14    11    15     8     7    12    10     9    12    15    13    13
 15    13    10    16
com49 com50 com51 com52 com53 com54 com55 com56 com57 com58 com59 com60
com61 com62 com63 com64
   14    12    13    13    14    13    15    13    11    12    16    13
9     8    11    15
com65 com66 com67 com68 com69 com70 com71 com72 com73 com74 com75 com76
com77 com78 com79 com80
   13    17    13    15    10    11    12    11    14     8    10    12
 11    12    14    13
com81 com82
    9    12

$FRic
        com1         com2         com3         com4         com5
com6         com7
3.669752e-04 6.898164e-04 6.893918e-04 3.935451e-05 1.436140e-04
1.012949e-03 2.934536e-04
        com8         com9        com10        com11        com12
 com13        com14
1.001556e-04 6.425547e-04 1.740235e-04 5.561802e-04 2.964362e-04
1.480860e-05 1.060512e-04
       com15        com16        com17        com18        com19
 com20        com21
4.121157e-04 5.346433e-04 1.108007e-06 5.726895e-05 8.593435e-06
1.452446e-05 1.855957e-05
       com22        com23        com24        com25        com26
 com27        com28
2.128971e-04 8.438329e-05 3.216279e-04 2.529525e-04 4.980317e-04
3.111325e-05 6.290088e-04
       com29        com30        com31        com32        com33
 com34        com35
3.559802e-05 5.907167e-05 8.906878e-05 2.510168e-05 1.929088e-04
1.234508e-04 2.784301e-04
       com36        com37        com38        com39        com40
 com41        com42
1.480560e-08 1.411752e-06 5.576549e-05 2.445569e-05 6.167242e-06
1.210002e-04 1.666034e-04
       com43        com44        com45        com46        com47
 com48        com49
1.203484e-04 7.347513e-05 8.991003e-05 8.691148e-05 6.718789e-05
1.357136e-04 1.821851e-04
       com50        com51        com52        com53        com54
 com55        com56
4.832203e-05 8.391627e-05 2.173971e-04 1.355160e-04 1.304425e-04
1.787888e-04 1.759204e-05
       com57        com58        com59        com60        com61
 com62        com63
9.307474e-05 1.185857e-04 2.776166e-04 1.277143e-04 5.905299e-06
9.606009e-08 1.019480e-04
       com64        com65        com66        com67        com68
 com69        com70
2.395355e-04 2.307081e-04 4.019309e-04 6.874506e-05 1.417622e-04
5.675463e-06 9.878848e-05
       com71        com72        com73        com74        com75
 com76        com77
6.907251e-05 8.938528e-05 2.493585e-04 1.214151e-09 2.419942e-05
1.183863e-04 7.457464e-05
       com78        com79        com80        com81        com82
6.284563e-05 1.741100e-04 2.128749e-04 2.920847e-06 9.368270e-05

$qual.FRic
[1] 0.7035642

$FEve
     com1      com2      com3      com4      com5      com6      com7
 com8      com9
0.2388515 0.3996566 0.3350494 0.2943431 0.3576785 0.3846561 0.4319967
0.5857688 0.4271764
    com10     com11     com12     com13     com14     com15     com16
com17     com18
0.3288544 0.4625139 0.4810921 0.3041395 0.5820621 0.6313595 0.5406627
0.2707035 0.4530424
    com19     com20     com21     com22     com23     com24     com25
com26     com27
0.3015171 0.5790744 0.7253301 0.5441404 0.4481694 0.6187607 0.5445650
0.4955940 0.5116752
    com28     com29     com30     com31     com32     com33     com34
com35     com36
0.5221560 0.5670513 0.4293040 0.4812907 0.4915317 0.3878949 0.4287726
0.2893205 0.5835605
    com37     com38     com39     com40     com41     com42     com43
com44     com45
0.7896749 0.5482274 0.4015703 0.5990018 0.5431955 0.6251919 0.6023954
0.4962892 0.3749658
    com46     com47     com48     com49     com50     com51     com52
com53     com54
0.4290664 0.4932756 0.5870607 0.3415984 0.3242199 0.4296702 0.4971491
0.3272834 0.4865427
    com55     com56     com57     com58     com59     com60     com61
com62     com63
0.3428716 0.4653631 0.5479140 0.5698272 0.4777804 0.4525375 0.5916255
0.4652363 0.4111973
    com64     com65     com66     com67     com68     com69     com70
com71     com72
0.3987632 0.3856989 0.3064660 0.4717288 0.3534531 0.4285679 0.6087836
0.3607790 0.5494437
    com73     com74     com75     com76     com77     com78     com79
com80     com81
0.4214327 0.4360703 0.3808632 0.2833824 0.2876808 0.3380949 0.3421757
0.2249389 0.6562824
    com82
0.6041267

$FDiv
     com1      com2      com3      com4      com5      com6      com7
 com8      com9
0.7423817 0.7458169 0.8679783 0.8226750 0.8373889 0.7877725 0.8070008
0.7379254 0.8131881
    com10     com11     com12     com13     com14     com15     com16
com17     com18
0.7050804 0.6976598 0.7512530 0.6806472 0.6994011 0.7276620 0.7870732
0.8793599 0.7562019
    com19     com20     com21     com22     com23     com24     com25
com26     com27
0.8983302 0.7681038 0.8163501 0.8198178 0.8489976 0.8922742 0.8442970
0.8269863 0.7891795
    com28     com29     com30     com31     com32     com33     com34
com35     com36
0.7569559 0.8674167 0.7436638 0.7317634 0.9541561 0.7466859 0.7087626
0.8006321 0.8511148
    com37     com38     com39     com40     com41     com42     com43
com44     com45
0.7729260 0.7509163 0.6905947 0.8466404 0.7677596 0.8791198 0.8211045
0.7259760 0.7992553
    com46     com47     com48     com49     com50     com51     com52
com53     com54
0.7573869 0.8788377 0.9036087 0.8287276 0.7762280 0.8064715 0.7775368
0.7828276 0.8151245
    com55     com56     com57     com58     com59     com60     com61
com62     com63
0.7503195 0.9213640 0.9141396 0.9150055 0.8348691 0.7271261 0.7875414
0.8338675 0.7070272
    com64     com65     com66     com67     com68     com69     com70
com71     com72
0.7189990 0.7043998 0.7768710 0.7264939 0.8140790 0.7532290 0.7309884
0.9190267 0.8540992
    com73     com74     com75     com76     com77     com78     com79
com80     com81
0.7531779 0.8520790 0.7649957 0.7319195 0.7578687 0.7915857 0.7600834
0.7303097 0.7693079
    com82
0.7487281

$FDis
      com1       com2       com3       com4       com5       com6
com7       com8
0.19178600 0.15352983 0.23419296 0.20315128 0.18604639 0.14348855
0.28989249 0.25752544
      com9      com10      com11      com12      com13      com14
 com15      com16
0.26174957 0.15962395 0.17907612 0.19642851 0.12827329 0.20114316
0.18128942 0.25731184
     com17      com18      com19      com20      com21      com22
 com23      com24
0.25855225 0.19576353 0.26366092 0.27728602 0.29546846 0.20720052
0.27212077 0.30880887
     com25      com26      com27      com28      com29      com30
 com31      com32
0.29440458 0.25396646 0.25647806 0.23422171 0.25464177 0.24311894
0.16182038 0.09958014
     com33      com34      com35      com36      com37      com38
 com39      com40
0.13095167 0.12983413 0.24224903 0.18239337 0.19817113 0.26320996
0.11766508 0.30940641
     com41      com42      com43      com44      com45      com46
 com47      com48
0.23583814 0.30624876 0.27750572 0.16747032 0.21445188 0.24327116
0.20589103 0.27339261
     com49      com50      com51      com52      com53      com54
 com55      com56
0.23614656 0.23678552 0.25641929 0.26260242 0.22516659 0.25243952
0.23674896 0.18732040
     com57      com58      com59      com60      com61      com62
 com63      com64
0.27202483 0.22947018 0.31342777 0.17997456 0.18461335 0.32429534
0.14840674 0.13731830
     com65      com66      com67      com68      com69      com70
 com71      com72
0.20437128 0.23298402 0.14830718 0.27194825 0.09289396 0.23196338
0.17920946 0.25265696
     com73      com74      com75      com76      com77      com78
 com79      com80
0.23525249 0.22171523 0.21972879 0.23523622 0.25336830 0.22477734
0.20430806 0.20674064
     com81      com82
0.14270928 0.22673005

$RaoQ
      com1       com2       com3       com4       com5       com6
com7       com8
0.05331536 0.03630438 0.07372825 0.06071274 0.05671961 0.05128404
0.10541586 0.08965742
      com9      com10      com11      com12      com13      com14
 com15      com16
0.09102682 0.04333067 0.04941515 0.05495308 0.03115535 0.06048519
0.06070379 0.08680368
     com17      com18      com19      com20      com21      com22
 com23      com24
0.07256118 0.05321952 0.08855815 0.10718949 0.10760039 0.07391960
0.09163325 0.11476244
     com25      com26      com27      com28      com29      com30
 com31      com32
0.10458183 0.08833300 0.07746703 0.07975863 0.08699710 0.07029682
0.04116800 0.02091466
     com33      com34      com35      com36      com37      com38
 com39      com40
0.03452371 0.03102533 0.07072961 0.04601163 0.05125527 0.08872861
0.03608639 0.11227991
     com41      com42      com43      com44      com45      com46
 com47      com48
0.07155343 0.10655043 0.09463142 0.04483107 0.05149290 0.06818611
0.05776898 0.08787335
     com49      com50      com51      com52      com53      com54
 com55      com56
0.06689262 0.06673575 0.07673498 0.08209786 0.06165892 0.07169030
0.07207671 0.05351944
     com57      com58      com59      com60      com61      com62
 com63      com64
0.10496706 0.07830439 0.11178032 0.05616672 0.04961674 0.11105321
0.03840657 0.03693797
     com65      com66      com67      com68      com69      com70
 com71      com72
0.05718178 0.07088485 0.03711119 0.08826702 0.02446860 0.08202483
0.05274964 0.07232899
     com73      com74      com75      com76      com77      com78
 com79      com80
0.06245748 0.05668243 0.06019524 0.07375344 0.07743079 0.06009721
0.05757830 0.05642231
     com81      com82
0.03665132 0.06852237

$CWM
        trait1                        trait2   trait3              trait4
      trait5
com1  Demersal Marine, brackish, freshwater  3.361717 Invertebrate Feeder
     Browser
com2  Demersal Marine, brackish, freshwater  3.391770 Invertebrate Feeder
     Browser
com3  Demersal Marine, brackish, freshwater  3.389626 Invertebrate Feeder
     Browser
com4  Demersal Marine, brackish, freshwater  3.437043 Invertebrate Feeder
     Browser
com5  Demersal Marine, brackish, freshwater  3.450760 Invertebrate Feeder
     Browser
com6  Demersal Marine, brackish, freshwater  3.354952 Invertebrate Feeder
     Browser
com7  Demersal Marine, brackish, freshwater  3.389917 Invertebrate Feeder
     Browser
com8  Demersal Marine, brackish, freshwater  3.382973 Invertebrate Feeder
     Browser
com9  Demersal Marine, brackish, freshwater  3.371722 Invertebrate Feeder
     Browser
com10 Demersal Marine, brackish, freshwater  3.371057 Invertebrate Feeder
     Browser
com11 Demersal Marine, brackish, freshwater  3.389740 Invertebrate Feeder
     Browser
com12 Demersal Marine, brackish, freshwater  3.416626 Invertebrate Feeder
     Browser
com13 Demersal Marine, brackish, freshwater  3.348563 Invertebrate Feeder
     Browser
com14 Demersal Marine, brackish, freshwater  3.310051 Invertebrate Feeder
     Browser
com15 Demersal Marine, brackish, freshwater  3.274433 Invertebrate Feeder
     Browser
com16 Demersal Marine, brackish, freshwater  3.366033 Invertebrate Feeder
     Browser
com17  Pelagic Marine, brackish, freshwater  3.284144 Invertebrate Feeder
Browser/Hunter
com18 Demersal Marine, brackish, freshwater  3.352978 Invertebrate Feeder
     Browser
com19 Demersal Marine, brackish, freshwater  3.313528 Invertebrate Feeder
     Browser
com20 Demersal Marine, brackish, freshwater  3.368486 Invertebrate Feeder
     Browser
com21 Demersal Marine, brackish, freshwater  3.346555 Invertebrate Feeder
     Browser
com22 Demersal Marine, brackish, freshwater  3.348779 Invertebrate Feeder
     Browser
com23 Demersal Marine, brackish, freshwater  3.316949 Invertebrate Feeder
     Browser
com24 Demersal Marine, brackish, freshwater  3.332521 Invertebrate Feeder
     Browser
com25 Demersal Marine, brackish, freshwater  3.398814 Invertebrate Feeder
     Browser
com26 Demersal Marine, brackish, freshwater  3.281393 Invertebrate Feeder
     Browser
com27 Demersal Marine, brackish, freshwater  3.325194 Invertebrate Feeder
     Browser
com28 Demersal Marine, brackish, freshwater  3.356956 Invertebrate Feeder
     Browser
com29 Demersal Marine, brackish, freshwater  3.282245 Invertebrate Feeder
     Browser
com30 Demersal Marine, brackish, freshwater  3.263298 Invertebrate Feeder
     Browser
com31 Demersal Marine, brackish, freshwater  3.304036 Invertebrate Feeder
     Browser
com32 Demersal              Marine, brackish 3.230522 Invertebrate Feeder
     Browser
com33 Demersal Marine, brackish, freshwater  3.347002 Invertebrate Feeder
     Browser
com34 Demersal Marine, brackish, freshwater  3.430373 Invertebrate Feeder
     Browser
com35 Demersal Marine, brackish, freshwater  3.318061 Invertebrate Feeder
     Browser
com36 Demersal Marine, brackish, freshwater  3.334512 Invertebrate Feeder
     Browser
com37 Demersal Marine, brackish, freshwater  3.354938 Invertebrate Feeder
     Browser
com38 Demersal Marine, brackish, freshwater  3.282320 Invertebrate Feeder
     Browser
com39 Demersal Marine, brackish, freshwater  3.307719 Invertebrate Feeder
     Browser
com40 Demersal              Marine, brackish 3.343822 Invertebrate Feeder
     Browser
com41 Demersal Marine, brackish, freshwater  3.347152 Invertebrate Feeder
     Browser
com42 Demersal Marine, brackish, freshwater  3.389799 Invertebrate Feeder
     Browser
com43 Demersal Marine, brackish, freshwater  3.400693 Invertebrate Feeder
     Browser
com44 Demersal Marine, brackish, freshwater  3.421323 Invertebrate Feeder
     Browser
com45 Demersal Marine, brackish, freshwater  3.329006 Invertebrate Feeder
     Browser
com46 Demersal Marine, brackish, freshwater  3.316793 Invertebrate Feeder
     Browser
com47  Benthic Marine, brackish, freshwater  3.309663 Invertebrate Feeder
     Browser
com48 Demersal Marine, brackish, freshwater  3.372207 Invertebrate Feeder
     Browser
com49  Benthic Marine, brackish, freshwater  3.332736 Invertebrate Feeder
     Browser
com50  Benthic Marine, brackish, freshwater  3.311616 Invertebrate Feeder
     Browser
com51 Demersal Marine, brackish, freshwater  3.319775 Invertebrate Feeder
     Browser
com52 Demersal Marine, brackish, freshwater  3.277058 Invertebrate Feeder
     Browser
com53 Demersal Marine, brackish, freshwater  3.354429 Invertebrate Feeder
     Browser
com54 Demersal Marine, brackish, freshwater  3.339532 Invertebrate Feeder
     Browser
com55 Demersal Marine, brackish, freshwater  3.357153 Invertebrate Feeder
     Browser
com56  Benthic Marine, brackish, freshwater  3.279952 Invertebrate Feeder
     Browser
com57  Benthic              Marine, brackish 3.126602 Invertebrate Feeder
     Browser
com58  Benthic              Marine, brackish 3.217454 Invertebrate Feeder
     Browser
com59 Demersal              Marine, brackish 3.307770 Invertebrate Feeder
     Browser
com60 Demersal              Marine, brackish 3.252970 Invertebrate Feeder
     Browser
com61 Demersal Marine, brackish, freshwater  3.404601 Invertebrate Feeder
     Browser
com62  Pelagic Marine, brackish, freshwater  2.806229 Invertebrate Feeder
     Browser
com63 Demersal Marine, brackish, freshwater  3.287427 Invertebrate Feeder
     Browser
com64 Demersal Marine, brackish, freshwater  3.292238 Invertebrate Feeder
     Browser
com65 Demersal              Marine, brackish 3.265497 Invertebrate Feeder
     Browser
com66 Demersal Marine, brackish, freshwater  3.317879 Invertebrate Feeder
     Browser
com67 Demersal              Marine, brackish 3.258586 Invertebrate Feeder
     Browser
com68 Demersal Marine, brackish, freshwater  3.203772 Invertebrate Feeder
     Browser
com69 Demersal Marine, brackish, freshwater  3.289830 Invertebrate Feeder
     Browser
com70 Demersal              Marine, brackish 3.326195 Invertebrate Feeder
     Browser
com71  Benthic Marine, brackish, freshwater  3.325590 Invertebrate Feeder
     Browser
com72  Benthic Marine, brackish, freshwater  3.297994 Invertebrate Feeder
     Browser
com73 Demersal Marine, brackish, freshwater  3.331968 Invertebrate Feeder
     Browser
com74 Demersal Marine, brackish, freshwater  3.395514 Invertebrate Feeder
     Browser
com75 Demersal Marine, brackish, freshwater  3.323936 Invertebrate Feeder
     Browser
com76 Demersal Marine, brackish, freshwater  3.201015 Invertebrate Feeder
     Browser
com77 Demersal Marine, brackish, freshwater  3.280311 Invertebrate Feeder
     Browser
com78 Demersal Marine, brackish, freshwater  3.318771 Invertebrate Feeder
     Browser
com79 Demersal Marine, brackish, freshwater  3.318253 Invertebrate Feeder
     Browser
com80 Demersal Marine, brackish, freshwater  3.374939 Invertebrate Feeder
     Browser
com81 Demersal Marine, brackish, freshwater  3.440927 Invertebrate Feeder
     Browser
com82 Demersal Marine, brackish, freshwater  3.381153 Invertebrate Feeder
     Browser
         trait6
com1  0.5 - 1.0
com2  1.0 - 2.0
com3  1.0 - 2.0
com4  1.0 - 2.0
com5  1.0 - 2.0
com6  1.0 - 2.0
com7  1.0 - 2.0
com8  1.0 - 2.0
com9  0.5 - 1.0
com10 1.0 - 2.0
com11 1.0 - 2.0
com12 1.0 - 2.0
com13 0.5 - 1.0
com14 0.5 - 1.0
com15 0.5 - 1.0
com16 0.5 - 1.0
com17 1.0 - 2.0
com18 0.5 - 1.0
com19 0.5 - 1.0
com20 0.5 - 1.0
com21 0.5 - 1.0
com22 0.5 - 1.0
com23 1.0 - 2.0
com24 1.0 - 2.0
com25 1.0 - 2.0
com26 1.0 - 2.0
com27 1.0 - 2.0
com28 0.5 - 1.0
com29 0.5 - 1.0
com30 0.5 - 1.0
com31 0.5 - 1.0
com32 0.5 - 1.0
com33 0.5 - 1.0
com34 1.0 - 2.0
com35 0.5 - 1.0
com36 0.5 - 1.0
com37 1.0 - 2.0
com38 0.5 - 1.0
com39 0.5 - 1.0
com40 0.5 - 1.0
com41 0.5 - 1.0
com42 1.0 - 2.0
com43 1.0 - 2.0
com44 1.0 - 2.0
com45     < 0.5
com46     < 0.5
com47     < 0.5
com48     < 0.5
com49     < 0.5
com50     < 0.5
com51     < 0.5
com52 0.5 - 1.0
com53 0.5 - 1.0
com54     < 0.5
com55     < 0.5
com56     < 0.5
com57     < 0.5
com58     < 0.5
com59 0.5 - 1.0
com60 0.5 - 1.0
com61 1.0 - 2.0
com62 1.0 - 2.0
com63 0.5 - 1.0
com64 0.5 - 1.0
com65 0.5 - 1.0
com66 0.5 - 1.0
com67 0.5 - 1.0
com68 0.5 - 1.0
com69 0.5 - 1.0
com70 0.5 - 1.0
com71     < 0.5
com72     < 0.5
com73     < 0.5
com74 1.0 - 2.0
com75 0.5 - 1.0
com76 0.5 - 1.0
com77 1.0 - 2.0
com78 0.5 - 1.0
com79 0.5 - 1.0
com80 1.0 - 2.0
com81 1.0 - 2.0
com82 1.0 - 2.0

2016-02-22 13:58 GMT+00:00 stephen sefick <ssefick at gmail.com>:
> If memory serves me, dbFD returns a lot of output. What do you want to
> plot? Also, please provide reproducible examples, so that we can help you
> solve your R related queries.
> kindest regards,
>
> Stephen
>
> On Mon, Feb 22, 2016 at 7:00 AM, Fabio Monteiro <
> fabio.monteiro1992 at gmail.com> wrote:
>
>> Hi
>>
>> thank you for your quick answer
>>
>> I finally managed to insert everything correctly and dbFD is
caltulated.
>>
>> I'm now trying to plot the results.
>>
>> My objects are matrices.
>>
>> x is a functional trait and species matrice. a is the species and
samples
>>
>> Thank you
>>
>> 2016-02-22 12:19 GMT+00:00 PIKAL Petr <petr.pikal at
precheza.cz>:
>>
>> > Hi
>> >
>> > comments inline
>> >
>> > > -----Original Message-----
>> > > From: R-help [mailto:r-help-bounces at r-project.org] On
Behalf Of Fabio
>> > > Monteiro
>> > > Sent: Monday, February 22, 2016 11:51 AM
>> > > To: r-help at r-project.org
>> > > Subject: [R] FD package
>> > >
>> > > Hi.
>> > >
>> > > First i would like to say that i'm really new in R. I
recently started
>> > > working with R and i'm using the FD package.
>> > >
>> > > I'm having some errors that doesn't make any sense.
>> > >
>> > > I have 2 matrix, one is the species with functional traits
and the
>> > > second one is the species and abundances.
>> >
>> > Your objects are matrices or data frames? From docs dbFD expects
various
>> > inputs byt they have to be properly formatted.
>> >
>> > >
>> > > When I try to run the dbFD to calculate the functional
diversity, the
>> > > error is the number of species is different in x and a.
>> > >
>> > > I checked a lot of times and the number of species is the
same and
>> > > there are no mistakes in their names like spaces or caps.
>> >
>> > How did you checked?
>> >
>> > dim(trait) and  dim(abund)
>> >
>> > shall give you the same number of rows in traits as columns in
abund.
>> >
>> > If trait is vector, you need to use length instead of dim.
>> >
>> > >
>> > > Can you help me?
>> >
>> > Without better description of your objects and code you used you
hardly
>> > get any answer. You can start by using examples from help page,
which
>> shall
>> > work and see how your data differ from those examples.
>> >
>> > Cheers
>> > Petr
>> >
>> >
>> > >
>> > > F?bio Monteiro
>> > >
>> > >       [[alternative HTML version deleted]]
>> > >
>> > > ______________________________________________
>> > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and
more, see
>> > > 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.
>> >
>> > ________________________________
>> > Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a
jsou
>> > ur?eny pouze jeho adres?t?m.
>> > Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav?
>> > neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a
jeho
>> kopie
>> > vyma?te ze sv?ho syst?mu.
>> > Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni
tento
>> email
>> > jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat.
>> > Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou
>> modifikacemi
>> > ?i zpo?d?n?m p?enosu e-mailu.
>> >
>> > V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?:
>> > - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o
uzav?en?
>> > smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu.
>> > - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn?
>> p?ijmout;
>> > Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze
strany
>> > p??jemce s dodatkem ?i odchylkou.
>> > - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve
>> > v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech.
>> > - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za
>> > spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl
p?semn?
>> zmocn?n
>> > nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly
adres?tovi
>> tohoto
>> > emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo
jejich
>> > existence je adres?tovi ?i osob? j?m zastoupen? zn?m?.
>> >
>> > This e-mail and any documents attached to it may be confidential
and are
>> > intended only for its intended recipients.
>> > If you received this e-mail by mistake, please immediately inform
its
>> > sender. Delete the contents of this e-mail with all attachments
and its
>> > copies from your system.
>> > If you are not the intended recipient of this e-mail, you are not
>> > authorized to use, disseminate, copy or disclose this e-mail in
any
>> manner.
>> > The sender of this e-mail shall not be liable for any possible
damage
>> > caused by modifications of the e-mail or by delay with transfer of
the
>> > email.
>> >
>> > In case that this e-mail forms part of business dealings:
>> > - the sender reserves the right to end negotiations about entering
into
>> a
>> > contract in any time, for any reason, and without stating any
reasoning.
>> > - if the e-mail contains an offer, the recipient is entitled to
>> > immediately accept such offer; The sender of this e-mail (offer)
>> excludes
>> > any acceptance of the offer on the part of the recipient
containing any
>> > amendment or variation.
>> > - the sender insists on that the respective contract is concluded
only
>> > upon an express mutual agreement on all its aspects.
>> > - the sender of this e-mail informs that he/she is not authorized
to
>> enter
>> > into any contracts on behalf of the company except for cases in
which
>> > he/she is expressly authorized to do so in writing, and such
>> authorization
>> > or power of attorney is submitted to the recipient or the person
>> > represented by the recipient, or the existence of such
authorization is
>> > known to the recipient of the person represented by the recipient.
>> >
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 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.
>
>
>
>
> --
> Stephen Sefick
> **************************************************
> Auburn University
> Biological Sciences
> 331 Funchess Hall
> Auburn, Alabama
> 36849
> **************************************************
> sas0025 at auburn.edu
> http://www.auburn.edu/~sas0025
> **************************************************
>
> Let's not spend our time and resources thinking about things that are
so
> little or so large that all they really do for us is puff us up and make us
> feel like gods.  We are mammals, and have not exhausted the annoying little
> problems of being mammals.
>
>                                 -K. Mullis
>
> "A big computer, a complex algorithm and a long time does not equal
> science."
>
>                               -Robert Gentleman
>
>
	[[alternative HTML version deleted]]

R help - Feb 2016 - FD package

[R] FD package

[R] FD package

[R] FD package