Censoring in rjags - Invalid parent values
I'm having troubles reimplementing a model from winbugs on rjags. I'm getting the Invalid parent values
error which is the error you get when censoring was not correctly setup, but I can't see my mistake.
This is the original model on WinBugs:
model
for(i in 1 : N)
times[i] ~ dweib(v, lambda[i]) T(censor[i],)
lambda[i] <- exp(beta0 + beta1*type[i])
S[i] <- exp(-lambda[i]*pow(times[i],v));
f[i] <- lambda[i]*v*pow(times[i],v-1)*S[i]
h[i] <- f[i]/S[i]
beta0 ~ dnorm(0.0, 0.0001)
beta1 ~ dnorm(0.0, 0.0001)
v ~ dexp(0.001)
median0 <- pow(log(2) * exp(-beta0), 1/v)
median1 <- pow(log(2) * exp(-beta0-beta1), 1/v)
Setting up a reproducible example:
type <- as.factor(c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0))
censor <- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,882,892,1031,
1033,1306,1335,0,1452,1472,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,381,0,0,0,0,0,0,0,0,0,529,0,
0,0,0,0,0,0,0,0,945,0,0,1180,0,0,1277,1397,1512,1519)
times <-c (17,42,44,48,60,72,74,95,103,108,122,144,167,170,183,185,193,195,197,208,234,235,254,307,315,401,
445,464,484,528,542,567,577,580,795,855,NA,NA,NA,NA,NA,NA,1366,NA,NA,1,63,105,129,182,216,250,262,
301,301,342,354,356,358,380,NA,383,383,388,394,408,460,489,499,524,NA,535,562,675,676,748,748,778,
786,797,NA,955,968,NA,1245,1271,NA,NA,NA,NA)
df <- tibble(type = type, censor = censor, time = times) %>%
mutate(censor_limit = replace(censor, censor == 0, max(times, na.rm = TRUE))) %>%
mutate(is_censored = ifelse(is.na(time), 1, 0)) %>%
mutate(time_init = ifelse(is_censored == 1, censor_limit + 1, NA))
df$censor <- NULL
head(df)
And this is the rjags part:
m <- textConnection("model
for(i in 1 : N)
isCensored[i] ~ dinterval(times[i], censorLimit[i])
times[i] ~ dweib(v, lambda[i])
lambda[i] <- exp(beta0 + beta1*type[i])
S[i] <- exp(-lambda[i]*pow(times[i],v));
f[i] <- lambda[i]*v*pow(times[i],v-1)*S[i]
h[i] <- f[i]/S[i]
beta0 ~ dnorm(0.0, 0.0001)
beta1 ~ dnorm(0.0, 0.0001)
v ~ dexp(0.001)
# Median survival time
median0 <- pow(log(2) * exp(-beta0), 1/v)
median1 <- pow(log(2) * exp(-beta0-beta1), 1/v)
")
d <- list(N = nrow(df), times = df$time, type = df$type, isCensored = df$is_censored,
censorLimit = df$censor_limit)
inits1 = function()
inits = list(v = 1, beta0 = 0, beta1=0, times = df$time_init)
mod <- jags.model(m, data = d, inits = inits1, n.chains = 3)
update(mod, 1e3)
mod_sim <- coda.samples(model = mod, variable.names = c("lambda", "median0", "median1"), n.iter = 5e3)
mod_csim <- as.mcmc(do.call(rbind, mod_sim))
Output:
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 164
Unobserved stochastic nodes: 19
Total graph size: 910
Initializing model
Deleting model
Error in jags.model(m, data = d, inits = inits1, n.chains = 3): Error in node h[35]
Invalid parent values
r bayesian rjags
add a comment |
I'm having troubles reimplementing a model from winbugs on rjags. I'm getting the Invalid parent values
error which is the error you get when censoring was not correctly setup, but I can't see my mistake.
This is the original model on WinBugs:
model
for(i in 1 : N)
times[i] ~ dweib(v, lambda[i]) T(censor[i],)
lambda[i] <- exp(beta0 + beta1*type[i])
S[i] <- exp(-lambda[i]*pow(times[i],v));
f[i] <- lambda[i]*v*pow(times[i],v-1)*S[i]
h[i] <- f[i]/S[i]
beta0 ~ dnorm(0.0, 0.0001)
beta1 ~ dnorm(0.0, 0.0001)
v ~ dexp(0.001)
median0 <- pow(log(2) * exp(-beta0), 1/v)
median1 <- pow(log(2) * exp(-beta0-beta1), 1/v)
Setting up a reproducible example:
type <- as.factor(c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0))
censor <- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,882,892,1031,
1033,1306,1335,0,1452,1472,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,381,0,0,0,0,0,0,0,0,0,529,0,
0,0,0,0,0,0,0,0,945,0,0,1180,0,0,1277,1397,1512,1519)
times <-c (17,42,44,48,60,72,74,95,103,108,122,144,167,170,183,185,193,195,197,208,234,235,254,307,315,401,
445,464,484,528,542,567,577,580,795,855,NA,NA,NA,NA,NA,NA,1366,NA,NA,1,63,105,129,182,216,250,262,
301,301,342,354,356,358,380,NA,383,383,388,394,408,460,489,499,524,NA,535,562,675,676,748,748,778,
786,797,NA,955,968,NA,1245,1271,NA,NA,NA,NA)
df <- tibble(type = type, censor = censor, time = times) %>%
mutate(censor_limit = replace(censor, censor == 0, max(times, na.rm = TRUE))) %>%
mutate(is_censored = ifelse(is.na(time), 1, 0)) %>%
mutate(time_init = ifelse(is_censored == 1, censor_limit + 1, NA))
df$censor <- NULL
head(df)
And this is the rjags part:
m <- textConnection("model
for(i in 1 : N)
isCensored[i] ~ dinterval(times[i], censorLimit[i])
times[i] ~ dweib(v, lambda[i])
lambda[i] <- exp(beta0 + beta1*type[i])
S[i] <- exp(-lambda[i]*pow(times[i],v));
f[i] <- lambda[i]*v*pow(times[i],v-1)*S[i]
h[i] <- f[i]/S[i]
beta0 ~ dnorm(0.0, 0.0001)
beta1 ~ dnorm(0.0, 0.0001)
v ~ dexp(0.001)
# Median survival time
median0 <- pow(log(2) * exp(-beta0), 1/v)
median1 <- pow(log(2) * exp(-beta0-beta1), 1/v)
")
d <- list(N = nrow(df), times = df$time, type = df$type, isCensored = df$is_censored,
censorLimit = df$censor_limit)
inits1 = function()
inits = list(v = 1, beta0 = 0, beta1=0, times = df$time_init)
mod <- jags.model(m, data = d, inits = inits1, n.chains = 3)
update(mod, 1e3)
mod_sim <- coda.samples(model = mod, variable.names = c("lambda", "median0", "median1"), n.iter = 5e3)
mod_csim <- as.mcmc(do.call(rbind, mod_sim))
Output:
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 164
Unobserved stochastic nodes: 19
Total graph size: 910
Initializing model
Deleting model
Error in jags.model(m, data = d, inits = inits1, n.chains = 3): Error in node h[35]
Invalid parent values
r bayesian rjags
add a comment |
I'm having troubles reimplementing a model from winbugs on rjags. I'm getting the Invalid parent values
error which is the error you get when censoring was not correctly setup, but I can't see my mistake.
This is the original model on WinBugs:
model
for(i in 1 : N)
times[i] ~ dweib(v, lambda[i]) T(censor[i],)
lambda[i] <- exp(beta0 + beta1*type[i])
S[i] <- exp(-lambda[i]*pow(times[i],v));
f[i] <- lambda[i]*v*pow(times[i],v-1)*S[i]
h[i] <- f[i]/S[i]
beta0 ~ dnorm(0.0, 0.0001)
beta1 ~ dnorm(0.0, 0.0001)
v ~ dexp(0.001)
median0 <- pow(log(2) * exp(-beta0), 1/v)
median1 <- pow(log(2) * exp(-beta0-beta1), 1/v)
Setting up a reproducible example:
type <- as.factor(c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0))
censor <- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,882,892,1031,
1033,1306,1335,0,1452,1472,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,381,0,0,0,0,0,0,0,0,0,529,0,
0,0,0,0,0,0,0,0,945,0,0,1180,0,0,1277,1397,1512,1519)
times <-c (17,42,44,48,60,72,74,95,103,108,122,144,167,170,183,185,193,195,197,208,234,235,254,307,315,401,
445,464,484,528,542,567,577,580,795,855,NA,NA,NA,NA,NA,NA,1366,NA,NA,1,63,105,129,182,216,250,262,
301,301,342,354,356,358,380,NA,383,383,388,394,408,460,489,499,524,NA,535,562,675,676,748,748,778,
786,797,NA,955,968,NA,1245,1271,NA,NA,NA,NA)
df <- tibble(type = type, censor = censor, time = times) %>%
mutate(censor_limit = replace(censor, censor == 0, max(times, na.rm = TRUE))) %>%
mutate(is_censored = ifelse(is.na(time), 1, 0)) %>%
mutate(time_init = ifelse(is_censored == 1, censor_limit + 1, NA))
df$censor <- NULL
head(df)
And this is the rjags part:
m <- textConnection("model
for(i in 1 : N)
isCensored[i] ~ dinterval(times[i], censorLimit[i])
times[i] ~ dweib(v, lambda[i])
lambda[i] <- exp(beta0 + beta1*type[i])
S[i] <- exp(-lambda[i]*pow(times[i],v));
f[i] <- lambda[i]*v*pow(times[i],v-1)*S[i]
h[i] <- f[i]/S[i]
beta0 ~ dnorm(0.0, 0.0001)
beta1 ~ dnorm(0.0, 0.0001)
v ~ dexp(0.001)
# Median survival time
median0 <- pow(log(2) * exp(-beta0), 1/v)
median1 <- pow(log(2) * exp(-beta0-beta1), 1/v)
")
d <- list(N = nrow(df), times = df$time, type = df$type, isCensored = df$is_censored,
censorLimit = df$censor_limit)
inits1 = function()
inits = list(v = 1, beta0 = 0, beta1=0, times = df$time_init)
mod <- jags.model(m, data = d, inits = inits1, n.chains = 3)
update(mod, 1e3)
mod_sim <- coda.samples(model = mod, variable.names = c("lambda", "median0", "median1"), n.iter = 5e3)
mod_csim <- as.mcmc(do.call(rbind, mod_sim))
Output:
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 164
Unobserved stochastic nodes: 19
Total graph size: 910
Initializing model
Deleting model
Error in jags.model(m, data = d, inits = inits1, n.chains = 3): Error in node h[35]
Invalid parent values
r bayesian rjags
I'm having troubles reimplementing a model from winbugs on rjags. I'm getting the Invalid parent values
error which is the error you get when censoring was not correctly setup, but I can't see my mistake.
This is the original model on WinBugs:
model
for(i in 1 : N)
times[i] ~ dweib(v, lambda[i]) T(censor[i],)
lambda[i] <- exp(beta0 + beta1*type[i])
S[i] <- exp(-lambda[i]*pow(times[i],v));
f[i] <- lambda[i]*v*pow(times[i],v-1)*S[i]
h[i] <- f[i]/S[i]
beta0 ~ dnorm(0.0, 0.0001)
beta1 ~ dnorm(0.0, 0.0001)
v ~ dexp(0.001)
median0 <- pow(log(2) * exp(-beta0), 1/v)
median1 <- pow(log(2) * exp(-beta0-beta1), 1/v)
Setting up a reproducible example:
type <- as.factor(c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0))
censor <- c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,882,892,1031,
1033,1306,1335,0,1452,1472,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,381,0,0,0,0,0,0,0,0,0,529,0,
0,0,0,0,0,0,0,0,945,0,0,1180,0,0,1277,1397,1512,1519)
times <-c (17,42,44,48,60,72,74,95,103,108,122,144,167,170,183,185,193,195,197,208,234,235,254,307,315,401,
445,464,484,528,542,567,577,580,795,855,NA,NA,NA,NA,NA,NA,1366,NA,NA,1,63,105,129,182,216,250,262,
301,301,342,354,356,358,380,NA,383,383,388,394,408,460,489,499,524,NA,535,562,675,676,748,748,778,
786,797,NA,955,968,NA,1245,1271,NA,NA,NA,NA)
df <- tibble(type = type, censor = censor, time = times) %>%
mutate(censor_limit = replace(censor, censor == 0, max(times, na.rm = TRUE))) %>%
mutate(is_censored = ifelse(is.na(time), 1, 0)) %>%
mutate(time_init = ifelse(is_censored == 1, censor_limit + 1, NA))
df$censor <- NULL
head(df)
And this is the rjags part:
m <- textConnection("model
for(i in 1 : N)
isCensored[i] ~ dinterval(times[i], censorLimit[i])
times[i] ~ dweib(v, lambda[i])
lambda[i] <- exp(beta0 + beta1*type[i])
S[i] <- exp(-lambda[i]*pow(times[i],v));
f[i] <- lambda[i]*v*pow(times[i],v-1)*S[i]
h[i] <- f[i]/S[i]
beta0 ~ dnorm(0.0, 0.0001)
beta1 ~ dnorm(0.0, 0.0001)
v ~ dexp(0.001)
# Median survival time
median0 <- pow(log(2) * exp(-beta0), 1/v)
median1 <- pow(log(2) * exp(-beta0-beta1), 1/v)
")
d <- list(N = nrow(df), times = df$time, type = df$type, isCensored = df$is_censored,
censorLimit = df$censor_limit)
inits1 = function()
inits = list(v = 1, beta0 = 0, beta1=0, times = df$time_init)
mod <- jags.model(m, data = d, inits = inits1, n.chains = 3)
update(mod, 1e3)
mod_sim <- coda.samples(model = mod, variable.names = c("lambda", "median0", "median1"), n.iter = 5e3)
mod_csim <- as.mcmc(do.call(rbind, mod_sim))
Output:
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 164
Unobserved stochastic nodes: 19
Total graph size: 910
Initializing model
Deleting model
Error in jags.model(m, data = d, inits = inits1, n.chains = 3): Error in node h[35]
Invalid parent values
r bayesian rjags
r bayesian rjags
edited Nov 12 '18 at 22:19
FranGoitia
asked Nov 12 '18 at 21:29
FranGoitiaFranGoitia
72621129
72621129
add a comment |
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