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Ricardo Honorato-Zimmer rhz

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View gist:945329
import qualified Data.Map as Map
type Mol = String
type Mixture = Map.Map Mol Integer
type Rxn = (Mixture, (Mixture -> Mixture), Double)
getActivities :: [Rxn] -> Mixture -> [Double]
getActivities rxns mixture =
let f acc mol sc = if sc == 1 -- sc is stoichiometric coefficient
then fromIntegral $ mixture Map.! mol
View gillespie.hs
import qualified Data.Map as Map
import Random (randomRIO)
type Mol = String
type Mixture = Map.Map Mol Integer
type Rxn = (Mixture, (Mixture -> Mixture)) -- (Lhs, Action)
type State = (Double, Integer, Mixture) -- (Time, NumSteps, Mixture)
getActivities :: [Rxn] -> Mixture -> [Integer]
getActivities rxns mixture = []
View gist:871248
(defn get-molecule [state mol]
(get-in state [:mixture mol] 0))
(defn get-activities [state] ;; FIXME this fn takes upto 80% of the time
(into {} (for [{:keys [lhs rate] :as r} (:rxns state)]
[r (apply * rate (for [[mol freq] lhs]
(* (get-molecule state mol) freq)))])))
View gillespie.clj
(ns mca.gillespie
(:require [clojure.contrib.generic.math-functions :as math]))
(defn choice [m]
(let [r (rand (apply + (vals m)))]
(loop [[[k w] & kws] (seq m)
sum 0]
(if (or (nil? kws) (< r (+ sum w))) k
(recur kws (+ sum w))))))
View gist:842663
(defprotocol AKappaExpression
"Kappa expression"
(agents [e] "get all agents in this expression")
(complexes [e] "get all complexes in this expression")
(subexpr [e ids] "get a subexpression for the given agent ids")
(merge [e1 e2] "merge two expressions")
(count-automorphisms [e] "count the number of automorphisms")
(expression? [e] "predicate for AKappaExpression")
(match [e1 e2] "returns a map from agent ids in e1 to their matching agent ids in e2")
;; should this methods be part of AKappaAgent?
View bienes-raices.clj
(require '[clojure.string :as s]
'[incanter.stats :as stats]
'[clojure.contrib.generic.math-functions :as m]
'[clojure.contrib.combinatorics :as c])
;;;; Conversion
(defn get-rows [s]
(let [[sep & ss] (.split s "\n")]
(take-nth 2 (partition-by #{sep} ss))))
View gist:834802
(defn prob-n [pred tol in n] ;; in is a csv's filename
(let [as (for [[_ _ p m] (map #(.split % ";") (rest (.split (slurp in) "\n"))) :when p]
(if (empty? m) [p] [p m])) ;; take the third and fourth (if possible) column of each row
conteo (for [as (c/combinations as n)]
(if (apply pred tol as) 1 0))]
(/ (reduce + conteo) (count conteo))))
(defn ningun-apellido-en-comun [tol & as]
(let [distinct-as (distinct (apply concat as))
conteo (for [a distinct-as]
View empty-counted-sorted-set-disj-get.patch
diff --git a/src/main/clojure/clojure/data/finger_tree.clj b/src/main/clojure/clojure/data/finger_tree.clj
index bc00343..557aaaf 100644
--- a/src/main/clojure/clojure/data/finger_tree.clj
+++ b/src/main/clojure/clojure/data/finger_tree.clj
@@ -537,13 +537,17 @@
(count [_] (:len (measured tree)))
(disjoin [this k]
- (let [[l x r] (split-tree tree #(>= 0 (cmpr k (:right %))))]
- (if (= x k)
rhz / gist:671969
Created Nov 11, 2010
pak -Ss QUERY
View gist:671969
diff --git a/main.lisp b/main.lisp
index 0dfaf15..ec5730e 100644
--- a/main.lisp
+++ b/main.lisp
@@ -270,6 +270,17 @@ Returns T upon successful installation, NIL otherwise."
(get-pkgbuild pkg-name)
+(defun search-packages (query)
+ (maybe-refresh-cache)
View gist:668678
No message.
[Thrown class java.lang.IndexOutOfBoundsException]
0: [QUIT] Quit to the SLIME top level
1: [ABORT] ABORT to SLIME level 0
0: clojure.lang.PersistentVector.arrayFor(
1: clojure.lang.PersistentVector.nth(
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