Hi
when trying your code I got
pval = summary(model)$coeff[2,4]
Error in summary(model)$coeff[2, 4] : subscript out of bounds
> str(summary(model)$coeff)
num [1, 1:4] 1.73e-17 7.07e-01 2.44e-17 1.00
- attr(*, "dimnames")=List of 2
..$ : chr "(Intercept)"
..$ : chr [1:4] "Estimate" "Std. Error" "z
value" "Pr(>|z|)">
You can see that this object is matrix with one row, so your subscript does not
work and you has to define it correctly. How it is beyond my understanding of
this topic.
There are also warnings when estimating model, so maybe model is nod defined
correctly
> model = glm.nb(count~habitat,link="log")
Warning messages:
1: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace
> :
iteration limit reached
2: In theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace
> :
iteration limit reached
I did not check further.
Regards
Petr
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Kalia Schuster
> Sent: Friday, October 03, 2014 4:19 AM
> To: r-help at r-project.org
> Subject: [R] (no subject)
>
> Hello,
> I'm new to R. I'm trying to run a power analysis in a for loop to
find
> an ideal sample size. The situation is I am doing counts of fish at 24
> different sites and rating those sites as 1 or 2 for good or poor
> habitat.
> So the counts are continuous but the habitat rating isn't. When I try
> to run a negative binomial general linearized model with given values
> for mu:
> exp1.302 and exp-0.32 and a given theta: exp(0.75), I get an error
> message before I can run the whole loop and plot the power of the
> sample size against sample. I used a template my teacher showed in
> class, but since he used a poisson dist., I'm stuck on the glm.nb.
> Please help! This is an assignment, so any suggestions would be
> wonderful and I don't expect anything more. But please remember, I am a
> beginner and only have a crude knowledge of R at this point.
> Much appreciated.
>
> #Power analysis
> rm(list=ls())
> graphics.off()
>
> set.seed(1)
> alpha=0.05
> m=200
>
> Ns = seq(2,40,2)
> nNs = length(Ns)
> NAs=rep(NA,nNs)
> results= data.frame(n=Ns, power=NAs)
>
> for(j in 1:nNs) {
> n=Ns[j]
> reject_count = 0
>
> for(i in 1:m ) {
>
>
> mu_poor=exp(-0.32)
> mu_suit=exp(1.302)
> mu=c(rep(mu_poor,n/2),rep(mu_suit,n/2))
> theta=exp(0.175)
> count=rnbinom(n=n,size=theta,mu=mu)
> hab_poor=1
> hab_suit=2
> habitat=sample(hab_poor:hab_suit, size=n, replace=T)
> model = glm.nb(count~habitat,link="log")
> summary(model)
>
>
> pval = summary(model)$coeff[2,4]
> pval
> reject = pval < alpha
> if (reject) reject_count = reject_count+1
> }
> reject_rate = reject_count/m
> power = reject_rate
> typeIIerror=1-reject_rate
>
> results[j,]$power=power
> }
> plot (x=Ns, y=results$power, xlab="Sample size",
ylab="Power")
> lines(Ns,rep(0.95,nNs))
> par(lty=2)
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> 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.
________________________________
Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny
pouze jeho adres?t?m.
Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho
odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho
syst?mu.
Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email
jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat.
Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i
zpo?d?n?m p?enosu e-mailu.
V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?:
- vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? smlouvy, a
to z jak?hokoliv d?vodu i bez uveden? d?vodu.
- a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout;
Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce
s dodatkem ?i odchylkou.
- trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve v?slovn?m
dosa?en?m shody na v?ech jej?ch n?le?itostech.
- odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za spole?nost
??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n nebo p?semn?
pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto emailu p??padn?
osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich existence je adres?tovi
?i osob? j?m zastoupen? zn?m?.
This e-mail and any documents attached to it may be confidential and are
intended only for its intended recipients.
If you received this e-mail by mistake, please immediately inform its sender.
Delete the contents of this e-mail with all attachments and its copies from your
system.
If you are not the intended recipient of this e-mail, you are not authorized to
use, disseminate, copy or disclose this e-mail in any manner.
The sender of this e-mail shall not be liable for any possible damage caused by
modifications of the e-mail or by delay with transfer of the email.
In case that this e-mail forms part of business dealings:
- the sender reserves the right to end negotiations about entering into a
contract in any time, for any reason, and without stating any reasoning.
- if the e-mail contains an offer, the recipient is entitled to immediately
accept such offer; The sender of this e-mail (offer) excludes any acceptance of
the offer on the part of the recipient containing any amendment or variation.
- the sender insists on that the respective contract is concluded only upon an
express mutual agreement on all its aspects.
- the sender of this e-mail informs that he/she is not authorized to enter into
any contracts on behalf of the company except for cases in which he/she is
expressly authorized to do so in writing, and such authorization or power of
attorney is submitted to the recipient or the person represented by the
recipient, or the existence of such authorization is known to the recipient of
the person represented by the recipient.