[R-br] Erro ao rodar Wibugs/Openbugs
Alisson Lucrécio
alisson.lucrecio em ifgoiano.edu.br
Sábado Novembro 8 16:32:01 BRST 2014
Lie a respeito deles há alguns meses, WinBugs, JAGS e Stan, não me lembro
muito bem mais todos funcionam com MCMC. Tinha lido que o Rtan era mais
eficiente que o WinBurgs pos tinha tido uma evolunção no amostradores de
Gibbs. Entretanto, não sei se o Jags também teve essa evolução, mas todos
fazem a mesma coisa, vc só tera uns 30 a 40 segundos a menos quando rodar o
código.
2014-11-08 16:31 GMT-02:00 Alisson Lucrécio <
alisson.lucrecio em ifgoiano.edu.br>:
> Lie a respeito deles há alguns meses, WinBugs, JAGS e Stan, não me lembro
> muito bem mais todos funcionam com MCMC. Tinha lido que o Rtan era mais
> eficiente que o WinBurgs pos tinha tido uma evolunção no amostradores de
> Gibbs. Entretanto, não sei se o Jags também teve essa evolução, mas todos
> fazem a mesma coisa, vc só tera uns 30 a 40 segundos a menos quando rodar o
> código.
>
> 2014-11-08 16:12 GMT-02:00 Victor Eduardo [via R-br] <
> ml-node+s2285057n4663488h64 em n4.nabble.com>:
>
> Oi Alisson, fui experimentar o JAGS, conhece? Com os mesmos códigos de
>> antes rodou normalmente o programa. Não sabia que o rbug era problemático,
>> fiquei horas quebrando a cabeça para solucionar e nada.
>>
>> Aparentemente está tudo ok!
>>
>>
>> O rstan não rodou de jeito nenhum aqui. Chegou a carregar o pacote pelo
>> comando que me passou, mas na hora de rodar aquele exemplo começou a
>> apresentar erro de funções não encontradas. Não sei se o problema foi no
>> meu pc.
>>
>>
>>
>>
>>
>> Valeu pela ajuda
>>
>> Em 8 de novembro de 2014 15:54, Alisson Lucrécio <[hidden email]
>> <http://user/SendEmail.jtp?type=node&node=4663488&i=0>> escreveu:
>>
>>> Victor,
>>>
>>> Minha sugestão é que vc sustituia o código rbug por rstan, o rbug é
>>> muito problemático e ineficente, mande um CMR. Vc conseguiu rodar o rstar?
>>>
>>> Att.
>>>
>>> 2014-11-08 15:52 GMT-02:00 Alisson Lucrécio <[hidden email]
>>> <http://user/SendEmail.jtp?type=node&node=4663488&i=1>>:
>>>
>>>> Victor,
>>>>
>>>> Minha sugestão é que vc sustituia o código rbug por rstan, o rbug é
>>>> muito problemático e ineficente, mande um CRM. Vc conseguiu rodar o rstar?
>>>> Att.
>>>>
>>>> 2014-11-08 15:38 GMT-02:00 Victor Eduardo [via R-br] <[hidden email]
>>>> <http://user/SendEmail.jtp?type=node&node=4663488&i=2>>:
>>>>
>>>> Não rodou aqui. =/
>>>>>
>>>>> O erro que tinha incialmente eu consegui arrumar, só que agora surgiu
>>>>> outro
>>>>>
>>>>> Error in handleRes(res) : NA
>>>>>
>>>>>
>>>>> Só que não tem NA na minha base de dados
>>>>>
>>>>> 2014-11-08 14:10 GMT-02:00 Alisson Lucrécio <[hidden email]
>>>>> <http://user/SendEmail.jtp?type=node&node=4663486&i=0>>:
>>>>>
>>>>>> Caro Victor,
>>>>>>
>>>>>> Se der certo teste esse exemplo.
>>>>>>
>>>>>> library(rstan)
>>>>>>
>>>>>> treatment_level <- c("0", "5", "10", "15")
>>>>>> repetition_number <- 20
>>>>>> response_mean <- c(100, 94, 88, 82)
>>>>>>
>>>>>> treatment <- gl(n = length(treatment_level), k = repetition_number,
>>>>>> labels = treatment_level)
>>>>>> str_error <- 2
>>>>>>
>>>>>> response_temp <- sapply(response_mean, function(x){
>>>>>> response <- rnorm(n = repetition_number, mean = x, sd = str_error)
>>>>>> })
>>>>>>
>>>>>> response <- c(response_temp)
>>>>>>
>>>>>> plot(response ~ treatment)
>>>>>>
>>>>>> summary(lm(response ~ treatment -1))
>>>>>>
>>>>>> mean(response)
>>>>>> sd(response)
>>>>>>
>>>>>> stan_data <- list(N = length(response), I = length(treatment_level),
>>>>>> Treatment=as.numeric(treatment), Response = response)
>>>>>>
>>>>>> # Bayesian method for estimate mean and standard error by treatment
>>>>>>
>>>>>> stan_modelcode <- "
>>>>>> data { // data setup
>>>>>> int<lower=0> N; // sample size
>>>>>> int<lower=1> I; // number of treatments
>>>>>> real Response[N]; // Response
>>>>>> int<lower=1, upper=I> Treatment[N]; // Treatment
>>>>>> }
>>>>>>
>>>>>> parameters {
>>>>>> real mu[I];
>>>>>> real<lower=0, upper=100> sigma[I];
>>>>>> }
>>>>>>
>>>>>> model {
>>>>>> //Priors
>>>>>> mu ~ normal(0, 100);
>>>>>> sigma ~ uniform(0, 100);
>>>>>> //Likelihood
>>>>>> for(i in 1:N) {
>>>>>> Response[i] ~ normal(mu[Treatment[i]], sigma[Treatment[i]]);
>>>>>> }
>>>>>> }
>>>>>> "
>>>>>>
>>>>>> fit <- stan(model_code = stan_modelcode, data = stan_data, iter =
>>>>>> 1000, chains = 3,
>>>>>> verbose = TRUE)
>>>>>>
>>>>>> plot(fit)
>>>>>>
>>>>>> 2014-11-08 14:09 GMT-02:00 Alisson Lucrécio <[hidden email]
>>>>>> <http://user/SendEmail.jtp?type=node&node=4663486&i=1>>:
>>>>>>
>>>>>> Use esse código.
>>>>>>>
>>>>>>> Sys.setenv(MAKEFLAGS = "-j4")
>>>>>>> source('http://mc-stan.org/rstan/install.R', echo = TRUE,
>>>>>>> max.deparse.length = 2000)
>>>>>>> install_rstan()
>>>>>>>
>>>>>>> 2014-11-08 13:41 GMT-02:00 Victor Eduardo [via R-br] <[hidden email]
>>>>>>> <http://user/SendEmail.jtp?type=node&node=4663486&i=2>>:
>>>>>>>
>>>>>>> Oi Alisson, o pacote deu erro para instalar. Tanto pelo arquivo
>>>>>>>> quando pelo código install.packages
>>>>>>>>
>>>>>>>>
>>>>>>>> Esse erro que está acontecendo comigo é no modelo? Porque
>>>>>>>> aparentemente está tudo ok com ele.
>>>>>>>>
>>>>>>>> Em 8 de novembro de 2014 13:01, Alisson Lucrécio <[hidden email]
>>>>>>>> <http://user/SendEmail.jtp?type=node&node=4663483&i=0>> escreveu:
>>>>>>>>
>>>>>>>>> Victor,
>>>>>>>>>
>>>>>>>>> Boa tarde.
>>>>>>>>>
>>>>>>>>> Use o pacote rstan.
>>>>>>>>>
>>>>>>>>> Att.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 2014-11-08 12:53 GMT-02:00 Victor Eduardo [via R-br] <[hidden
>>>>>>>>> email] <http://user/SendEmail.jtp?type=node&node=4663483&i=1>>:
>>>>>>>>>
>>>>>>>>> Pessoal, estou rodando um modelo de regressão pelo Openbugs. Na
>>>>>>>>>> hora de rodar ele da o seguinte erro durante o processo
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Error in BRugs::samplesSet(parametersToSave) :
>>>>>>>>>> model must be initialized before monitors used
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> O que seria exatamente isso? Já mexi em tudo quanto é
>>>>>>>>>> configuração e código do meu modelo e nada até agora
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Atenciosamente,
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Victor Eduardo
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
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>>>>>>>>>> forneça código mínimo reproduzível.
>>>>>>>>>>
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>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Alisson Lucrecio da Costa
>>>>>>>>>
>>>>>>>>> _______________________________________________
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>>>>>>>>>
>>>>>>>>
>>>>>>>>
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>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Alisson Lucrecio da Costa
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Alisson Lucrecio da Costa
>>>>>>
>>>>>> _______________________________________________
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>>>>>>
>>>>>
>>>>>
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>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Alisson Lucrecio da Costa
>>>>
>>>
>>>
>>>
>>> --
>>> Alisson Lucrecio da Costa
>>>
>>> _______________________________________________
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>>
>>
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>
>
>
> --
> Alisson Lucrecio da Costa
>
--
Alisson Lucrecio da Costa
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