From c9af75a8a4a3ca6488ccf22541bbbb6bbb7b3859 Mon Sep 17 00:00:00 2001
From: Paco Zamora Martinez <pakozm@gmail.com>
Date: Tue, 30 Jun 2015 10:41:43 +0200
Subject: [PATCH] Simplified bootstrap pvalue interface

---
 packages/basics/stats/lua_src/statistics.lua  | 36 +++++--------------
 packages/basics/stats/test/test_bootstrap.lua |  4 ---
 2 files changed, 9 insertions(+), 31 deletions(-)

diff --git a/packages/basics/stats/lua_src/statistics.lua b/packages/basics/stats/lua_src/statistics.lua
index 23cc40177..9aca7d579 100644
--- a/packages/basics/stats/lua_src/statistics.lua
+++ b/packages/basics/stats/lua_src/statistics.lua
@@ -1366,10 +1366,16 @@ stats.boot.percentile =
 -- Taylor Berg-Kirkpatrick David Burkett Dan Klein.
 -- http://www.cs.berkeley.edu/~tberg/papers/emnlp2012.pdf
 stats.boot.pvalue =
-  function(data, pivot, index, alternative, h0)
-    local h0  = h0 or 0.0
+  function(data, pivot, index, params)
+    local params = get_table_fields(
+      {
+        h0 = { mandatory = false, default = 0.0, type_match = "number" },
+        alternative = { mandatory = false, default = "two-sided", type_match = "string" },
+      },
+      params or {})
+    local h0  = params.h0
     local p50 = stats.boot.percentile(data, 0.50, index)
-    local alternative = alternative or "two-sided"
+    local alternative = params.alternative
     april_assert(alternatives[alternative],
                  "Unknown alternative value %s", alternative)
     local data = data:select(2, index or 1)
@@ -1393,30 +1399,6 @@ stats.boot.pvalue =
     return pvalue
   end
 
-stats.boot.rprob =
-  april_doc{
-    class = "function",
-    summary = "Computes one-sided probability for a given pivot in a bootstrap sample",
-    description = {
-      "This function returns the one-sided probability of given pivot, that is, the",
-      "probability of the sample to be greater than the pivot. The probability",
-      "is computed to avoid bias problems as: (C(>pivot)+1)/(N+1)",
-    },
-    params = {
-      "The result of stats.boot function.",
-      "The pivot [optional], by default it is 0.0",
-      "The statistic index for which you want compute the percentile [optional], by default it is 1",
-    },
-    outputs = {
-      "The one-sided right probability",
-    },
-  } ..
-  function(data, pivot, index)
-    assert(data, "Needs a data argument as first argument")
-    local ge_pivot = data:select(2, index or 1):gt(pivot or 0.0):count_ones()
-    return (1+ge_pivot) / (data:dim(1)+1)
-  end
-
 ----------------------------------------------------------------------------
 
 stats.percentile =
diff --git a/packages/basics/stats/test/test_bootstrap.lua b/packages/basics/stats/test/test_bootstrap.lua
index 19ae05b88..78fb4c87c 100644
--- a/packages/basics/stats/test/test_bootstrap.lua
+++ b/packages/basics/stats/test/test_bootstrap.lua
@@ -47,8 +47,4 @@ T("BootstrapTest",
     check.number_eq(m,  -0.012237)
     check.number_eq(p0, -0.117945)
     check.number_eq(pn,  0.092709)
-    -- p-value tests
-    check.number_eq(stats.boot.rprob(boot_result, b), 0.025, 0.05)
-    check.number_eq(1.0 - stats.boot.rprob(boot_result, a), 0.025, 0.05)
-    check.number_eq(stats.boot.rprob(boot_result, m, 1), 0.500)
 end)