tpapp

using AMDB
using DataStructures            
using GZip
using UnicodePlots

# replace this line with the path on your own machine
records = GZip.open(deserialize,
                    expanduser("~/research/AMDB/data/AMDB_subsample.jls.gz"), "r")

long_samples = [data for (id,data) in records if length(data.AMP_spells) > 1000]

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type ParseErrorLoc
    T
    string
    column
    line
end

function Base.show(io::IO, pel::ParseErrorLoc)
    print("could not parse \"$(pel.string)\" as $(pel.T)")
    if pel.column > 0

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module Foos
type Foo{T <: Tuple} 
end 
m1{T}(f::Foo{Tuple{T}}, index::T...) = 42 # suggested by Bill Hart
m2{T}(f::Foo{T}, index::T...) = 42 # what I thought would work
_m3{T}(f::Foo{T}, index::T) = 42 # indirect solution
m3{T}(f::Foo{T}, index...) = _m3(f, index)
end

f1 = Foos.Foo{Tuple{Int}}()

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>      stanmodelcode <- "
     data {
       int<lower=0> N;
       real y[N];
     } 
     
     parameters {
       real mu;
     } 
     

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N <- 100
w <- rlnorm(N,0,1)
a <- runif(N,0,1)
m <- 2
keep <- w < a*m
w_kept <- w[keep]
a_kept <- a[keep]
N_kept <- sum(keep)

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@doc "All length `n` permutations of `v` in a matrix, with repetitions."->
function perm_matrix{T}(v::Vector{T}, n)
  l = length(v)
  m = l^n
  a = Array(T, m, n)
  for i = 1:m
    k = i-1
    j = n
    while (j > 0)
      (d,r) = divrem(k,l)

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data {
  int N;
  int a_N;                      //  number of categories in a
  int b_N;                      //  number of categories in b
  int c_N;                      //  number of c coefficients (continuous)
  int<lower=1, upper=a_N> a[N];
  int<lower=1, upper=b_N> b[N];
  matrix[N, c_N] c;
  int<lower=0, upper=1> y[N];
}

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## A simple study in implementing univariate censoring
library(rstan)
 
## simulated data
m <- 1 # boundary
z <- rlnorm(100) # latent variable
z <- z[z > m] # only kept when above m
N <- length(z)
z_hat <- rlnorm(N, log(z), 0.1) # observed with noise

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array_or_vector_p <- function(object) {
  ## Test if object is what we consider an array for the purposes of
  ## the code below.
  ##
  ## Lists are not arrays, but vectors are, even if they don't have a
  ## dim attribute. The following give an error:
  ## - objects which are neither lists, (non-list) vectors, or arrays
  ## - vectors and arrays with zero length
  ## - arrays with rank lower than 1
  if (is.list(object))