Re: [R-sig-eco] doubt in generating loops with For
Hello Thiago,
You keep doing the same mistake. When you pass z as subset to comm z will be
the z th column and you only has 10 columns so you will always receive the
out of bound. If I understood correctly you are trying to repeat a process
1000 times if yes follow a code above. I'm not sure that the nested loop is
the right thing but it works.
I don't know the diversity index that you are computing so I'm sorry if it's
not the result that you are looking for. But anyways the code now works so I
believe that you can fix it if i did wrong.
regards
library(vegan)
comm-t(data.frame(sp1=rpois(10, 1), sp2=rpois(10,1), sp3=rpois(10,1),
sp4=rpois(10,1), sp5=rpois(10,1)))
traits-t(data.frame(sp1=rnorm(5,1.2,.2),sp2=rnorm(5,2,.5),
sp3=rnorm(5,3,.3), sp4=rnorm(5,0.5,.2),
sp5=rnorm(5,.9,.6)))
dist-vegdist(traits,gower)
comm-as.matrix(comm)
results-list()
for (i in 1:1000){
for (z in ncol(comm)){
comm1-apply(comm,2,sample)
results[i]-(((t(comm1[, z]) %*% (as.matrix(dist)^2) %*%
comm1[,z])/2/(sum(comm1[, z])^2))[1,1])
}
}
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[R-sig-eco] Help with a function
Dear R users,
I’m trying to build a function to select random samples idf’s from a
database.
So, my data frame had 2 columns and 575 rows. Follow bellow an example of my
database
Idf1casod
12 1
14 1
15 1
16 1
17 3
18 3
19 3
21 3
25 1
24 1
26 1
28 1
29 3
32 3
33 3
35 1
36 3
37 1
48 3
So my function is
blinding=function(sample){
sort=sample(idf1,10,replace=F)
return(sort2)
}
It is pretty simple and I would like to add one more step in my choice. I
would like to link my choice to casod stats. Thus if casod==3 sample would
be random idfs could not be an idf with casod=1. Does someone can help me?
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Re: [R-sig-eco] Help with a function
Hello,
I would like to thanks everyone for the help.
I did this one:
blinding=function(sampling){
sort1=sample(idf[casod==1],30,replace=F)
sort2=sample(idf[casod==3],30,replace=F)
var1=factor(c(rep(1,30),rep(2,30)),labels=c(Positivo,Negativo))
var2=cbind(c(pos=sort1,neg=sort2))
var3=sample(1:60,replace=F)
df=data.frame(Status=var1,IDF=var2,TRP=var3)
return(write.csv(df,file=Piloto.csv,row.names=F))
It`s not exactly a function but works for me.
BTW I found this site:
http://manuals.bioinformatics.ucr.edu/home/programming-in-r
I`ll try to learn a little more about r functions
Regards,
Moreno
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Re: [R-sig-eco] R-sig-ecology (72-19): Plot question
Dear Michal, In this case they have only two variables: (i) time spend in each prey and (ii) prey type. Would be better if he use bar graphs. So if are necessary show the time spend for each spider I suggest the follow commands: spider2=as.factor(spider) plot(time~prey) library(gplots) mt=tapply(time,prey,mean) ept=tapply(time,prey,sd)/sqrt(tapply(time,prey,length)) barplot2(mt,plot.ci=T,ci.u=mt+ept,ci.l=mt-ept,ylim=c(0,200),ylab=Mean of time spending in each prey) barplot(tapply(time,list(prey,spider),mean),beside=T,ylim=c(0,250),col=c(Gray,Gray10,Gray20,Gray30,Gray40,Gray50),xlab=Spider,ylab=Time spend in each prey) levels(prey) labs=c(Ant,CocKroach,Fly,Isopod,Termite) legend(topleft,labs,fill=c(Gray,Gray10,Gray20,Gray30,Gray40,Gray50),bty=n) If u dont like bar use stripchart function for bars :) -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/Re-R-sig-ecology-72-19-Plot-question-tp7578769p7578775.html Sent from the r-sig-ecology mailing list archive at Nabble.com. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] R-sig-ecology (72-19): Plot question
Ok my bad. Stripchart doenst plot bar... Just like this time=(c(rnorm(10,2),rnorm(10,3),rnorm(10,1.5),rnorm(10,.5),rnorm(10,1))) prey=factor(c(rep(1,10),rep(2,10),rep(3,10),rep(4,10),rep(5,10)),labels=c(Ants,Cockroach,Fly,Isopod,Mite)) stripchart(time~prey,vertical=T,pch=1,method=jitter,ylab=Time spend in each prey type,cex.axis=1.4,cex.lab=1.4,cex=1.2) Regadrs, Moreno -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/Re-R-sig-ecology-72-19-Plot-question-tp7578769p7578778.html Sent from the r-sig-ecology mailing list archive at Nabble.com. ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] richness estimators
Hello everyone, I get two questions about richness estimators .. When I use the command below poolaccum from library (vegan) I have the following result estimator - poolaccum (est, permutations = 100, minsize = 1) summary (estimator, display = jack1) N Jackknife 1 2.5% 97.5% Std.Dev 1 5.21 2.000 8.525000 1.79952294 2 9.60 4.2125000 14.50 2.65622958 3 12.116667 6.667 17.508333 2.83689616 4 13.607500 8.500 18.25 2.86595635 5 14.10 9.600 18.60 2.62628516 6 14.751667 9.833 18.17 2.34706099 7 15.408571 10.7142857 18.285714 2.11297296 8 15.54 11.750 19.25 2.10607886 9 15.77 12.311 18.44 1.80268052 10 15.974000 12.900 18.50 1.40105444 11 16.198182 13.3409091 19.022727 1.36031920 12 16.089167 14.833 17.67 0.93069726 13 16.012308 14.8461538 17.692308 0.72956962 14 15.857143 15.8571429 15.857143 0. 1) I would like to know which command I have to use to get the mean and standard deviation ... What command I use to use these data as vectors separately .. 2) For the ACE and ICE estimators they consider the abundance of 10 individuals or incidence in 10 samples as being rare, I wonder if anyone know how to change this value. Thank you for your attention. Best regards, FERNANDO RODRIGUES DA SILVA === Doutor em Biologia Animal Lab. de Ecologia Animal, UNESP - São José do Rio Preto - Cep 15054-000 Celular:(17) 8126-4085 (17) 9774-3163 MSN: bigos...@hotmail.com Skype: presidentedalaponia Lattes:http://buscatextual.cnpq.br/buscatextual/visualizacv.jsp?id=K4777878T8 [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
