rtirrell

require "dm-core"
require "dm-types"
require "noorm"

module NOORM
  class Disease
    property :concept_id, String, :key => true
    property :name, String
  end

rtirrell

(ns oba-client
  (:use [clojure-http.resourcefully :as res]
        [clojure.contrib.str-utils :only [str-join]])
  (:refer-clojure :exclude [get]))

(def default-timeout 30) 
(def default-uri     "http://rest.bioontology.org/obs/annotator")

(def all-annotator-parameters #{
 	"email"

rtirrell

(ns oba-client
  (:use [clojure-http.resourcefully :as res]
        [clojure.contrib.str-utils :only [str-join]])
  (:refer-clojure :exclude [get]))

(def default-timeout 30) 
(def default-uri     "http://rest.bioontology.org/obs/annotator")

(def all-annotator-parameters #{
 	:email

rtirrell

(ns oba-client
  (:use [clojure-http.resourcefully :as res]
        [clojure.contrib.str-utils :only [str-join]])
  (:refer-clojure :exclude [get]))

(def default-timeout 30) 
(def default-uri     "http://rest.bioontology.org/obs/annotator")

(def all-annotator-parameters #{
 	:email

rtirrell

(ns clojure-playground.core
  (:require [clojure.contrib.math :as math]))

(defmacro not== [& body]
  `(not (== ~@body)))

(defn parent [i] (math/floor (/ (- i 1) 2)))

(defn left-child [i] (+ (* 2 i) 1))

rtirrell

(ns clojure-playground.core)

(defn play 
  ([] (play 10))
  ([n]
    (loop [i 0 
           state false
           turned-on (vec (repeat n false))
           turned-off 0]
      (if (== turned-off (dec n))

rtirrell

    def self.correct_correlations(klass, method)
      all = CLASSES[klass].all(:method => method)
      p_values = $r.p_adjust(all.map {|c| c.p_value}, {:method => "holm"})
        
      all.each_index do |i|
        all[i].update :adjusted_p_value => p_values[i]
      end
    end

rtirrell

transactions = lapply(strsplit(readLines('Data/retail.dat'), ' '), as.numeric)
transactions.unlisted = unlist(transactions)
nitems = length(transactions.unlisted)
counts = table(transactions.unlisted)

threshold.count = 0.02 * length(transactions)
frequent = list(
  single = (1:length(counts))[counts > threshold.count]
)
frequent$cdouble = t(combn(frequent$single, 2))

rtirrell

c("0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 ", 
"30 31 32 ", "33 34 35 ", "36 37 38 39 40 41 42 43 44 45 46 ", 
"38 39 47 48 ", "38 39 48 49 50 51 52 53 54 55 56 57 58 ", "32 41 59 60 61 62 ", 
"3 39 48 ", "63 64 65 66 67 68 ", "32 69 ", "48 70 71 72 ", "39 73 74 75 76 77 78 79 ", 
"36 38 39 41 48 79 80 81 ", "82 83 84 ", "41 85 86 87 88 ", "39 48 89 90 91 92 93 94 95 96 97 98 99 100 101 ", 
"36 38 39 48 89 ", "39 41 102 103 104 105 106 107 108 ", "38 39 41 109 110 ", 
"39 111 112 113 114 115 116 117 118 ", "119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 ", 
"48 134 135 136 ", "39 48 137 138 139 140 141 142 143 144 145 146 147 148 149 ", 
"39 150 151 152 ", "38 39 56 153 154 155 ", "48 156 157 158 159 160 ", 
"39 41 48 ", "161 162 163 164 165 166 167 ", "38 39 48 168 169 170 171 172 173 ", 

rtirrell

# Read a list of about about 100K vectors, each with fewer than 30 items 
# (most with a few). These are supermarket-type transactions.
transactions = lapply(strsplit(readLines('Data/retail.dat'), ' '), as.numeric)
transactions.unlisted = unlist(transactions)

# Count the total number of items over all transactions.
nitems = length(transactions.unlisted)
# And the number of occurrences of each item.
counts = table(transactions.unlisted)