Merge pull request #295 from turion/dev_transformer_naming

Make transformer naming idiomatic. Fixes #189. Fixes #242.

benchmark/SSM.hs

@@ -7,7 +7,7 @@ import Control.Monad.Bayes.Inference.RMSMC (rmsmcDynamic)
 import Control.Monad.Bayes.Inference.SMC
 import Control.Monad.Bayes.Inference.SMC2 as SMC2 (smc2)
 import Control.Monad.Bayes.Population
-import Control.Monad.Bayes.Population (population, resampleMultinomial)
+import Control.Monad.Bayes.Population (resampleMultinomial, runPopulationT)
 import Control.Monad.Bayes.Sampler.Strict (sampleIO, sampleIOfixed, sampleWith)
 import Control.Monad.Bayes.Weighted (unweighted)
 import Control.Monad.IO.Class (MonadIO (liftIO))

benchmark/Speed.hs

@@ -8,7 +8,7 @@ import Control.Monad.Bayes.Class (MonadMeasure)
 import Control.Monad.Bayes.Inference.MCMC (MCMCConfig (MCMCConfig, numBurnIn, numMCMCSteps, proposal), Proposal (SingleSiteMH))
 import Control.Monad.Bayes.Inference.RMSMC (rmsmcDynamic)
 import Control.Monad.Bayes.Inference.SMC (SMCConfig (SMCConfig, numParticles, numSteps, resampler), smc)
-import Control.Monad.Bayes.Population (population, resampleSystematic)
+import Control.Monad.Bayes.Population (resampleSystematic, runPopulationT)
 import Control.Monad.Bayes.Sampler.Strict (SamplerIO, sampleIOfixed)
 import Control.Monad.Bayes.Traced (mh)
 import Control.Monad.Bayes.Weighted (unweighted)
@@ -59,10 +59,10 @@ instance Show Alg where
 
 runAlg :: Model -> Alg -> SamplerIO String
 runAlg model (MH n) = show <$> unweighted (mh n (buildModel model))
-runAlg model (SMC n) = show <$> population (smc SMCConfig {numSteps = (modelLength model), numParticles = n, resampler = resampleSystematic} (buildModel model))
+runAlg model (SMC n) = show <$> runPopulationT (smc SMCConfig {numSteps = (modelLength model), numParticles = n, resampler = resampleSystematic} (buildModel model))
 runAlg model (RMSMC n t) =
   show
-    <$> population
+    <$> runPopulationT
       ( rmsmcDynamic
           MCMCConfig {numMCMCSteps = t, numBurnIn = 0, proposal = SingleSiteMH}
           SMCConfig {numSteps = modelLength model, numParticles = n, resampler = resampleSystematic}

docs/docs/notebooks/Diagrams.html

@@ -14729,8 +14729,8 @@ <h2 id="Viewing-traces">Viewing traces<a class="anchor-link" href="#Viewing-trac
 <div class="jp-InputPrompt jp-InputArea-prompt">In&nbsp;[3]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
      <div class="CodeMirror cm-s-jupyter">
-<div class=" highlight hl-Haskell"><pre><span></span><span class="nf">getTrace</span><span class="w"> </span><span class="ow">::</span><span class="w"> </span><span class="kt">Weighted</span><span class="w"> </span><span class="p">(</span><span class="kt">Density</span><span class="w"> </span><span class="kt">SamplerIO</span><span class="p">)</span><span class="w"> </span><span class="n">a</span><span class="w"> </span><span class="ow">-&gt;</span><span class="w"> </span><span class="kt">SamplerIO</span><span class="w"> </span><span class="p">([</span><span class="kt">Double</span><span class="p">],</span><span class="w"> </span><span class="kt">Log</span><span class="w"> </span><span class="kt">Double</span><span class="p">)</span>
-<span class="nf">getTrace</span><span class="w"> </span><span class="n">m</span><span class="w"> </span><span class="ow">=</span><span class="w"> </span><span class="n">fmap</span><span class="w"> </span><span class="p">(</span><span class="nf">\</span><span class="p">((</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">),</span><span class="n">z</span><span class="p">)</span><span class="w"> </span><span class="ow">-&gt;</span><span class="w"> </span><span class="p">(</span><span class="n">z</span><span class="p">,</span><span class="n">y</span><span class="p">)</span><span class="w"> </span><span class="p">)</span><span class="w"> </span><span class="o">$</span><span class="w"> </span><span class="n">runWriterT</span><span class="w"> </span><span class="o">$</span><span class="w"> </span><span class="n">weighted</span><span class="w"> </span><span class="o">$</span><span class="w"> </span><span class="kt">Weighted</span><span class="o">.</span><span class="n">hoist</span><span class="w"> </span><span class="p">(</span><span class="kt">WriterT</span><span class="w"> </span><span class="o">.</span><span class="w"> </span><span class="n">density</span><span class="w"> </span><span class="kt">[]</span><span class="p">)</span><span class="w"> </span><span class="n">m</span>
+<div class=" highlight hl-Haskell"><pre><span></span><span class="nf">getTrace</span><span class="w"> </span><span class="ow">::</span><span class="w"> </span><span class="kt">WeightedT</span><span class="w"> </span><span class="p">(</span><span class="kt">DensityT</span><span class="w"> </span><span class="kt">SamplerIO</span><span class="p">)</span><span class="w"> </span><span class="n">a</span><span class="w"> </span><span class="ow">-&gt;</span><span class="w"> </span><span class="kt">SamplerIO</span><span class="w"> </span><span class="p">([</span><span class="kt">Double</span><span class="p">],</span><span class="w"> </span><span class="kt">Log</span><span class="w"> </span><span class="kt">Double</span><span class="p">)</span>
+<span class="nf">getTrace</span><span class="w"> </span><span class="n">m</span><span class="w"> </span><span class="ow">=</span><span class="w"> </span><span class="n">fmap</span><span class="w"> </span><span class="p">(</span><span class="nf">\</span><span class="p">((</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">),</span><span class="n">z</span><span class="p">)</span><span class="w"> </span><span class="ow">-&gt;</span><span class="w"> </span><span class="p">(</span><span class="n">z</span><span class="p">,</span><span class="n">y</span><span class="p">)</span><span class="w"> </span><span class="p">)</span><span class="w"> </span><span class="o">$</span><span class="w"> </span><span class="n">runWriterT</span><span class="w"> </span><span class="o">$</span><span class="w"> </span><span class="n">runWeightedT</span><span class="w"> </span><span class="o">$</span><span class="w"> </span><span class="kt">Weighted</span><span class="o">.</span><span class="n">hoist</span><span class="w"> </span><span class="p">(</span><span class="kt">WriterT</span><span class="w"> </span><span class="o">.</span><span class="w"> </span><span class="n">runDensityT</span><span class="w"> </span><span class="kt">[]</span><span class="p">)</span><span class="w"> </span><span class="n">m</span>
 </pre></div>
 
      </div>

docs/docs/notebooks/Histogram.html

@@ -14642,7 +14642,7 @@ <h1 id="Distributions-over-anything">Distributions over <strong>anything</strong
 <span class="w">    </span><span class="n">return</span><span class="w"> </span><span class="n">y</span>
 <span class="w">    </span>
 <span class="nf">distributionOverWeightedSamples</span><span class="w"> </span><span class="ow">::</span><span class="w"> </span><span class="kt">Distribution</span><span class="w"> </span><span class="p">(</span><span class="kt">Double</span><span class="p">,</span><span class="w"> </span><span class="kt">Log</span><span class="w"> </span><span class="kt">Double</span><span class="p">)</span>
-<span class="nf">distributionOverWeightedSamples</span><span class="w"> </span><span class="ow">=</span><span class="w"> </span><span class="n">weighted</span><span class="w"> </span><span class="n">unnormalizedDistribution</span>
+<span class="nf">distributionOverWeightedSamples</span><span class="w"> </span><span class="ow">=</span><span class="w"> </span><span class="n">runWeightedT</span><span class="w"> </span><span class="n">unnormalizedDistribution</span>
 <span class="w">    </span>
 <span class="nf">iidDistribution</span><span class="w"> </span><span class="ow">::</span><span class="w"> </span><span class="kt">Distribution</span><span class="w"> </span><span class="p">[(</span><span class="kt">Double</span><span class="p">,</span><span class="w"> </span><span class="kt">Log</span><span class="w"> </span><span class="kt">Double</span><span class="p">)]</span>
 <span class="nf">iidDistribution</span><span class="w"> </span><span class="ow">=</span><span class="w"> </span><span class="n">replicateM</span><span class="w"> </span><span class="mi">100000</span><span class="w"> </span><span class="n">distributionOverWeightedSamples</span>

docs/docs/notebooks/Parsing.html

@@ -14701,7 +14701,7 @@ <h1 id="Probabilistic-Parser-Combinators">Probabilistic Parser Combinators<a cla
 
 <span class="nf">runWordParser</span><span class="w"> </span><span class="n">w</span><span class="w"> </span><span class="ow">=</span><span class="w"> </span><span class="kr">do</span>
 <span class="w">    </span><span class="n">x</span><span class="w"> </span><span class="ow">&lt;-</span><span class="w"> </span><span class="n">sampler</span><span class="w"> </span>
-<span class="w">        </span><span class="o">.</span><span class="w"> </span><span class="n">population</span><span class="w"> </span>
+<span class="w">        </span><span class="o">.</span><span class="w"> </span><span class="n">runPopulationT</span><span class="w"> </span>
 <span class="w">        </span><span class="o">.</span><span class="w"> </span><span class="n">smc</span><span class="w"> </span><span class="kt">SMCConfig</span><span class="w"> </span><span class="p">{</span><span class="n">numSteps</span><span class="w"> </span><span class="ow">=</span><span class="w"> </span><span class="mi">5</span><span class="p">,</span><span class="w"> </span><span class="n">numParticles</span><span class="w"> </span><span class="ow">=</span><span class="w"> </span><span class="mi">3000</span><span class="p">,</span><span class="w"> </span><span class="n">resampler</span><span class="w"> </span><span class="ow">=</span><span class="w"> </span><span class="n">resampleMultinomial</span><span class="p">}</span><span class="w"> </span>
 <span class="w">        </span><span class="o">$</span><span class="w"> </span><span class="n">run</span><span class="w"> </span><span class="n">word</span><span class="w"> </span><span class="n">w</span>
 <span class="w">    </span><span class="n">pPrintCustom</span><span class="w"> </span><span class="o">$</span><span class="w"> </span><span class="n">toEmpiricalWeighted</span><span class="w"> </span><span class="n">x</span>

docs/docs/notebooks/Streaming.html

@@ -14906,7 +14906,7 @@ <h2 id="Conditioning">Conditioning<a class="anchor-link" href="#Conditioning">&#
 <div class="jp-InputPrompt jp-InputArea-prompt">In&nbsp;[7]:</div>
 <div class="jp-CodeMirrorEditor jp-Editor jp-InputArea-editor" data-type="inline">
      <div class="CodeMirror cm-s-jupyter">
-<div class=" highlight hl-Haskell"><pre><span></span><span class="nf">particles</span><span class="w"> </span><span class="ow">&lt;-</span><span class="w"> </span><span class="n">sampleIOfixed</span><span class="w"> </span><span class="o">$</span><span class="w"> </span><span class="n">runPopulation</span><span class="w"> </span><span class="o">$</span><span class="w"> </span>
+<div class=" highlight hl-Haskell"><pre><span></span><span class="nf">particles</span><span class="w"> </span><span class="ow">&lt;-</span><span class="w"> </span><span class="n">sampleIOfixed</span><span class="w"> </span><span class="o">$</span><span class="w"> </span><span class="n">runPopulationT</span><span class="w"> </span><span class="o">$</span><span class="w"> </span>
 <span class="w">    </span><span class="n">smc</span><span class="w"> </span><span class="kt">SMCConfig</span><span class="w"> </span><span class="p">{</span>
 <span class="w">        </span><span class="n">numSteps</span><span class="w"> </span><span class="ow">=</span><span class="w"> </span><span class="mi">100</span><span class="p">,</span><span class="w"> </span>
 <span class="w">        </span><span class="n">numParticles</span><span class="w"> </span><span class="ow">=</span><span class="w"> </span><span class="mi">1000</span><span class="p">,</span><span class="w"> </span>