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data {
  int<lower = 1> N_D;
  int<lower = 1> N_ind;
  real B;
  int <lower = 1, upper = N_D>  D_class[N_ind];
  real<lower = 0, upper = B> Delta;           // Width of distance bins
  vector<lower = 0, upper = B>[N_D] Midpt;    // Interval mid-points
}
transformed data {
  vector<lower = 0, upper = 1>[N_D] pi = 2 * Midpt / square(B) * Delta;

ito4303

data {
  int<lower = 1> N_ind;                     // Number of individuals
  int<lower = 1> N_z;                       // Number of augment observed data
  int<lower = 0, upper = 1> Y[N_ind + N_z]; // Augumented inds. have y=0 by
                                            // definition
  int<lower = 1> N_D;
  real B;
  int <lower = 1, upper = N_D> D_class[N_ind];
  real<lower = 0, upper = B> Delta;           // Width of distance bins
  vector<lower = 0, upper = B>[N_D] Midpt;    // Interval mid-points

ito4303

data {
  int<lower = 1> N_sites;
  int<lower = 0> N_ind;
  int<lower = 0> N_z;
  real<lower = 0> B;
  vector[N_sites] Habitat;
  vector[N_sites] Wind;
  int<lower = 0, upper = 1> Y[N_ind + N_z];
  vector<lower = 0, upper = B>[N_ind] D;
  int<lower = 1, upper = N_sites> Site[N_ind];

ito4303

data {
  int<lower = 1> N_sites;
  int<lower = 0> N_ind;
  int<lower = 0> N_z;
  int<lower = 1> N_D;
  real<lower = 0> B;
  real<lower = 0> Delta;
  vector<lower = 0, upper = B>[N_D] Midpt;
  vector[N_sites] Habitat;
  vector[N_sites] Wind;

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library(ggplot2)
library(sf)
library(ggspatial)

# Data source: http://www.pref.hokkaido.lg.jp/sr/srk/OPD.htm
#     CC-BY 北海道水産林務部林務局森林計画課
houkai <- read_sf("山腹崩壊.shp", options = "ENCODING=CP932")

sum(st_area(houkai))

ito4303

library(GGally)

sc <- 4
ht <- 3
wd <- 4

set.seed(101)
N <- 100
X <- rnorm(N, 0, 1)
Y <- rnorm(N, 0, 1)

ito4303

library(rstan)
options(mc.cores = parallel::detectCores())
rstan_options(auto_write = TRUE)

set.seed(105)
N <- 100
X <- rnorm(N, 0, 1)
Y <- rnorm(N, 0, 1)
Z <- rnorm(N, 0, 1)

ito4303

/**
 * N-mixture model with 2 replicated observations
 *
 * References
 * Dennis et al. (2015) Computational aspects of N-mixture models.
 *   Biometrics 71:237--246. DOI:10.1111/biom.12246
 * Stan users mailing list
 *   https://groups.google.com/forum/#!topic/stan-users/9mMsp1oB69g
 */

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---
title: "Rounding"
output: html_notebook
---

```{r}
library(rstan)
options(mc.cores = parallel::detectCores())
rstan_options(auto_write = TRUE)
```

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library(coda)
library(readr)

read_cmdstan <- function(files) {
  m <- lapply(files, function(f) {
    d <- read_csv(f, comment = "#")
    as.mcmc(d)
  })
  as.mcmc.list(m)
}