rbbt-util 5.17.18 → 5.17.19

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: df2f1977b609e8ee620bf7f2a5318664c7ed7cbf
-  data.tar.gz: f8107c1ea077494713357cfe4b37289fcb1103ba
+  metadata.gz: 8086326d7f2641311bb29a47622ed665b7810bbf
+  data.tar.gz: bb5058f3d0f22653fb8f01bcb2ff7660e581eb17
 SHA512:
-  metadata.gz: 5dfbc75b5b4cb08522333f438d0a40a240c29a17d3ebd37139a67d4dc7a5b236d6424b09eeb7a533d9e6f1fda1e133cca9db102de06d56ed9d9667a1c5be3855
-  data.tar.gz: 98a1e891119afbf2a454efd0e5ebc690be36f6deadb474c8ed9b3294f866522f3c568fe1571624015ca6653e29dffb229fef6d4074dc7d5a7ab702f06fadd1c5
+  metadata.gz: ab07516d71e624866421fbd4041e27ea9964d871f13bbda1ceb6871215815d7e847eb2f6af2f21e001417d1a933804e08d28db3e26b4596365a29747dc4d48d2
+  data.tar.gz: f58d0cad5b049f1fdc902a0d14b9cd39ffe3b0104017e08ce4941cf1f73014d95e0989e26e9d3878a9e62948f7928c1b7ed0fec5864e5e3cafbfc761dcc28110

data/lib/rbbt/resource/path.rb

@@ -167,7 +167,7 @@ module Path
 
     search_paths.keys.
       collect{|where| Dir.glob(find(where, Path.caller_lib_dir, search_paths))}.
-      compact.flatten.collect{|path| Path.setup(path, self.resource, self.pkgdir)}
+      compact.flatten.uniq.collect{|path| Path.setup(path, self.resource, self.pkgdir)}
   end
   #{{{ Methods
 

data/lib/rbbt/tsv/stream.rb

@@ -18,7 +18,7 @@ module TSV
  
   def self.paste_streams(streams, options = {})
     options = Misc.add_defaults options, :sep => "\t", :sort => true
-    sort, sep, preamble = Misc.process_options options, :sort, :sep, :preamble
+    sort, sep, preamble, same_fields = Misc.process_options options, :sort, :sep, :preamble, :same_fields
 
     out = Misc.open_pipe do |sin|
 
@@ -67,7 +67,11 @@ module TSV
       end
 
       key_field = key_fields.compact.first
-      fields = fields.compact.flatten
+      if same_fields
+        fields = fields.first
+      else
+        fields = fields.compact.flatten
+      end
       options = options.merge(input_options.first)
       options[:type] = :list if options[:type] == :single
 
@@ -150,13 +154,30 @@ module TSV
             end
           end
 
-          values = str.inject(nil) do |acc,part| 
-            if acc.nil?
-              acc = part.dup
-            else
-              acc << sep << part
+          if same_fields
+
+            values = nil
+            str.each do |part|
+              next if part.nil? or part.empty?
+              _p = part.split(sep,-1)
+              if values.nil?
+                values = _p.collect{|v| [v]}
+              else
+                _p.each_with_index{|v,i| values[i] << v}
+              end
+            end
+
+            values = values.collect{|list| list * "|" } * sep
+
+          else
+            values = str.inject(nil) do |acc,part| 
+              if acc.nil?
+                acc = part.dup
+              else
+                acc << sep << part
+              end
+              acc
             end
-            acc
           end
           text = [min, values] * sep
           sin.puts text

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

@@ -70,6 +70,19 @@ data = NULL
       tsv
     end
 
+    def predict_interval(value, interval='confidence')
+      field = formula.split("~").last.strip
+      field.gsub!(/log\((.*)\)/,'\1')
+
+      script = <<-EOF
+model = rbbt.model.load('#{model_file}');
+predict(model, data.frame(#{field} = #{R.ruby2R value}), interval=#{R.ruby2R interval});
+      EOF
+
+      res = R.eval_a script
+      Hash[*%w(fit lower upper).zip(res).flatten]
+    end
+
     def predict(tsv, field = "Prediction")
       case tsv
       when TSV

data/lib/rbbt/util/misc/inspect.rb

@@ -118,8 +118,6 @@ module Misc
   def self.hash2md5(hash)
     return "" if hash.nil? or hash.empty?
 
-    hash = Annotated.purge(hash)
-
     str = ""
     keys = hash.keys
     keys = keys.clean_annotations if keys.respond_to? :clean_annotations
@@ -133,7 +131,11 @@ module Misc
 
     keys.each do |k|
       next if k == :monitor or k == "monitor" or k == :in_situ_persistence or k == "in_situ_persistence"
-      v = hash[k]
+      _v = hash[k]
+      _k = k
+      v = Annotated.purge(_v)
+      k = Annotated.purge(k)
+
       case
       when TrueClass === v
         str << k.to_s << "=>true" 
@@ -168,8 +170,8 @@ module Misc
         end
       end
 
-      if defined? Annotated and Annotated === v and not (defined? AssociationItem and AssociationItem === v)
-        info = Annotated.purge(v.info)
+      if defined? Annotated and Annotated === _v and not (defined? AssociationItem and AssociationItem === _v)
+        info = Annotated.purge(_v.info)
         str << "_" << hash2md5(info) 
       end
     end

data/test/rbbt/tsv/test_stream.rb

@@ -176,6 +176,28 @@ row1 A B C
     assert_equal ["AA", "BB", "CC", ""], tsv["row2"]
   end
 
+  def test_paste_stream_same_field
+    text1=<<-EOF
+#: :sep=" "
+#Row LabelA
+row1 A
+row2 AA
+    EOF
+
+    text2=<<-EOF
+#: :sep=" "
+#Row LabelA
+row2 AAA
+    EOF
+
+    s1 = StringIO.new text1
+    s2 = StringIO.new text2
+    tsv = TSV.open TSV.paste_streams([s1,s2], :sep => " ", :type => :double, :sort => false, :same_fields => true)
+    ppp tsv.to_s
+    assert_equal "Row", tsv.key_field
+    assert_equal ["AA", "AAA"], tsv["row2"][0]
+  end
+
   def test_flat2double
     text1=<<-EOF
 #: :sep= #:type=:flat

data/test/rbbt/util/R/test_model.rb

@@ -109,4 +109,22 @@ data = rbbt.model.inpute(data, CI ~ Dose, method=drm, classes='numeric', fct=LL.
     pred = model.predict "Dose" => x
     assert pred > y and pred < y + 4
   end
+
+  def test_interval
+    data = TSV.setup({}, :key_field => "Dose", :fields => ["Response"], :type => :single)
+    10.times do 
+      x = rand(10)
+      y = 10 + 3 * x + rand * 4
+      data[x] = y
+    end
+
+    model = R::Model.new "Test fit 2", "Response ~ Dose", data, :fit => 'lm'
+
+    x = 5
+    y = 10 + 3 * x 
+
+    pred = model.predict x
+    iii model.predict_interval(x)
+    assert pred > y and pred < y + 4
+  end
 end

data/test/rbbt/util/test_open.rb

@@ -3,7 +3,7 @@ require 'rbbt/util/open'
 require 'rbbt/util/tmpfile'
 require 'rbbt/persist'
 require 'test/unit'
-require 'iconv'
+
 
 class TestOpen < Test::Unit::TestCase
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.18
+  version: 5.17.19
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-04-16 00:00:00.000000000 Z
+date: 2015-04-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake