Merge pull request #109 from paxtonfitzpatrick/master

updated examples
ContextLab · Aug 16, 2018 · dbb0302 · dbb0302
2 parents f561ac9 + 5f04f69
commit dbb0302
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Showing 15 changed files with 847 additions and 815 deletions.
diff --git a/docs/tutorial/.ipynb_checkpoints/naturalistic-analyses-checkpoint.ipynb b/docs/tutorial/.ipynb_checkpoints/naturalistic-analyses-checkpoint.ipynb
diff --git a/docs/tutorial/naturalistic-analyses.ipynb b/docs/tutorial/naturalistic-analyses.ipynb
diff --git a/examples/crack_egg.py b/examples/crack_egg.py
@@ -18,21 +18,6 @@
 egg = quail.load('example')
 
 #crack egg
-cracked_egg = quail.crack_egg(egg, subjects=[0], lists=[0])
+cracked_egg = egg.crack(subjects=[0], lists=[0])
 
 cracked_egg.info()
-
-pres = cracked_egg.get_pres_items().as_matrix()[0]
-rec = cracked_egg.get_rec_items().as_matrix()[0]
-
-def distmat(egg, feature, distdict):
-    f = [xi[feature] for xi in egg.get_pres_features()]
-    return cdist(f, f, distdict[feature])
-
-
-for idx in range(len(rec)-1):
-    ind1 = np.where(pres==rec[idx])[0][0]
-    ind2 = np.where(pres==rec[idx+1])[0][0]
-    dists = dist[ind1, :]
-    cdist = dist[ind1, ind2]
-    rank = np.mean(np.where(np.sort(dists)[::-1] == cdist))
diff --git a/examples/create_egg.py b/examples/create_egg.py
@@ -17,40 +17,69 @@
 
 
 # generate some fake data
-next_presented = ['CAT', 'DOG', 'SHOE', 'HORSE']
-next_recalled = ['HORSE', 'DOG', 'CAT']
-
-next_features = [{
+presented = [{
+                    'item' : 'CAT',
                     'category' : 'animal',
                     'size' : 'bigger',
                     'starting letter' : 'C',
                     'length' : 3
                  },
                  {
+                    'item' : 'DOG',
                     'category' : 'animal',
                     'size' : 'bigger',
                     'starting letter' : 'D',
                     'length' : 3
                  },
                  {
+                    'item' : 'SHOE',
                     'category' : 'object',
                     'size' : 'smaller',
                     'starting letter' : 'S',
                     'length' : 4
                  },
                  {
+                    'item' : 'HORSE',
                     'category' : 'animal',
                     'size' : 'bigger',
                     'starting letter' : 'H',
                     'length' : 5
                  }
 ]
+
+recalled = [{
+                    'item' : 'HORSE',
+                    'category' : 'animal',
+                    'size' : 'bigger',
+                    'starting letter' : 'H',
+                    'length' : 5
+                 },
+                 {
+                    'item' : 'DOG',
+                    'category' : 'animal',
+                    'size' : 'bigger',
+                    'starting letter' : 'D',
+                    'length' : 3
+                 },
+                 {
+                    'item' : 'CAT',
+                    'category' : 'animal',
+                    'size' : 'bigger',
+                    'starting letter' : 'C',
+                    'length' : 3
+                 }
+]
+
+# set some custom distance functions
 dist_funcs = {
                 'category' : 'lambda a, b: int(a!=b)',
                 'size' : 'lambda a, b: int(a!=b)',
                 'starting letter' : 'lambda a, b: int(a!=b)',
                 'length' : 'lambda a, b: np.linalg.norm(np.subtract(a,b))'
 }
-egg = quail.Egg(pres=[next_presented], rec=[next_recalled], features=[next_features], dist_funcs=dist_funcs)
 
-egg.analyze('lagcrp').plot()
+egg = quail.Egg(pres=[presented], rec=[recalled], dist_funcs=dist_funcs)
+
+fegg = egg.analyze('lagcrp')
+
+fegg.plot()
diff --git a/examples/create_multisubject_egg.py b/examples/create_multisubject_egg.py
@@ -26,4 +26,6 @@
 egg = quail.Egg(pres=presented_words, rec=recalled_words)
 
 # analyze and plot
-egg.analyze('accuracy').plot(plot_style='violin', title='Average Recall Accuracy')
+fegg = egg.analyze('accuracy')
+
+fegg.plot(plot_style='violin', title='Average Recall Accuracy')
diff --git a/examples/decode_speech.py b/examples/decode_speech.py
@@ -17,7 +17,7 @@
 # decode speech
 recall_data = quail.decode_speech('../data/sample.wav', save=True,
                                   speech_context=['DONKEY', 'PETUNIA'],
-                                  keypath='/Users/andyheusser/Documents/cdl/credentials/efficient-learning-553bf474f805.json')
+                                  keypath='path/to/key.json')
 
 # print results
 print(recall_data)
diff --git a/examples/fingerprint_optimalpresenter.py b/examples/fingerprint_optimalpresenter.py
@@ -16,35 +16,66 @@
 from quail import Fingerprint, OptimalPresenter
 
 # generate some fake data
-next_presented = ['CAT', 'DOG', 'SHOE', 'BAT']
-next_recalled = ['DOG', 'CAT', 'BAT', 'SHOE']
-
-next_features = [{
+next_presented = [{
+                    'item' : 'CAT',
                     'category' : 'animal',
                     'size' : 'bigger',
                     'starting letter' : 'C',
                     'length' : 3
                  },
                  {
+                    'item' : 'DOG',
                     'category' : 'animal',
                     'size' : 'bigger',
                     'starting letter' : 'D',
                     'length' : 3
                  },
                  {
+                    'item' : 'SHOE',
                     'category' : 'object',
                     'size' : 'smaller',
                     'starting letter' : 'S',
                     'length' : 4
                  },
                  {
+                    'item' : 'BAT',
                     'category' : 'animal',
                     'size' : 'bigger',
                     'starting letter' : 'B',
                     'length' : 3
                  }]
 
-egg = quail.Egg(pres=[next_presented], rec=[next_recalled], features=[next_features])
+next_recalled = [{
+                    'item' : 'DOG',
+                    'category' : 'animal',
+                    'size' : 'bigger',
+                    'starting letter' : 'D',
+                    'length' : 3
+                 },
+                 {
+                    'item' : 'CAT',
+                    'category' : 'animal',
+                    'size' : 'bigger',
+                    'starting letter' : 'C',
+                    'length' : 3
+                 },
+                 {
+                    'item' : 'BAT',
+                    'category' : 'animal',
+                    'size' : 'bigger',
+                    'starting letter' : 'B',
+                    'length' : 3
+                 },
+                 {
+                    'item' : 'SHOE',
+                    'category' : 'object',
+                    'size' : 'smaller',
+                    'starting letter' : 'S',
+                    'length' : 4
+                 }
+]
+
+egg = quail.Egg(pres=[next_presented], rec=[next_recalled])
 
 # initialize fingerprint
 fingerprint = Fingerprint(init=egg)

diff --git a/examples/plot_fingerprint.py b/examples/plot_fingerprint.py
@@ -23,4 +23,6 @@
 egg = quail.load('example')
 
 # analyze and plot
-egg.analyze('fingerprint', listgroup=['average']*8, features=['temporal']).plot(title='Memory Fingerprint')
+fegg = egg.analyze('fingerprint', listgroup=['average']*8, features=['temporal'])
+
+fegg.plot(title='Memory Fingerprint')
diff --git a/examples/plot_lagcrp.py b/examples/plot_lagcrp.py
@@ -20,4 +20,6 @@
 egg = quail.load('example')
 
 # analyze and plot
-egg.analyze('lagcrp', listgroup=['average']*8).plot(title='Lag-CRP')
+fegg = egg.analyze('lagcrp', listgroup=['average']*8)
+
+fegg.plot(title='Lag-CRP')
diff --git a/examples/plot_pfr.py b/examples/plot_pfr.py
@@ -16,10 +16,9 @@
 import quail
 
 #load data
-egg = quail.load_example_data()
+egg = quail.load('example')
 
-# analysis
-analyzed_data = quail.analyze(egg, analysis='pfr', listgroup=['average']*8)
+# analyze and plot
+fegg = egg.analyze('pfr', listgroup=['average']*8)
 
-# plot
-quail.plot(analyzed_data, title='Probability of First Recall')
+fegg.plot(title='Probability of First Recall')
diff --git a/examples/plot_pnr.py b/examples/plot_pnr.py
@@ -16,11 +16,10 @@
 import quail
 
 #load data
-egg = quail.load_example_data()
+egg = quail.load('example')
 
-# analysis
-analyzed_data = quail.analyze(egg, analysis='pnr', listgroup=['average']*8,
+# analyze and plot
+fegg = egg.analyze('pnr', listgroup=['average']*8,
                               position=5)
 
-# plot
-quail.plot(analyzed_data, title='Probability of Recall')
+fegg.plot(title='Probability of Recall')
diff --git a/examples/plot_spc.py b/examples/plot_spc.py
@@ -16,7 +16,9 @@
 import quail
 
 #load data
-egg = quail.load_example_data()
+egg = quail.load('example')
 
 # analyze and plot
-egg.analyze('spc', listgroup=['average']*8).plot(title='Serial Position Curve')
+fegg = egg.analyze('spc', listgroup=['average']*8)
+
+fegg.plot(title='Serial Position Curve')
diff --git a/examples/plot_temporal.py b/examples/plot_temporal.py
@@ -16,10 +16,9 @@
 import quail
 
 #load data
-egg = quail.load_example_data()
+egg = quail.load('example')
 
-#analysis
-analyzed_data = quail.analyze(egg, analysis='temporal', listgroup=['early']*4+['late']*4)
+#analyze and plot
+fegg = egg.analyze('temporal', listgroup=['early']*4+['late']*4)
 
-#plot
-quail.plot(analyzed_data, title='Temporal Clustering')
+fegg.plot(title='Temporal Clustering')
diff --git a/quail/data/naturalistic.egg b/quail/data/naturalistic.egg
diff --git a/quail/fingerprint.py b/quail/fingerprint.py
@@ -103,7 +103,7 @@ def update(self, egg, permute=False, nperms=1000,
                           pass_features=True,
                           permute=permute,
                           n_perms=nperms,
-                          parallel=parallel).as_matrix(), 0)
+                          parallel=parallel).values, 0)
 
         if self.state is not None: