Occupancy estimate per site

[Yuri Kaneoya Arcova]

Hi guys, I hope you can help me.

 On single species- single season model, unmarked presents one single value for occupancy(psi) and one for detectability (p). I also need  the psi and p for each individual site but don't know how. 

Appreciate it in advance.

Yuri

[Jim Baldwin]

If you only have a single value for each, then those are the values for every site.  Your model would need to include covariates to have varying estimates for each site.  Sharing your model would allow for more specific advice.

Jim

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[Yuri Kaneoya Arcova]

Hey Jim. Thanks for your answer. 

But what I actually mean, is that unmarked provides one single value for the model (an average), even though I have for exemple, 12 sampling units. I'm now interested in each of the psi and p value per sampling unit. How do I do that? 

Thank you once again. 

Yuri

[Yuri Kaneoya Arcova]

Here is the script, and the detection history :

Unit S1 S2 S3 S4 S5 S6 S7 S8 S9 S10 S11 S12 S13 S14 S15 S16 S17 S18 S19 S20 S21 S22 S23 S24 S25 S26 S27 S28 S29
1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
2 0 0 0 1 1 0 0 0 1 1 1 1 1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0
3 0 0 0 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
5 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
6 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
9 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
10 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0
11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
12 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0

Script: 

library(unmarked)

dados=read.delim("ocupacao_semana.csv", sep=";", header=TRUE)

amb=read.delim("variaveis.csv", sep=";", header=TRUE)


dados <- dados[ -c(1) ]

amb<-amb[ -c(1) ]

dados_oficial <- unmarkedFrameOccu(y = as.matrix(dados))
summary(dados_oficial)

m2 <- unmarkedFrameOccu(y = as.matrix(dados), siteCovs = amb)

summary(m2)

m1 <- occu(formula =~1~1, data = dados_oficial)   
summary(m1)                                      


predict(m1, newdata = data.frame(site = 1), type = "state")
predict(m1,  newdata = data.frame(site = 1), type = "det")


boot::inv.logit(coef(m1)
boot::inv.logit(coef(m1)

mf <- occu(formula = ~X + Y ~X + A+ Y+P , data = m2, se=TRUE)
summary(mf)

predict(mf, newdata = data.frame(site = 1), type = "state")

[Yaelle Blais]

Hello Yuri, 

Have you tried this code :

predict(mf, type = "state")

It should give you the psi for your 12 sites

Best, 

Yaelle Blais