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## Development utilities for XX
##
## Usage:
## 		make <target> [<arg>=<value> ...]
##
## Targets:
## 		help:		Show this help message.
##		env: 		Create or update conda environment "XX"
ENV?=XX

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import os
import pandas as pd

def read_auto(datapath):
    _, ext = os.path.splitext(datapath)

    if ext == ".csv":
        return pd.read_csv(datapath)
    elif ext == ".tsv":
        return pd.read_csv(datapath, sep="\t")

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#! /usr/bin/bash
repos=$(gh repo list -L=9999 | awk '{print $1}')
for r in $repos; do gh repo clone $r; done

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---
title: "Stan templates"
output: html_notebook
---

**Things to keep in mind:**

- Stan uses the *standard deviation* to parameterize the normal distribution. Use `normal(mu, sigma)` instead of `normal(mu, sigma^2)`.
- Leave a blank line at the end of the chunk defining Stan code.

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library(assert)
source("multinorm.R")

rnormalgamma <- (function(k, b, Sigma, nu, kappa) {
  # Sample from a Normal-Gamma distribution Attaches both `rnormalgamma` and 
  # `rnormalgamma.fast` to the current environment.
  # 
  # Usage:
  #   rnormalgamma(b, Sigma, nu, kappa)
  #   rnormalgamma.fast(b, Sigma, nu, kappa)

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#
# Work in progress.
#

cmap.seaborn <- function(n) {
  colors.seaborn <-
    c(rgb(0.12156862745098039, 0.4666666666666667, 0.7058823529411765),
      rgb(1.0, 0.4980392156862745, 0.054901960784313725),
      rgb(0.17254901960784313, 0.6274509803921569, 0.17254901960784313),
      rgb(0.8392156862745098, 0.15294117647058825, 0.1568627450980392),

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library(assert)

rmultinorm.fast <- function(k, mu, sigma) {
  p = length(mu)
  t(chol(sigma)) %*% matrix(rnorm(p*k, 0, 1), nrow=p) + mu
}

#' Sample from a multivariate normal distribution. Attaches both `rmultinorm`
#' and `rmultinorm.fast` to the current environment.
#' 

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assert <- function(..., msg=NULL) {
  # Assert that each of the provided expression is true. Otherwise returns a
  # description of each failed assertion.
  # 
  # Args:
  #   ...: List of logical assertions
  #   msg: Optional parameter printed when one of the assertions fails.
  # 
  # Returns:
  #   Nothing if all assertions pass. Otherwise throws an error describing which