[R-br] Erro ao rodar Wibugs/Openbugs
Alisson Lucrécio
alisson.lucrecio em ifgoiano.edu.br
Sábado Novembro 8 16:50:35 BRST 2014
Ok, bom trabalho.
Att.
P.S. Vc precisa ler um bom material sobre o assunto, esses códigos são
definidos em data, parameters e model, vc precisa sempre declarar todas
essas variáveis.
2014-11-08 16:40 GMT-02:00 Victor Eduardo [via R-br] <
ml-node+s2285057n4663490h26 em n4.nabble.com>:
> Acredito que o JAGS também seja tão eficiente quanto o stan, até porque
> ele é atual também. Ele rodou super rápido. Agora a luta aqui é a
> convergência dos parâmetros. rs
>
> Em 8 de novembro de 2014 16:32, Alisson Lucrécio <[hidden email]
> <http://user/SendEmail.jtp?type=node&node=4663490&i=0>> escreveu:
>
>> 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 <[hidden email]
>> <http://user/SendEmail.jtp?type=node&node=4663490&i=1>>:
>>
>>> 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] <[hidden email]
>>> <http://user/SendEmail.jtp?type=node&node=4663490&i=2>>:
>>>
>>> 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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>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Alisson Lucrecio da Costa
>>>>>>>>>>>
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>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Alisson Lucrecio da Costa
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Alisson Lucrecio da Costa
>>>>>>>>
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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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--
Alisson Lucrecio da Costa
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