[R] accumulation curves

[Michael Bedward]

Hi Kyran,

Please reply via the list - you'll get more answers that way :)

My example had the data in vectors, you are using a data.frame.  Try
replacing the relevant bits of your code (below) with these lines and
see if that helps...

rich.lm ~ lm(Chao1 ~ log(N.obs), data=table1)
smooth.effort <- seq(0,54,0.1)
lines(smooth.effort,
    predict(rich.lm, newdata=list(N.obs=smooth.effort)), col="red")

Michael

On 23 September 2010 18:06, Kyran Staunton <staunton.k at gmail.com> wrote:
> Ok so using your additions my script is......
>
> library(adehabitat)
> in.dir = in.dir="D:/R output/Richness/BK12SR.csv"
> out.dir = "D:/R output/Richness/"
> table1= read.csv(file =in.dir)
>
> y_range <- range(1:15)
> x_range = range(0,60)
>
> png(filename="D:/R output/Richness/BK12SR.png", height=800,
> width=1500, bg="white")
> par(mfrow = c(1, 1), pty = "m", ps=15,cex.main=0.9,mar=c(5,7,4,7))
>
> plot(table1$Chao1~table1$N.obs, ann=FALSE, axes=TRUE, ylim=y_range,
> xlim=x_range, cex=1)
> rich.lm <- lm(table1$Chao1~ log (table1$N.obs))
> smooth.effort <- seq(0,54,0.1)
> lines(smooth.effort, predict(rich.lm,
> newdata=list(table1$N.obs=smooth.effort)), col="red")
>
> title(xlab= "Samples")
> title(ylab= "Chao1 (mean)")
> box()
> dev.off()
>
> #I have 54 samples (N.obs) and about 14 species (Chao1)
>
> R won't run the line as it states......
>
> Error: unexpected '=' in "lines(smooth.effort, predict(rich.lm,
> newdata=list(table1$N.obs="
>
> Can you please decipher this error,
>
> Thank you very much for your time
>
> Kyran.
>
> On 23 September 2010 17:36, Michael Bedward <michael.bedward at gmail.com> wrote:
>> OK, assuming a trend in estimated spp richness vs log(effort) you
>> could do this...
>>
>> plot(effort, richness)
>> rich.lm <- lm( richness ~ log(effort) )
>> smooth.effort <- seq(1, 10, 0.1)  # or whatever is appropriate
>> lines( smooth.effort, predict(rich.lm,
>> newdata=list(effort=smooth.effort)), col="red" )
>>
>> Is that the sort of thing that you're after ?
>>
>> Michael
>>
>>
>> On 23 September 2010 17:07, Kyran Staunton <staunton.k at gmail.com> wrote:
>>> Sorry Michael,
>>>
>>> Yes it surely is, Chao1 species richness increase per sampling effort
>>> run through fossil.
>>>
>>> cheers,
>>>
>>> Kyran
>>>
>>> On 23 September 2010 16:58, Michael Bedward <michael.bedward at gmail.com> wrote:
>>>> Hello Kyran,
>>>>
>>>> Some more details of your data would be helpful. For example, is it
>>>> cumulative species count over time ?
>>>>
>>>> Michael
>>>>
>>>> On 23 September 2010 15:05, Kyran Staunton <staunton.k at gmail.com> wrote:
>>>>> Hi,
>>>>>
>>>>> I am trying to fit a logarithmic trendline to a scatterplot of a
>>>>> species accumulation curve. I've tried abline, lines, curve and
>>>>> scatter.smooth but none of these work.
>>>>>
>>>>> Can anyone help please,
>>>>>
>>>>> Kyran
>>>>>
>>>>> ______________________________________________
>>>>> R-help at r-project.org mailing list
>>>>> 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.
>>>>>
>>>>
>>>
>>
>