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---
title: "R Notebook"
output: html_notebook
---

## Fitting diameter class data to Weibull distribution

```{r setup}
library(cmdstanr)
library(ggplot2)

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---
title: "R Notebook"
output: html_notebook
---

## Fitting truncated and censored data to Weibull distribution

Supposing tree diameter data, fitting truncated and censored data to Weibull distribution.

See Chapter 4 [Truncated or Censored Data](https://mc-stan.org/docs/2_28/stan-users-guide/truncated-or-censored-data.html) in the Stan User's Guide.

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---
title: "R Notebook"
output: html_notebook
---

Three parameter Weibull distribution

```{r}
library(ggplot2)
library(cmdstanr)

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/*
 * 2-d integral using Simpson's rule
 * based on
 * https://statmodeling.hatenablog.com/entry/waic-with-hierarchical-models
 */

functions {
  real f(real z, array[] real theta, real x, real y) {
    real v;

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library(ggplot2)
library(cmdstanr)
library(posterior)
library(bayesplot)

# data
set.seed(1234)
n <- 160
n_block <- 8
x <- runif(n, 0, 1)

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---
title: "R Notebook"
output: html_notebook
---

## Library

```{r}
library(cmdstanr)
```

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functions {
  /**
   * Returns log likelihood of N-mixture model
   * with 2 replicated observations using
   * bivariate Poisson distibution
   *
   * References
   * Dennis et al. (2015) Computational aspects of N-mixture models.
   *   Biometrics 71:237--246. DOI:10.1111/biom.12246
   * Stan users mailing list

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# The simplest possible N-mixture model from Section 6.3 of
# Applied Hierarchical Modeling in Ecology.

library(cmdstanr)
set_cmdstan_path("/usr/local/cmdstan")

# generate simulated data

lambda <- 2.5 # mean abundance
p <- 0.4      # detection probability

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functions {
  real partial_sum(int[] dummy_k,
                   int start, int end,
                   int[] count,
                   real lambda,
                   real p) {
    vector[end - start + 1] lp;

    for (k in start:end) {
      if (k - 1 < max(count))

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#
# HMM Test for CmdStan 2.24
#

library(rstan)
options(mc.cores = parallel::detectCores())
library(cmdstanr)
set_cmdstan_path("/usr/local/cmdstan")
library(extraDistr)