[R] package FD

Jeff Newmiller jdnewmil at dcn.davis.ca.us
Sun Mar 6 17:08:12 CET 2016 

That code doesn't show what a$x IS, just what comes out after you force things. The fact that you felt compelled to apply those functions just makes it seem more likely that Jim is onto something. The output of

str( a$x )

would show what kind of data it is, and

dput( a$x )

would let us put the data column into our copy of R and guess about why it might not already be numeric, and

dput( a )

followed by your actual code that uses `a` would give us a possibility to reproduce your actual error.  At this point the cause of the problem seems likely to be in the original input data or the code that you are using to import and manipulate that data, which is where most questions like this seem to end up. 
-- 
Sent from my phone. Please excuse my br
evity.

On March 6, 2016 3:57:04 AM PST, Fabio Monteiro <fabio.monteiro1992 at gmail.com> wrote:
>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.
>> >>> >
>> >>> >
>> >>
>> >>
>> >
>>
>
>	[[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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