Andrea,
  The argument na.action controls how missings are treated. is this what
you wanted?

aggregate(cbind(IND, DUM)~.,data=net1,sum, na.action=na.pass)

Dave

>Date: Mon, 16 Sep 2013 11:42:07 -0400
>From: Andrea Goijman <agoijman@cnia.inta.gov.ar>
>To: arun <smartpink111@yahoo.com>
>Cc: R help <r-help@r-project.org>
>Subject: Re: [R] Aggregate rows with same fields, within factors
>Message-ID:
>        <
CA+vCKnXekYBkfvcQYTxGwh1WGPxJM8Yj>O2YCPv7FKDszTvcn6Q@mail.gmail.com<CA%2BvCKnXekYBkfvcQYTxGwh1WGPxJM8YjO2YCPv7FKDszTvcn6Q@mail.gmail.com>
>Content-Type: text/plain
>
>it works, but it eliminates the rows with NA
>
>is there a way to keep those?
>
>
>On Mon, Sep 16, 2013 at 11:22 AM, arun <smartpink111@yahoo.com> wrote:
>
> Hi,
> Try:
>
>
>  aggregate(IND~.,data=net1,sum)
>    CAMP LOTE HAB TRANS       ORDEN IND
> 1    C1   B1   C    C1               0
> 2    C1   B1   B    B3       ACARI   3
> 3    C1   B1   B    B1     ARANEAE   1
> 4    C1   B1   B    B3     ARANEAE   2
> 5    C1   B1   B    B3  COLEOPTERA   2
> 6    C1   B1   B    B1     DIPTERA  27
> 7    C1   B1   B    B3     DIPTERA  11
> 8    C1   B1   C    C2     DIPTERA   3
> 9    C1   B1   B    B1   HEMIPTERA  11
> 10   C1   B1   B    B3   HEMIPTERA 231
> 11   C1   B1   C    C2   HEMIPTERA 147
> 12   C1   B1   B    B1 HYMENOPTERA   8
> 13   C1   B1   B    B3 HYMENOPTERA   2
> 14   C1   B1   C    C2 HYMENOPTERA   1
> 15   C1   B1   B    B1 LEPIDOPTERA   1
> 16   C1   B1   B    B1  NEUROPTERA   1
> 17   C1   B1   B    B1  ORTHOPTERA   2
> 18   C1   B1   B    B3  ORTHOPTERA   1
>
>
> A.K.
>
> ----- Original Message -----
> From: Andrea Goijman <agoijman@cnia.inta.gov.ar>
> To: R help <r-help@r-project.org>
> Cc:
> Sent: Monday, September 16, 2013 11:09 AM
> Subject: [R] Aggregate rows with same fields, within factors
>
> Dear R list,
>
> I want to aggregate the number of individuals 'IND' of the same ORDER,
> within each site and season CAMP,TRANS... but I also want to keep record
of
> the habitat HAB and LOTE
>
> For example I have this:
>
>          CAMP LOTE HAB TRANS IND       ORDEN
> 1765   C1   B1   B    B1   7   HEMIPTERA
> 1766   C1   B1   B    B1   7     DIPTERA
> 1767   C1   B1   B    B1   1     DIPTERA
> 1768   C1   B1   B    B1   1  NEUROPTERA
> 1769   C1   B1   B    B1   1   HEMIPTERA
> 1770   C1   B1   B    B1   5     DIPTERA
> 1771   C1   B1   B    B1   1     DIPTERA
>
> And I want this
>
>           CAMP LOTE HAB TRANS IND       ORDEN
> 1765   C1   B1   B    B1   8   HEMIPTERA
> 1766   C1   B1   B    B1   14     DIPTERA
> 1768   C1   B1   B    B1   1  NEUROPTERA
>
>
> I'm using aggregate the way I show below, but it is not working, and I
> cannot figure out why.
>
> Thanks!
>
> Andrea
>
>
>
> net1<-structure(list(CAMP = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = c("C1",
> "C2", "C3", "C4"), class = "factor"), LOTE = structure(c(1L,
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
> 1L), .Label = c("B1", "B4", "B5", "F7", "G6", "G8", "R10", "W9",
> "Z2", "Z3"), class = "factor"), HAB = structure(c(1L, 1L, 1L,
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
> 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label =
> c("B",
> "C"), class = "factor"), TRANS = structure(c(1L, 1L, 1L, 1L,
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,
> 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
> 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), .Label = c("B1",
> "B2", "B3", "C1", "C2", "C3"), class = "factor"), IND = c(2L,
> 6L, 7L, 1L, 1L, 7L, 7L, 1L, 1L, 1L, 5L, 1L, 1L, 1L, 4L, 1L, 2L,
> 1L, 1L, NA, NA, NA, NA, 28L, 4L, 2L, 1L, 3L, 193L, 1L, 2L, 7L,
> 2L, 1L, 5L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 62L, 1L, 1L, 1L, 80L,
> 1L, 1L, 4L), ORDEN = structure(c(9L, 10L, 8L, 8L, 15L, 9L, 8L,
> 8L, 12L, 9L, 8L, 8L, 11L, 3L, 8L, 8L, 10L, 9L, 15L, 1L, 1L, 1L,
> 1L, 9L, 8L, 8L, 5L, 2L, 9L, 10L, 3L, 9L, 9L, 9L, 8L, 10L, 5L,
> 15L, 1L, 1L, 1L, 1L, 9L, 8L, 10L, 9L, 9L, 8L, 8L, 9L), .Label = c("",
> "ACARI", "ARANEAE", "CHILOGNATHA", "COLEOPTERA", "DERMAPTERA",
> "DICTYOPTERA", "DIPTERA", "HEMIPTERA", "HYMENOPTERA", "LEPIDOPTERA",
> "NEUROPTERA", "NN", "ODONATA", "ORTHOPTERA", "PSOCOPTERA", "STREPSIPTERA",
> "THYSANOPTERA", "TRICHOPTERA"), class = "factor")), .Names = c("CAMP",
> "LOTE", "HAB", "TRANS", "IND", "ORDEN"), row.names = c(1760L,
> 1761L, 1762L, 1763L, 1764L, 1765L, 1766L, 1767L, 1768L, 1769L,
> 1770L, 1771L, 1772L, 1773L, 1920L, 1921L, 1922L, 1923L, 1924L,
> 1774L, 1775L, 1776L, 1777L, 1778L, 1779L, 1780L, 1781L, 1782L,
> 1783L, 1784L, 1785L, 1786L, 1787L, 1788L, 1789L, 1790L, 1791L,
> 1925L, 1731L, 1732L, 1733L, 1734L, 1735L, 1736L, 1737L, 1738L,
> 1739L, 1740L, 1741L, 1742L), class = "data.frame")
>
> #generate grouping list
> b <- list(net1$CAMP, net1$LOTE, net1$HAB, net1$TRANS, net1$ORDEN)
>
> #aggregate data
> net2 <- aggregate(x = net1, by =(b), FUN = "sum")
>
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