ml_ratiosolve 1.0.0 → 1.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 50e5f40213dec0644ad76c57672c031139f516a7
+  metadata.gz: 690cbbb17382e88e829a3ee728d173ec3fce5ed3
+  data.tar.gz: 6fbc77aa4726d5cb1ae06432126b2859c9880f72
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data/Gemfile

@@ -2,3 +2,4 @@ source 'https://rubygems.org'
 
 # Specify your gem's dependencies in ml_ratiosolve.gemspec
 gemspec
+#gem 'nmatrix', path: '/home/cfuller/git/nmatrix'

data/bin/ml_ratiosolve

@@ -13,6 +13,8 @@ opts = Trollop::options do
   opt :ci_level, "Float in the range 0-1 specifiying the level of confidence interval to calculate.  E.g. 0.95 will calculate a 95% confidence interval", type: :float, default: 0.95
   opt :skip, "If some experiments are missing datapoints, specifiy which ones here.  These should be specified as (0-indexed) treatment,experiment pairs, with a comma separating treatment and experiment and a colon separating successive pairs.  E.g. to skip the first and second treatments in the first experiment: '0,0:1,0'", type: :string, default: ""
   opt :norm_index, "Normalize so that the mean value of the specified treatment is set to 1.", type: :integer, default: 0
+  opt :stdin, "Read from standard input rather than a file."
+  opt :quiet, "Only write the final result to standard output."
 end
 
 MLRatioSolveBin.go(opts)

data/lib/ml_ratiosolve/ml_ratiosolve.rb

@@ -49,11 +49,19 @@ require 'nmatrix'
 module MLRatioSolve
   class << self
 
+    #
+    # Set whether to use quiet mode.  In quiet mode, no intermediate results
+    # are written to output.
+    # @param q [Boolean] whether to activate quiet mode
+    def quiet_mode(q)
+      @quiet_mode = q
+    end
+
     # 
     # The normal probability distribution.
-    # @param  x [Numeric] The point at which to calculate the probability density
-    # @param  m [Numeric] The mean of the distribution
-    # @param  s2 [Numeric] The variance of the distribution
+    # @param x [Numeric] The point at which to calculate the probability density
+    # @param m [Numeric] The mean of the distribution
+    # @param s2 [Numeric] The variance of the distribution
     # 
     # @return [Float] The probability density at the specified point
     def normpdf(x, m, s2)
@@ -231,6 +239,7 @@ module MLRatioSolve
     # 
     # @return [void]
     def print_parameters(mu, sig2, gamma, x, iternum)
+      return nil if @quiet_mode
       puts "="*10
       puts "At iteration number #{iternum}:"
       puts "mu = #{mu.to_s}"
@@ -505,7 +514,7 @@ module MLRatioSolve
         end
         counter += 1
         if best[:mu] then
-          puts "Best solution found so far:"
+          puts "Best solution found so far:" unless @quiet_mode
           print_parameters(best[:mu], best[:sig2], best[:gamma], x, counter)
         end
       end
@@ -553,7 +562,19 @@ module MLRatioSolve
     # 
     # @return [NMatrix] an IxN nmatrix containing the experimental data
     def read_data_from_file(fn)
-      N[*(CSV.read(fn).map{ |e| e.map{ |i| i.to_f } })]
+      File.open(fn) do |f|
+        read_data_from_io(f)
+      end
+    end
+
+    # 
+    # Reads csv-formatted datapoints from an IO object.  Data should be
+    # arranged with columns as independent experiments and rows as treatments.
+    # @param io [IO] The IO from which to read the data.
+    # 
+    # @return [NMatrix] an IxN nmatrix containing the experimental data
+    def read_data_from_io(io)
+      N[*(CSV.new(io).map{ |e| e.map{ |i| i.to_f } })]
     end
   end
 end

data/lib/ml_ratiosolve/version.rb

@@ -1,3 +1,3 @@
 module MlRatiosolve
-  VERSION = "1.0.0"
+  VERSION = "1.1.0"
 end

data/lib/ml_ratiosolve.rb

@@ -37,7 +37,17 @@ module MLRatioSolveBin
 
     MLRatioSolve.set_skip_indices(opts[:skip])
 
-    x = MLRatioSolve.read_data_from_file(opts[:file])
+    x = nil
+
+    if opts[:stdin] then
+      x = MLRatioSolve.read_data_from_io(STDIN)
+    else
+      x = MLRatioSolve.read_data_from_file(opts[:file])
+    end
+
+    if opts[:quiet] then
+      MLRatioSolve.quiet_mode(true)
+    end
 
     n_gammas_to_fit = x.shape[1] - 1
 

data/ml_ratiosolve.gemspec

@@ -10,7 +10,7 @@ Gem::Specification.new do |spec|
   spec.email         = ["cjfuller@gmail.com"]
   spec.description   = %q{Methods for using maximum likelihood calculations to estimate parmeters of ratios of gaussian variates}
   spec.summary       = %q{Methods for using maximum likelihood calculations to estimate parmeters of ratios of gaussian variates}
-  spec.homepage      = "https://github.com/cjfuller/ml_ratiosolve"
+  spec.homepage      = ""
   spec.license       = "MIT"
 
   spec.files         = `git ls-files`.split($/)
@@ -19,8 +19,8 @@ Gem::Specification.new do |spec|
   spec.require_paths = ["lib"]
 
   spec.add_dependency "trollop", "~> 2.0"
-  spec.add_dependency "nmatrix", "~> 0.1"
-  spec.add_development_dependency "bundler", "~> 1.3"
-  spec.add_development_dependency "rake"
-  spec.add_development_dependency "rspec"
+  spec.add_dependency "nmatrix", ">= 0.1.0.rc1"
+  spec.add_development_dependency "bundler", "~> 1"
+  spec.add_development_dependency "rake", "> 0"
+  spec.add_development_dependency "rspec", "> 0"
 end

metadata

@@ -1,83 +1,83 @@
 --- !ruby/object:Gem::Specification
 name: ml_ratiosolve
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.1.0
 platform: ruby
 authors:
 - Colin J. Fuller
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-11 00:00:00.000000000 Z
+date: 2014-03-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: trollop
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
 - !ruby/object:Gem::Dependency
   name: nmatrix
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '0.1'
+        version: 0.1.0.rc1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '0.1'
+        version: 0.1.0.rc1
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: '1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: '1'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">"
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">"
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">"
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - ">"
       - !ruby/object:Gem::Version
         version: '0'
 description: Methods for using maximum likelihood calculations to estimate parmeters
@@ -89,7 +89,7 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
-- .gitignore
+- ".gitignore"
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -102,7 +102,7 @@ files:
 - ml_ratiosolve.gemspec
 - spec/error_bootstrapping_spec.rb
 - spec/ml_ratiosolve_spec.rb
-homepage: https://github.com/cjfuller/ml_ratiosolve
+homepage: ''
 licenses:
 - MIT
 metadata: {}
@@ -112,17 +112,17 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.3
+rubygems_version: 2.2.1
 signing_key: 
 specification_version: 4
 summary: Methods for using maximum likelihood calculations to estimate parmeters of