rbbt-util 5.17.12 → 5.17.13

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 49810dd833a5c40846bfe91fd20a79bf4e7782f0
-  data.tar.gz: b2db2759542144fbfc6071956161fccf93244512
+  metadata.gz: 899623e0f5927a7d4f7464374483875dfc1f0df7
+  data.tar.gz: 3ad22d09d6d094fbea8fa89280973b5fced6c5a8
 SHA512:
-  metadata.gz: 98a969cd68398ccb3b27c90946fc70920638649d7d028088834d94dc194e6df9b82dffa407426151fd0c38a852ebf0d51f4e6bc5b74b4290ede658a509364250
-  data.tar.gz: 9df8b38bada0e06fcd690e171fc25b7cec722c341d92279a336018ac985342b3619b34c7ed7aa64e2c4033e65f3c94fa976d7cea6ca5ab5cfea07197ea985b86
+  metadata.gz: 09c486addcb8a341d9fe352412cdacd225960647904479a0c7250565aa0a42c463ee81ca57d99fcc07bb1a48045f63be69b3d83acb5de52a7fb0f6ddf83d41fe
+  data.tar.gz: 4429c44655f3ee70112b544d907c44a2cc768036c402e1aa41b4c386c2f1c172fe73e579297b8648ce5fd486f37f3e80d3c3927c38f4d6f42d7180a5ea3bdaa3

data/lib/rbbt/util/R.rb

@@ -8,7 +8,11 @@ module R
   UTIL    = File.join(LIB_DIR, 'util.R')
   PLOT    = File.join(LIB_DIR, 'plot.R')
 
-  def self.run(command, source = nil, options = {})
+  def self.run(command, source = nil, options = nil)
+    source, options = nil, source if options.nil? and Hash === source
+    options = {} if options.nil?
+    monitor = options.delete :monitor
+
     cmd =<<-EOF
 # Loading basic rbbt environment
 source('#{UTIL}');
@@ -33,7 +37,7 @@ source('#{UTIL}');
 
     Log.debug{"R Script:\n#{ cmd }"}
 
-    if options.delete :monitor
+    if monitor
       io = CMD.cmd('R --vanilla --quiet', options.merge(:in => cmd, :pipe => true, :log => true))
       while line = io.gets
         puts line

data/lib/rbbt/util/R/model.rb

@@ -87,11 +87,14 @@ predict(model, data.frame(#{R.ruby2R tsv}));
         Array === tsv.values.first ? res : res.first
       when Fixnum, Array, Float, String
         field = formula.split("~").last.strip
+        field.gsub!(/log\((.*)\)/,'\1')
 
-        res = R.eval_a <<-EOF
+        script = <<-EOF
 model = rbbt.model.load('#{model_file}');
 predict(model, data.frame(#{field} = #{R.ruby2R tsv}));
         EOF
+
+        res = R.eval_a script
         Array === tsv ? res : res.first
       else
         raise "Unknown object for predict: #{Misc.fingerprint tsv}"
@@ -110,7 +113,8 @@ predict(model, data.frame(#{field} = #{R.ruby2R tsv}));
       tsv = Model.groom(tsv, formula)
 
       FileUtils.mkdir_p File.dirname(model_file) unless File.exists?(File.dirname(model_file))
-      tsv.R <<-EOF, r_options(tsv)
+      roptions = r_options(tsv)
+      tsv.R <<-EOF, roptions
 model = rbbt.model.fit(data, #{formula}, method=#{method}#{args_str})
 save(model, file='#{model_file}')
 data = NULL

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.12
+  version: 5.17.13
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-03-27 00:00:00.000000000 Z
+date: 2015-04-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -431,7 +431,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 2.4.6
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)