'scales' calculates ranges per alternative now

To support filling of effects table - API-incompatible, so renaming service to smaa_v2 - Make the Patavi service name configurable - The 95% CI hulls are calculated client side - Modified a test since the previous method didn't really calculate the hull of the 95% CIs...
ademirjs · May 5, 2014 · 2c42acc · 2c42acc
1 parent 9136da7
commit 2c42acc
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diff --git a/Makefile b/Makefile
@@ -1,7 +1,4 @@
-all: R/service.R SCSSC
-
-R/service.R: R/measurements.R R/smaa.R R/macbethSolve.R
-	cat $^ > $@
+all: SCSSC
 
 SCSSC:
 	compass compile

diff --git a/Dockerfile → R/Dockerfile b/Dockerfile → R/Dockerfile
@@ -9,8 +9,11 @@ RUN DEBIAN_FRONTEND=noninteractive apt-get install -y -q libgmp-dev
 RUN R -e 'install.packages("hitandrun", repos="http://cran.rstudio.com/"); if (!require("hitandrun")) quit(save="no", status=8)'
 RUN R -e 'install.packages("smaa", repos="http://cran.rstudio.com/"); if (!require("smaa")) quit(save="no", status=8)'
 
-ADD R/service.R /var/lib/patavi/smaa_service.R
+ADD measurements.R /tmp/
+ADD macbethSolve.R /tmp/
+ADD smaa.R /tmp/
+RUN cat /tmp/*.R > /var/lib/patavi/smaa_service.R
 
 USER patavi
 ENV HOME /var/lib/patavi
-ENTRYPOINT ["/var/lib/patavi/bin/patavi-worker", "--method", "smaa", "-n", "1", "--file", "/var/lib/patavi/smaa_service.R", "--rserve", "--packages", "MASS,rcdd,hitandrun,smaa"]
+ENTRYPOINT ["/var/lib/patavi/bin/patavi-worker", "--method", "smaa_v2", "-n", "1", "--file", "/var/lib/patavi/smaa_service.R", "--rserve", "--packages", "MASS,rcdd,hitandrun,smaa"]
diff --git a/R/smaa.R b/R/smaa.R
@@ -8,7 +8,7 @@ wrap.matrix <- function(m) {
   l
 }
 
-smaa <- function(params) {
+smaa_v2 <- function(params) {
   allowed <- c('scales', 'smaa', 'macbeth')
   if(params$method %in% allowed) {
     do.call(paste("run", params$method, sep="_"), list(params))
@@ -22,7 +22,8 @@ run_scales <- function(params) {
   crit <- names(params$criteria)
   alts <- names(params$alternatives)
   meas <- sample(alts, crit, params$performanceTable, N)
-  list(wrap.matrix(t(apply(meas, 3, function(e) { quantile(e, c(0.025, 0.975)) }))))
+  scales <- apply(meas, c(2, 3), function(e) { quantile(e, c(0.025, 0.5, 0.975)) })
+  apply(aperm(scales, c(3,2,1)), 1, wrap.matrix)
 }
 
 ratioConstraint <- function(n, i1, i2, x) {

diff --git a/R/test/thrombo.R b/R/test/thrombo.R
@@ -11,20 +11,18 @@ params <- fromJSON('../../examples/thrombolytics.json')
 
 print("=== CI hulls ===")
 
-expected <- list(structure(
-  list(
-    `Prox DVT` = structure(
-      c(0.0312317469487807, 0.202267162805509),
-      .Names = c("2.5%", "97.5%")),
-    `Dist DVT` = structure(
-      c(0.189206533230964, 0.359563082546533),
-      .Names = c("2.5%", "97.5%")),
-    Bleed = structure(
-      c(0.000383785658019692, 0.0704173191411898),
-      .Names = c("2.5%", "97.5%"))),
-  .Names = c("Prox DVT", "Dist DVT", "Bleed")))
-
-actual <- run_scales(params)
+expected <- structure(list(
+  `Prox DVT` = structure(c(0.0273829683645853, 0.211008623949751), .Names = c("2.5%", "97.5%")),
+  `Dist DVT` = structure(c(0.179207896860712, 0.372992144610352), .Names = c("2.5%", "97.5%")),
+  Bleed = structure(c(0.000174242898524121, 0.0774123400973682), .Names = c("2.5%", "97.5%"))),
+  .Names = c("Prox DVT", "Dist DVT", "Bleed"))
+
+scales <- run_scales(params)
+actual <- lapply(scales, function(y) {
+  lower <- min(unlist(lapply(y, function(z) { z["2.5%"] })))
+  upper <- max(unlist(lapply(y, function(z) { z["97.5%"] })))
+  c("2.5%"=lower, "97.5%"=upper)
+})
 print(all.equal(expected, actual, tolerance=0.05))
 
 print("=== Preference Free ===")

diff --git a/app/js/config.js b/app/js/config.js
@@ -50,6 +50,7 @@ define([], function() {
 
   return {
     tasks: tasks,
-    defaultView: defaultView
+    defaultView: defaultView,
+    pataviService: 'smaa_v2'
   };
 });
diff --git a/app/js/controllers/helpers/wizard.js b/app/js/controllers/helpers/wizard.js
@@ -1,12 +1,12 @@
 'use strict';
-define(['angular', 'underscore', 'mcda/lib/patavi', 'NProgress'], function(angular, _, patavi, NProgress) {
+define(['mcda/config', 'angular', 'underscore', 'mcda/lib/patavi', 'NProgress'], function(Config, angular, _, patavi, NProgress) {
   return ['$rootScope', '$scope', 'handler', function($rootScope, $scope, handler) {
     $rootScope.noProgress = true;
 
     var calculateIntermediateResults = function(state, standardizeFn) {
       var prefs = standardizeFn(state.prefs);
       var data = _.extend(state.problem, { "preferences": prefs, "method": "smaa" });
-      var task = patavi.submit('smaa', data);
+      var task = patavi.submit(Config.pataviService, data);
 
       var successHandler = function(results) {
         $scope.$root.$safeApply($scope, function() {

diff --git a/app/js/controllers/partialValueFunction.js b/app/js/controllers/partialValueFunction.js
@@ -1,5 +1,5 @@
 'use strict';
-define(['mcda/controllers/helpers/wizard', 'angular', 'mcda/lib/patavi', 'underscore'], function(Wizard, angular, patavi, _) {
+define(['mcda/config', 'mcda/controllers/helpers/wizard', 'angular', 'mcda/lib/patavi', 'underscore'], function(Config, Wizard, angular, patavi, _) {
   return function($scope, $injector, currentScenario, taskDefinition, PartialValueFunction) {
     var standardize = function(state) {
       // Copy choices to problem
@@ -35,7 +35,7 @@ define(['mcda/controllers/helpers/wizard', 'angular', 'mcda/lib/patavi', 'unders
         }
 
         var preferences = rewritePreferences(choice.data[choice.criterion].preferences);
-        var task = patavi.submit("smaa", { method: "macbeth", preferences: preferences });
+        var task = patavi.submit(Config.pataviService, { method: "macbeth", preferences: preferences });
         task.results.then(function(results) {
           $scope.$root.$safeApply($scope, function() {
             currentState.results = results.results;

diff --git a/app/js/controllers/results.js b/app/js/controllers/results.js
@@ -1,5 +1,5 @@
 'use strict';
-define(['angular', 'mcda/lib/patavi', 'underscore', 'NProgress'], function(angular, patavi, _, NProgress) {
+define(['mcda/config', 'angular', 'mcda/lib/patavi', 'underscore', 'NProgress'], function(Config, angular, patavi, _, NProgress) {
   return function($rootScope, $scope, currentScenario, taskDefinition) {
     var alternatives;
     var criteria;
@@ -9,7 +9,7 @@ define(['angular', 'mcda/lib/patavi', 'underscore', 'NProgress'], function(angul
     var run = function(state) {
       state = angular.copy(state);
       var data = _.extend(state.problem, { "preferences": state.prefs, "method": "smaa" });
-      var task = patavi.submit('smaa', data);
+      var task = patavi.submit(Config.pataviService, data);
 
       var successHandler = function(results) {
         $scope.$root.$safeApply($scope, function() {

diff --git a/app/js/controllers/scaleRange.js b/app/js/controllers/scaleRange.js
@@ -1,5 +1,5 @@
 'use strict';
-define(['angular', 'mcda/lib/patavi', 'underscore'], function(angular, patavi, _) {
+define(['mcda/config', 'angular', 'mcda/lib/patavi', 'underscore'], function(Config, angular, patavi, _) {
 
   return function($scope, currentScenario, taskDefinition) {
     $scope.title = taskDefinition.title;
@@ -22,20 +22,26 @@ define(['angular', 'mcda/lib/patavi', 'underscore'], function(angular, patavi, _
         code: (code && code.desc) ? code.desc : code,
         cause: error
       };
-      $scope.$root.$broadcast('error', message);
+      $scope.$root.$broadcast('patavi.error', message);
     };
 
     var successHandler = function(state, results) {
       var scales = {};
       var choices = {};
       $scope.$root.$safeApply($scope, function() {
-        _.map(_.pairs(results.results[0]), function(criterion) {
+        _.map(_.pairs(results.results), function(criterion) {
+
+          // Calculate interval hulls
+          var criterionRange = [
+            Math.min.apply(null, _.map(_.values(criterion[1]), function(alt) { return alt["2.5%"] })),
+            Math.max.apply(null, _.map(_.values(criterion[1]), function(alt) { return alt["97.5%"] }))
+          ];
 
           // Set inital model value
           var pvf = state.problem.criteria[criterion[0]].pvf;
           var problemRange = pvf ? pvf.range : null;
-          var from = problemRange ? problemRange[0] : criterion[1]['2.5%'];
-          var to = problemRange ? problemRange[1] : criterion[1]['97.5%'];
+          var from = problemRange ? problemRange[0] : criterionRange[0];
+          var to = problemRange ? problemRange[1] : criterionRange[1];
 
           choices[criterion[0]] = {
             lower: from,
@@ -55,8 +61,8 @@ define(['angular', 'mcda/lib/patavi', 'underscore'], function(angular, patavi, _
             return val > scale[1] ? scale[1] : val;
           };
           scales[criterion[0]] = {
-            restrictFrom: criterion[1]['2.5%'],
-            restrictTo: criterion[1]['97.5%'],
+            restrictFrom: criterionRange[0],
+            restrictTo: criterionRange[1],
             from: boundFrom(nice(from) - margin),
             to: boundTo(nice(to) + margin),
             increaseFrom: function() {
@@ -78,7 +84,7 @@ define(['angular', 'mcda/lib/patavi', 'underscore'], function(angular, patavi, _
     var scenario = currentScenario;
     var state = taskDefinition.clean(scenario.state);
 
-    var calculateScales = patavi.submit('smaa', _.extend(state.problem, {
+    var calculateScales = patavi.submit(Config.pataviService, _.extend(state.problem, {
       'method': 'scales'
     }));
     calculateScales.results.then(_.partial(successHandler, state), errorHandler);
@@ -112,4 +118,4 @@ define(['angular', 'mcda/lib/patavi', 'underscore'], function(angular, patavi, _
       scenario.redirectToDefaultView();
     };
   };
-});
+});