[R-sig-eco] Multiple count if style "queries"
Chris Mcowen
chrismcowen at gmail.com
Sat May 21 00:20:36 CEST 2011
Thank you.
Chris
On 20 May 2011, at 23:14, Peter Solymos wrote:
On Fri, May 20, 2011 at 4:04 PM, Chris Mcowen <chrismcowen at gmail.com> wrote:
> Thanks Peter,
>
> This is what i am after but i would like this ( the counts) for each ECO_NAME not the total for the entire data set.
>
> A sample of my data is below
>
> data2 <- structure(list(ECO_NAME = structure(c(1L, 1L, 2L, 2L, 2L, 2L,
> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L,
> 3L, 3L, 3L, 3L, 3L), .Label = c("Biak-Numfoor rain forests",
> "Central Range montane rain forests", "Huon Peninsula montane rain forests"
> ), class = "factor"), Order = structure(c(1L, 2L, 1L, 2L, 2L,
> 2L, 2L, 2L, 2L, 2L, 2L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L,
> 2L, 2L, 2L, 2L, 4L, 4L), .Label = c("Alismatales", "Asparagales",
> "Commelinales", "Poales", "Zingiberales"), class = "factor"),
> Family = structure(c(1L, 7L, 1L, 6L, 7L, 7L, 7L, 7L, 7L,
> 7L, 7L, 3L, 2L, 4L, 4L, 5L, 8L, 8L, 9L, 9L, 9L, 7L, 7L, 7L,
> 7L, 2L, 8L), .Label = c("Araceae", "Centrolepidaceae", "Commelinaceae",
> "Cyperaceae", "Eriocaulaceae", "Lomandraceae", "Orchidaceae",
> "Poaceae", "Zingiberaceae"), class = "factor"), Genus = structure(c(13L,
> 3L, 13L, 6L, 19L, 9L, 20L, 4L, 4L, 9L, 9L, 15L, 5L, 14L,
> 10L, 11L, 17L, 16L, 1L, 8L, 2L, 18L, 7L, 19L, 12L, 5L, 16L
> ), .Label = c("Alpinia", "Amomum", "Bromheadia", "Bulbophyllum",
> "Centrolepis", "Cordyline", "Corybas", "Curcuma", "Dendrobium",
> "Eleocharis", "Eriocaulon", "Glomera", "Homalomena", "Machaerina",
> "Murdannia", "Poa", "Schizostachyum", "Taeniophyllum", "Thelymitra",
> "Vanda"), class = "factor")), .Names = c("ECO_NAME", "Order",
> "Family", "Genus"), class = "data.frame", row.names = c(NA, -27L
> ))
Chris,
How about this? (Note that summed incidences are the same for all
taxonomic levels.)
> data.frame(unique.Genus=rowSums(xtabs(~ ECO_NAME + Genus, data2) > 0),
+ unique.Family=rowSums(xtabs(~ ECO_NAME + Family, data2) > 0),
+ unique.Order=rowSums(xtabs(~ ECO_NAME + Order, data2) > 0),
+ incidences.Genus=rowSums(xtabs(~ ECO_NAME + Genus, data2)),
+ incidences.Family=rowSums(xtabs(~ ECO_NAME + Family, data2)),
+ incidences.Order=rowSums(xtabs(~ ECO_NAME + Order, data2)))
unique.Genus unique.Family unique.Order
Biak-Numfoor rain forests 2 2 2
Central Range montane rain forests 16 9 5
Huon Peninsula montane rain forests 6 3 2
incidences.Genus incidences.Family
Biak-Numfoor rain forests 2 2
Central Range montane rain forests 19 19
Huon Peninsula montane rain forests 6 6
incidences.Order
Biak-Numfoor rain forests 2
Central Range montane rain forests 19
Huon Peninsula montane rain forests 6
Peter
>
>
> On 20 May 2011, at 22:32, Peter Solymos wrote:
>
> Chris,
>
> Something like this should do the job:
>
> 1.
> rowSums(xtabs(~ ECO_NAME + Genus, x) > 0)
> 2.
> rowSums(xtabs(~ ECO_NAME + Genus, x))
>
> Cheers,
>
> Peter
>
>
>
> On Fri, May 20, 2011 at 3:19 PM, Chris Mcowen <chrismcowen at gmail.com> wrote:
>> Dear List,
>>
>> I am looking to calculate two things from my data frame and was after some advice. For the example below i want to know.
>>
>> 1. How many unique Orders/Families and Genera there are per eco-name
>>
>> 2. How many incidences are there for each Order/Family and Genus there are per eco-region
>>
>> I have 650 econame.
>>
>> I.e for Biak-Numfoor rain forests there are 2 orders, 2 families and two genera. Also, Alismatales are represented once, Asparagales once etc etc.
>>
>> Thanks for any advice.
>>
>> Chris
>>
>>
>> ECO_NAME Order Family Genus
>> Biak-Numfoor rain forests Alismatales Araceae Homalomena
>> Biak-Numfoor rain forests Asparagales Orchidaceae Bromheadia
>> Central Range montane rain forests Alismatales Araceae Homalomena
>> Central Range montane rain forests Asparagales Lomandraceae Cordyline
>> Central Range montane rain forests Asparagales Orchidaceae Thelymitra
>> Central Range montane rain forests Asparagales Orchidaceae Dendrobium
>> Central Range montane rain forests Asparagales Orchidaceae Vanda
>> Central Range montane rain forests Asparagales Orchidaceae Bulbophyllum
>> Central Range montane rain forests Asparagales Orchidaceae Bulbophyllum
>> Central Range montane rain forests Asparagales Orchidaceae Dendrobium
>> Central Range montane rain forests Asparagales Orchidaceae Dendrobium
>> Central Range montane rain forests Commelinales Commelinaceae Murdannia
>> Central Range montane rain forests Poales Centrolepidaceae Centrolepis
>> Central Range montane rain forests Poales Cyperaceae Machaerina
>> Central Range montane rain forests Poales Cyperaceae Eleocharis
>> Central Range montane rain forests Poales Eriocaulaceae Eriocaulon
>> Central Range montane rain forests Poales Poaceae Schizostachyum
>> Central Range montane rain forests Poales Poaceae Poa
>> Central Range montane rain forests Zingiberales Zingiberaceae Alpinia
>> Central Range montane rain forests Zingiberales Zingiberaceae Curcuma
>> Central Range montane rain forests Zingiberales Zingiberaceae Amomum
>> Huon Peninsula montane rain forests Asparagales Orchidaceae Taeniophyllum
>> Huon Peninsula montane rain forests Asparagales Orchidaceae Corybas
>> Huon Peninsula montane rain forests Asparagales Orchidaceae Thelymitra
>> Huon Peninsula montane rain forests Asparagales Orchidaceae Glomera
>> Huon Peninsula montane rain forests Poales Centrolepidaceae Centrolepis
>> Huon Peninsula montane rain forests Poales Poaceae Poa
>>
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>
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