I need to express species accumulation curve in percentage terms, i.e. the
vertical axis is from 1% to 100%
I have community data similar to BCI (from vegan package).
I can construct the 'usual' species curve (see below) but I need to
convert
the species number to percentage.
data("BCI")
bcispec<-specaccum(BCI, method = "random",
permutations = 100)
plot(bcispec)
--
Eddie Tsyrlin, PhD Candidate | PEARG | Building 404, Grd Floor, Rm G21
School of Biosciences | University of Melbourne
*Post:* Bio21, Flemington Rd, Parkville VIC 3052
*m: *0413 995525
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Probably: ?sum ?cumsum e.g.> x <- runif(100, 10,20) > cumsum(x)/sum(x) *100Cheers, Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Tue, Jun 16, 2020 at 8:15 AM Eddie Tsyrlin < tsyrline at student.unimelb.edu.au> wrote:> I need to express species accumulation curve in percentage terms, i.e. the > vertical axis is from 1% to 100% > I have community data similar to BCI (from vegan package). > I can construct the 'usual' species curve (see below) but I need to convert > the species number to percentage. > > data("BCI") > bcispec<-specaccum(BCI, method = "random", > permutations = 100) > plot(bcispec) > > -- > Eddie Tsyrlin, PhD Candidate | PEARG | Building 404, Grd Floor, Rm G21 > > School of Biosciences | University of Melbourne > *Post:* Bio21, Flemington Rd, Parkville VIC 3052 > *m: *0413 995525 > ______________________________________________ > 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]]
Hi Eddie, I don't have the vegan package, but this may help: accum<-function(x,y) return(x+(y-x)/7) nspec<-90 for(i in 2:50) nspec[i]<-accum(nspec[i-1],220) plot(nspec/nspec[1]*100,type="l",xlab="Sites", ylab="Species accumulation (%)") Jim On Wed, Jun 17, 2020 at 1:15 AM Eddie Tsyrlin <tsyrline at student.unimelb.edu.au> wrote:> > I need to express species accumulation curve in percentage terms, i.e. the > vertical axis is from 1% to 100% > I have community data similar to BCI (from vegan package). > I can construct the 'usual' species curve (see below) but I need to convert > the species number to percentage. > > data("BCI") > bcispec<-specaccum(BCI, method = "random", > permutations = 100) > plot(bcispec) > > -- > Eddie Tsyrlin, PhD Candidate | PEARG | Building 404, Grd Floor, Rm G21 > > School of Biosciences | University of Melbourne > *Post:* Bio21, Flemington Rd, Parkville VIC 3052 > *m: *0413 995525 > ______________________________________________ > 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.
Hi Eddie, Upon reading your initial request more carefully, the last command should be: plot(nspec/nspec[50]*100,type="l",xlab="Sites", ylab="Species accumulation (%)",ylim=c(1,100)) Jim On Wed, Jun 17, 2020 at 8:23 AM Jim Lemon <drjimlemon at gmail.com> wrote:> > Hi Eddie, > I don't have the vegan package, but this may help: > > accum<-function(x,y) return(x+(y-x)/7) > nspec<-90 > for(i in 2:50) nspec[i]<-accum(nspec[i-1],220) > plot(nspec/nspec[1]*100,type="l",xlab="Sites", > ylab="Species accumulation (%)") > > Jim > > On Wed, Jun 17, 2020 at 1:15 AM Eddie Tsyrlin > <tsyrline at student.unimelb.edu.au> wrote: > > > > I need to express species accumulation curve in percentage terms, i.e. the > > vertical axis is from 1% to 100% > > I have community data similar to BCI (from vegan package). > > I can construct the 'usual' species curve (see below) but I need to convert > > the species number to percentage. > > > > data("BCI") > > bcispec<-specaccum(BCI, method = "random", > > permutations = 100) > > plot(bcispec) > > > > -- > > Eddie Tsyrlin, PhD Candidate | PEARG | Building 404, Grd Floor, Rm G21 > > > > School of Biosciences | University of Melbourne > > *Post:* Bio21, Flemington Rd, Parkville VIC 3052 > > *m: *0413 995525 > > ______________________________________________ > > 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.