[R] package FD

[Fabio Monteiro]

Hey Jim

they are all numeric as you can see

as.numeric(as.character(a$x))
 [1]  20.0  50.0   7.9  25.0  20.0  20.0  15.0  30.0  48.0  75.0  75.0
 25.0 300.0
[14] 103.0  20.0  45.0  15.0  20.0  50.0   6.0  18.0  59.0  70.0  80.0
100.0  40.0
[27]  15.0  30.0  40.0  60.0   9.0  11.0  27.5  75.0  60.0  70.0  70.0
 60.0  20.0
[40]  21.0  50.0  35.0  46.0

Fábio

2016-03-05 9:38 GMT+00:00 Jim Lemon <drjimlemon at gmail.com>:

> Hi Fabio,
> What has probably happened is that ft$trait3 looks like numbers but
> when it was read in at least one value could not be read as a number.
> The default behavior in R is to transform the variable into a factor:
>
> testcase<-read.table(text="1 2 3 4
>  1 2 3 4
>  1 2 B 4")
> > testcase
>  V1 V2 V3 V4
> 1  1  2  3  4
> 2  1  2  3  4
> 3  1  2  B  4
> > sapply(testcase,class)
>       V1        V2        V3        V4
> "integer" "integer"  "factor" "integer"
>
> So testcase$V3 was read in as a factor. There are a couple of things
> you can do. First, try to convert the factor to numeric and live with
> the NA values that will be generated:
>
> as.numeric(as.character(testcase$V3))
> [1]  3  3 NA
> Warning message:
> NAs introduced by coercion
>
> If the number of non0numeric values in the original data is small and
> you can find them:
>
> testcase$V3[3]<-3
> as.numeric(as.character(testcase$V3))
> [1] 3 3 3
>
> correct the original data and read it in again. I don't really know
> enough to answer your second question.
>
> JIm
>
>
> On Sat, Mar 5, 2016 at 2:58 AM, Fabio Monteiro
> <fabio.monteiro1992 at gmail.com> wrote:
> > I still have another question. apart from that one
> >
> > in the dbFD function in FD package there is one option which is if FRic
> > should be standardized or not. What does that mean? Why should our
> shouldn't
> > I have the FRic Standardized?
> >
> > Thank you Jim
> >
> > 2016-03-04 14:52 GMT+00:00 Fabio Monteiro <fabio.monteiro1992 at gmail.com
> >:
> >>
> >> class(ft$trait3)
> >> [1] "factor
> >>
> >>
> >> Yes is a factor. And now?
> >>
> >> Thank you
> >>
> >> Kind Regards
> >> Fábio
> >>
> >> 2016-03-04 7:15 GMT+00:00 Jim Lemon <drjimlemon at gmail.com>:
> >>>
> >>> Hi Fabio,
> >>> You should write:
> >>>
> >>> class(...)
> >>>
> >>> where ... is the same as what you would type to have the variable
> >>> displayed on the console. Looking at your earlier message, it might
> >>> be:
> >>>
> >>> x$trait3
> >>>
> >>> so try:
> >>>
> >>> class(x$trait3)
> >>>
> >>> Jim
> >>>
> >>>
> >>> On Fri, Mar 4, 2016 at 11:30 AM, Fabio Monteiro
> >>> <fabio.monteiro1992 at gmail.com> wrote:
> >>> > i just called trait3 to my variable.
> >>> >
> >>> > Is this what i'm suppose to wright? class(trait3), or class
> >>> > (my_trait3_variable?
> >>> >
> >>> > both give error
> >>> >
> >>> > 2016-03-03 23:42 GMT+00:00 Jim Lemon <drjimlemon at gmail.com>:
> >>> >>
> >>> >> Hi Fabio,
> >>> >> It is possible that your remaining "numeric" variable is a factor.
> >>> >> What
> >>> >> does:
> >>> >>
> >>> >> class(my_numeric_variable)
> >>> >>
> >>> >> say? (where you substitute the name of your "numeric" variable)
> >>> >>
> >>> >> Jim
> >>> >>
> >>> >>
> >>> >> On Fri, Mar 4, 2016 at 2:25 AM, Fabio Monteiro
> >>> >> <fabio.monteiro1992 at gmail.com> wrote:
> >>> >> > Hello, my name is Fábio and I'm a Marine Ecology student in
> >>> >> > Portugal.
> >>> >> >
> >>> >> > I'm currently using the FD package for my work and yesterday one
> >>> >> > message
> >>> >> > appeared that I wasn't expecting and I really need your help to
> try
> >>> >> > to
> >>> >> > figure out what's happening.
> >>> >> > I'm using the dbFD function and the following message appeared:
> >>> >> >
> >>> >> > FRic: Only categorical and/or ordinal trait(s) present in 'x'.
> FRic
> >>> >> > was
> >>> >> >  measured as the number of unique trait combinations, NOT as the
> >>> >> > convex
> >>> >> > hull volume.
> >>> >> > FDiv: Cannot be computed when only categorical and/or ordinal
> >>> >> > trait(s)
> >>> >> > present in 'x'.
> >>> >> >
> >>> >> > My data:
> >>> >> > x is a matrix with species vs functional traits
> >>> >> > a is a matrix with species vs sampling (in abundances)
> >>> >> >
> >>> >> > Previously I used the dbFD function and was working just fine.
> >>> >> > Yesterday
> >>> >> > I
> >>> >> > removed 2 traits and this message appeared.
> >>> >> >
> >>> >> > My traits now are 3 categorical traits and 1 numeric. The 2 trais
> >>> >> > that I
> >>> >> > removed were numeric traits as well. I really need to remove those
> >>> >> > trait,
> >>> >> > but I still need the FDiv to be calculated. Can you explain to me
> >>> >> > why is
> >>> >> > this error occurring? I need to know how the dbFD is measuring the
> >>> >> > indexes
> >>> >> > so I can understanding the error and if I can or can't continue to
> >>> >> > use
> >>> >> > this
> >>> >> > package (if it applies or not to my goals)
> >>> >> >
> >>> >> > Kind regards
> >>> >> >
> >>> >> > Fábio 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.
> >>> >
> >>> >
> >>
> >>
> >
>

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