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Dealing with rounded data in Stan
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--- | |
title: "Rounding" | |
output: html_notebook | |
--- | |
```{r} | |
library(rstan) | |
options(mc.cores = parallel::detectCores()) | |
rstan_options(auto_write = TRUE) | |
``` | |
# Model | |
https://mc-stan.org/docs/2_18/stan-users-guide/bayesian-measurement-error-model.html | |
```{stan, output.var=rounding} | |
data { | |
int<lower=0> N; | |
vector[N] y; | |
} | |
parameters { | |
real mu; | |
real<lower=0> sigma_sq; | |
vector<lower=-0.5, upper=0.5>[N] y_err; | |
} | |
transformed parameters { | |
real<lower=0> sigma; | |
vector[N] z; | |
sigma = sqrt(sigma_sq); | |
z = y + y_err; | |
} | |
model { | |
target += -2 * log(sigma); | |
z ~ normal(mu, sigma); | |
} | |
``` | |
# Run Stan | |
```{r} | |
set.seed(12) | |
y <- rnorm(20, 10, 2) | |
y_r <- round(y, 0) | |
N <- length(y) | |
fit <- sampling(rounding, data = list(N = N, y = y_r)) | |
print(fit) | |
plot(fit, pars = "y_err") | |
``` | |
```{r} | |
df <- data.frame(Y = rep(y, 2), | |
Y2 = c(y_r, get_posterior_mean(fit, pars = "z")[, "mean-all chains"]), | |
Var = rep(c("Rounded", "Estimated"), each = length(y))) | |
ggplot(df) + | |
geom_point(aes(x = Y, y = Y2, colour = Var)) + | |
geom_abline(aes(slope = 1, intercept = 0), colour = "gray") + | |
labs(x = "True", y = "Rounded and estimated") + | |
coord_fixed() | |
``` | |
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