survival 0.0.1 → 0.0.3

data/README.md

@@ -18,10 +18,14 @@ Or install it yourself as:
 
 ## Usage
 
-To generate a Kaplan-Meier survival plot:
-
-    #survivals is an array of hashes. Each represents a sample, and must define :event (the event time) and :censored (boolean describing whether this sample is censored)
-    points = KaplanMeier.generate_plot_points(SurvivalSample.create_survival_objects(survivals))
+To generate a Kaplan-Meier survival curve:
+
+    #survivals is an array of hashes. Each hash represents a sample, and must define 
+    #   :event (the event time)
+    #   :censored (boolean describing whether this sample is right-censored)
+    survivals = [{:event => 21, :censored => false}, {:event => 13, :censored => true}, ... ]
+    survival_objs = SurvivalSample.create_survival_objects(survivals) #Create survival sample objects
+    points = KaplanMeier.generate_plot_points(survival_objs) #Generate the x,y coordinates of the survival curve
 
     #points is an array of [x,y] pairs for plotting. Use your favorite plotting library to plot the line graph.
 

data/lib/survival/KaplanMeier.rb

@@ -9,11 +9,12 @@ class KaplanMeier
 
   #Creates the x,y pairs for plotting a survival curve, 
   #using the Kaplan-Meier method.
-  def self.generate_plot_points(survivals)
+  def self.generate_plot_points(survivals, include_horizontal=true)
 
     bins = SurvivalSample.bin_survivals(survivals)
 
     points = [[0,100]]
+    median = nil
 
     terms = Array.new
     n = survivals.length #Number we are considering at this time point (total surviving minus censored)
@@ -43,14 +44,22 @@ class KaplanMeier
 
       s_t = s_t * 100.0
 
+      #The median survival time is calculated as the smallest survival time 
+      #for which the survivor function is less than or equal to 0.5
+      if ( (s_t <= 50.0) && (median.nil?) ){
+        median = t
+      }
+
       #Add to plot points
-      points << [t, prev] #Horizontal line from previous point
+      if include_horizontal
+        points << [t, prev] #Horizontal line from previous point
+      end
       points << [t, s_t] #Current point
       prev = s_t
 
     end
 
-    return points
+    return points, median
   end
 
 end

data/lib/survival/SurvivalSample.rb

@@ -15,7 +15,7 @@ class SurvivalSample
     @event = event
   end
 
-    def to_s
+  def to_s
     "Survival: {Event: #{@event}, Censored: #{@censored}}"
   end
 

data/lib/survival/version.rb

@@ -1,3 +1,3 @@
 module Survival
-  VERSION = "0.0.1"
+  VERSION = "0.0.3"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: survival
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-11-23 00:00:00.000000000 Z
+date: 2013-09-17 00:00:00.000000000 Z
 dependencies: []
 description: A gem that provides survival analysis functionality
 email: