Frist pass at sizing help.

refs #66

requirements.txt

@@ -1,3 +1,4 @@
+Cython==0.19.1
 Django==1.5.1
 Jinja2==2.7
 MarkupSafe==0.18
@@ -38,8 +39,10 @@ lxml==3.1.1
 mailtools==2.1
 meld3==0.6.10
 mock==1.0.1
+numpy==1.7.1
 oauth2==1.5.211
 oauthlib==0.4.0
+pandas==0.11.0
 psutil==0.7.0
 psycopg2==2.4.6
 py==1.4.13
@@ -51,6 +54,8 @@ pyzmq==13.0.2
 regex==2013-03-11
 requests==1.2.0
 requests-oauthlib==0.3.0
+scipy==0.12.0
 six==1.3.0
 supervisor==3.0b1
 wsgiref==0.1.2
+patsy

rm/static/css/rm.css

@@ -514,6 +514,10 @@ ul.parsley-error-list {
     color: #e54f25;
 }
 
+ul.parsley-error-list li {
+    list-style-type: none;
+}
+
 .controls ul li {
     list-style-type: none;
 }

rm/static/js/rm.carousel.js

@@ -87,10 +87,12 @@
       return this.$items.index(this.$active)
     }
 
-  , to: function (pos) {
+  , to: function (pos, force) {
 
-      if(!this.validp()){
-          return this.pause().cycle()
+      if(!force){
+          if(!this.validp()){
+              return this.pause().cycle()
+          }
       }
       var activeIndex = this.getActiveIndex()
         , that = this
@@ -221,14 +223,14 @@
 
   var old = $.fn.carousel
 
-  $.fn.carousel = function (option) {
+  $.fn.carousel = function (option, force) {
     return this.each(function () {
       var $this = $(this)
         , data = $this.data('carousel')
         , options = $.extend({}, $.fn.carousel.defaults, typeof option == 'object' && option)
         , action = typeof option == 'string' ? option : options.slide
       if (!data) $this.data('carousel', (data = new Carousel(this, options)))
-      if (typeof option == 'number') data.to(option)
+      if (typeof option == 'number') data.to(option, force)
       else if (action) data[action]()
       else if (options.interval) data.pause().cycle()
     })

rm/static/js/rm.js

@@ -144,6 +144,41 @@ var RM = {
             })
         },
 
+        // Bind the power calculation form to an ajax call
+        init_power: function(){
+
+            $('form#power-form').ajaxForm({
+
+                beforeSubmit: function(){
+                    if(!$('form#power-form').parsley().validate()){
+                        return false
+                    }
+                    $('#power-btn').attr('disabled', true).text(
+                        'calculating required participants...')
+                },
+
+                success: function(data){
+                    var msg = 'You need ' + data + ' participant';
+                    if(parseInt(data) > 1){
+                        msg += 's'
+                    }
+                    $('#power-btn').attr('disabled', false).text(
+                    'run the numbers');
+                    $('#power-answer').text(msg);
+                    $('#id_min_participants').attr('value', data);
+                    $('#power-done').text('done')
+                },
+
+                error: function(data){
+                    console.log(data);
+                    console.log('Power calculation - something went wrong :()')
+                    $('#power-btn').attr('disabled', false).text(
+                    'run the numbers');
+                },
+
+            })
+        },
+
     },
 
     graphs: {

rm/stats/models.py

@@ -0,0 +1,3 @@
+from django.db import models
+
+# Create your models here.

rm/stats/tests.py

@@ -0,0 +1,16 @@
+"""
+This file demonstrates writing tests using the unittest module. These will pass
+when you run "manage.py test".
+
+Replace this with more appropriate tests for your application.
+"""
+
+from django.test import TestCase
+
+
+class SimpleTest(TestCase):
+    def test_basic_addition(self):
+        """
+        Tests that 1 + 1 always equals 2.
+        """
+        self.assertEqual(1 + 1, 2)

rm/stats/urls.py

@@ -0,0 +1,8 @@
+from django.conf.urls import patterns, include, url
+
+from rm.stats.views import PowerCalcView
+
+urlpatterns = patterns(
+    '',
+    url(r'power-calc$', PowerCalcView.as_view(), name='power-calc'),
+)

rm/stats/utils.py

@@ -0,0 +1,25 @@
+"""
+Utility functions for statistical calculations on Randomise Me
+"""
+from statsmodels.stats.power import tt_ind_solve_power
+
+def nobs(estimated=None, impressive=None):
+    """
+    Given the estimated and impressive figures,
+    conduct a power calculation and return the
+    number of required observations.
+
+    Arguments:
+    - `estimated`: int
+    - `impressive`: int
+
+    Return: int
+    Exceptions: None
+    """
+    estimated, impressive = float(estimated), float(impressive)
+    if abs(estimated/impressive) > 1:
+        effect_size = abs(estimated/impressive)
+    else:
+        effect_size = abs(impressive/estimated)
+    num = tt_ind_solve_power(effect_size=effect_size, alpha=0.05, power=0.8, nobs1=None)
+    return int(num) * 2

rm/stats/views.py

@@ -0,0 +1,24 @@
+"""
+Views to do server-side stats help
+"""
+from django.http import HttpResponse
+from django.views.generic import View
+
+from rm.stats.utils import nobs
+
+class PowerCalcView(View):
+    """
+    Run a power calculation
+    """
+    def post(self, *args, **kwargs):
+        """
+        Calculate the required number of participants
+        for the variables given
+
+        Return: str(int)
+        Exceptions: None
+        """
+        estimated, impressive = [int(self.request.POST.get(k))
+                                 for k in ['impressive', 'estimated']]
+        num = nobs(estimated=estimated, impressive=impressive)
+        return HttpResponse(str(num))

rm/templates/trials/_trial_form.html

@@ -105,12 +105,60 @@ <h2>
 
 </form>
 
+  <!-- Modal power -->
+  <div id="power" class="modal hide fade" tabindex="-1"
+       role="dialog" aria-labelledby="myModalLabel" aria-hidden="true">
+       <div class="modal-header">
+         <h3 id="myModalLabel">How many people do you need?</h3>
+       </div>
+       <div class="modal-body">
+         <form method="POST" action="{% url 'power-calc' %}"
+               id="power-form"
+               data-validate="parsley">
+           {% csrf_token %}
+           <p class="muted">
+             Roughly what score/proportion/count do you expect in group A?
+           </p>
+           <input type="text" name="estimated" value=""
+                  placeholder="estimated number"
+                  data-required="true" data-type="digits"
+                  />
+           <p class="muted">
+             What score in treatment group B would be meaningfully different enough
+             for you to be impressed?
+           </p>
+           <input type="text" name="impressive" value=""
+                  placeholder="impressive number"
+                  data-required="true" data-type="digits"
+                  />
+            <p>
+              <button class="btn btn-danger" type="submit" id="power-btn">
+                run the numbers
+              </button>
+            </p>
+            <h3 id="power-answer">How many participants do you need?</h3>
+         </form>
+
+       </div>
+       <div class="modal-footer">
+         <button id="power-done" class="btn" data-dismiss="modal" aria-hidden="true">
+           cancel
+         </button>
+       </div>
+  </div>
+
+
 <script type="text/javascript">
 
 $(document).ready( function(){
   RM.forms.init_instruction_toggles();
   RM.forms.init_enter_sliding();
   RM.forms.init_focus();
+  RM.forms.init_power();
+  if(window.location.search.search(/step=(\d+)/) != -1){
+     var step = (parseInt(window.location.search.match(/step=(\d+)/)[1]) -1);
+     $('.carousel').carousel(step, true).carousel('pause');
+  }
 });
 
 </script>

rm/templates/trials/steps/step_sizing.html

@@ -3,6 +3,7 @@
 <div class="item">
   <h2>3. <span class="red bold">SIZE</span> <span class="light">OF YOUR TRIAL</span></h2>
   {% if n1trial %}
+
     <h3>Would you like help to decide how many observations you'll need?</h3>
     <p class="muted">
       IMPLEMENT THIS PLEASE.
@@ -11,15 +12,24 @@ <h3>No, you think you've got it?</h3>
     {{ form.ending_reports|bootstrap }}
 
   {% else %}
+
+      <h3>Minimum number of participants</h3>
+      {{ form.min_participants|bootstrap }}
+      <p class="muted">
+        This is the minimum number of people you need in your trial
+        in order to obtain statistically significant results
+      </p>
+
+
     <h3>Would you like help to decide how many people you will need in your trial? </h3>
-    <p class="muted">
-      Roughly what score/proportion/count do you expect in group A?
-      What score in treatment group B would be meaningfully different enough
-      for you to be impressed? <br>
-      > simple power calculation
-    </p>
-  <p>IMPLEMENT THIS</p>
-  <h3>No, you think you've got it?</h3>
-  {{ form.min_participants|bootstrap }}
+
+    <a href="#power" class="btn btn-warning" data-toggle="modal" role="button">
+      help me decide
+    </a>
+
+
 {% endif %}
+
+
+
 </div>

rm/urls.py

@@ -60,6 +60,7 @@
     url(r'^trials/', include('rm.trials.urls')),
     url(r'search$', TrialSearchView.as_view(), name='search'),
 
+    url(r'^stats/', include('rm.stats.urls')),
 )
 
 urlpatterns += staticfiles_urlpatterns()