species names on a RDA plot

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species names on a RDA plot

Antonio Silva
Dear R users

I'm trying to do a RDA analysis based on Borcard et al. 2011 Numerical
Ecology with R examples.

What I cannot understand is why when I run the script (RDA.R) using the
dataset from book (dataset1.rar) RDA triplot shows species names and when I
use my dataset (dataset2.rar) species names are not shown.

Data and script can be downloaded at
https://app.box.com/s/oayq7tglbmdsu72fj05h83dlzclsiglg

Does anyone know why this happens? Thanks for any clue.

Best regards

Antônio Olinto Ávila da Silva
Fisheries Institute
São Paulo, Brasil

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Re: species names on a RDA plot

Antonio Silva
Hello everybody

The problem is that species names are shown in the ordination diagram when
the data set has a maximum of 80 rows, and mine has 81 (!!!).

So now the question is: it is possible to go through this limitation?

Thanks again,

Antônio Olinto


2015-04-03 20:08 GMT-03:00 Antonio Silva <[hidden email]>:

> Dear R users
>
> I'm trying to do a RDA analysis based on Borcard et al. 2011 Numerical
> Ecology with R examples.
>
> What I cannot understand is why when I run the script (RDA.R) using the
> dataset from book (dataset1.rar) RDA triplot shows species names and when I
> use my dataset (dataset2.rar) species names are not shown.
>
> Data and script can be downloaded at
> https://app.box.com/s/oayq7tglbmdsu72fj05h83dlzclsiglg
>
> Does anyone know why this happens? Thanks for any clue.
>
> Best regards
>
> Antônio Olinto Ávila da Silva
> Fisheries Institute
> São Paulo, Brasil
>

        [[alternative HTML version deleted]]

______________________________________________
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Re: species names on a RDA plot

Jim Lemon-4
Hi Antonio,
Is it possible to use "add=TRUE" and display the plot in two passes?

Jim


On Sat, Apr 4, 2015 at 11:44 PM, Antonio Silva <[hidden email]>
wrote:

> Hello everybody
>
> The problem is that species names are shown in the ordination diagram when
> the data set has a maximum of 80 rows, and mine has 81 (!!!).
>
> So now the question is: it is possible to go through this limitation?
>
> Thanks again,
>
> Antônio Olinto
>
>
> 2015-04-03 20:08 GMT-03:00 Antonio Silva <[hidden email]>:
>
> > Dear R users
> >
> > I'm trying to do a RDA analysis based on Borcard et al. 2011 Numerical
> > Ecology with R examples.
> >
> > What I cannot understand is why when I run the script (RDA.R) using the
> > dataset from book (dataset1.rar) RDA triplot shows species names and
> when I
> > use my dataset (dataset2.rar) species names are not shown.
> >
> > Data and script can be downloaded at
> > https://app.box.com/s/oayq7tglbmdsu72fj05h83dlzclsiglg
> >
> > Does anyone know why this happens? Thanks for any clue.
> >
> > Best regards
> >
> > Antônio Olinto Ávila da Silva
> > Fisheries Institute
> > São Paulo, Brasil
> >
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] 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.

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: species names on a RDA plot

Antonio Silva
Thanks for your attention Jim

Following your idea of adding one more step to construct the diagram, I used

text(spe2.rdaspe, row.names(spe2.rdaspe), pos=3, col="red",cex=0.8)

and I could add species names.

It seems that there's nothing we can do in the plot line.

Have a nice week, best regards

Antonio Olinto


2015-04-04 22:22 GMT-03:00 Jim Lemon <[hidden email]>:

> Hi Antonio,
> Is it possible to use "add=TRUE" and display the plot in two passes?
>
> Jim
>
>
> On Sat, Apr 4, 2015 at 11:44 PM, Antonio Silva <[hidden email]>
> wrote:
>
>> Hello everybody
>>
>> The problem is that species names are shown in the ordination diagram when
>> the data set has a maximum of 80 rows, and mine has 81 (!!!).
>>
>> So now the question is: it is possible to go through this limitation?
>>
>> Thanks again,
>>
>> Antônio Olinto
>>
>>
>> 2015-04-03 20:08 GMT-03:00 Antonio Silva <[hidden email]>:
>>
>> > Dear R users
>> >
>> > I'm trying to do a RDA analysis based on Borcard et al. 2011 Numerical
>> > Ecology with R examples.
>> >
>> > What I cannot understand is why when I run the script (RDA.R) using the
>> > dataset from book (dataset1.rar) RDA triplot shows species names and
>> when I
>> > use my dataset (dataset2.rar) species names are not shown.
>> >
>> > Data and script can be downloaded at
>> > https://app.box.com/s/oayq7tglbmdsu72fj05h83dlzclsiglg
>> >
>> > Does anyone know why this happens? Thanks for any clue.
>> >
>> > Best regards
>> >
>> > Antônio Olinto Ávila da Silva
>> > Fisheries Institute
>> > São Paulo, Brasil
>> >
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] 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.
>
>
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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Re: species names on a RDA plot

Jari Oksanen
Antonio Silva <aolinto.lst <at> gmail.com> writes:

>
> Thanks for your attention Jim
>
> Following your idea of adding one more step to construct the diagram, I used
>
> text(spe2.rdaspe, row.names(spe2.rdaspe), pos=3, col="red",cex=0.8)
>
> and I could add species names.
>
> It seems that there's nothing we can do in the plot line.
>
> Have a nice week, best regards
>

I haven't followed this list, and therefore my answer is a bit
(a big big) late: the help page of plot function suggests to
use type="t" (that is type is text) in your plot command.

Best wishes, Jari Oksanen

______________________________________________
[hidden email] 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.