sciruby 0.1.3 → 0.2.1

Sign up to get free protection for your applications and to get access to all the features.
Files changed (131) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +2 -0
  3. data/CHANGES +3 -0
  4. data/CONTRIBUTING.md +46 -0
  5. data/Gemfile +34 -0
  6. data/LICENSE.txt +21 -0
  7. data/README.rdoc +28 -0
  8. data/lib/sciruby/gems.rb +27 -0
  9. data/lib/sciruby/version.rb +3 -0
  10. data/lib/sciruby.rb +2 -77
  11. data/sciruby.gemspec +35 -0
  12. metadata +51 -413
  13. data/.autotest +0 -23
  14. data/.gemtest +0 -0
  15. data/History.txt +0 -6
  16. data/Manifest.txt +0 -119
  17. data/Rakefile +0 -178
  18. data/bin/sciruby-plotter +0 -12
  19. data/data/r/man/AirPassengers.Rd +0 -51
  20. data/data/r/man/BJsales.Rd +0 -34
  21. data/data/r/man/BOD.Rd +0 -53
  22. data/data/r/man/ChickWeight.Rd +0 -68
  23. data/data/r/man/DNase.Rd +0 -63
  24. data/data/r/man/EuStockMarkets.Rd +0 -28
  25. data/data/r/man/Formaldehyde.Rd +0 -44
  26. data/data/r/man/HairEyeColor.Rd +0 -77
  27. data/data/r/man/Harman23.cor.Rd +0 -25
  28. data/data/r/man/Harman74.cor.Rd +0 -28
  29. data/data/r/man/Indometh.Rd +0 -57
  30. data/data/r/man/InsectSprays.Rd +0 -45
  31. data/data/r/man/JohnsonJohnson.Rd +0 -37
  32. data/data/r/man/LakeHuron.Rd +0 -27
  33. data/data/r/man/LifeCycleSavings.Rd +0 -54
  34. data/data/r/man/Loblolly.Rd +0 -56
  35. data/data/r/man/Nile.Rd +0 -78
  36. data/data/r/man/Orange.Rd +0 -57
  37. data/data/r/man/OrchardSprays.Rd +0 -62
  38. data/data/r/man/PlantGrowth.Rd +0 -39
  39. data/data/r/man/Puromycin.Rd +0 -84
  40. data/data/r/man/Theoph.Rd +0 -84
  41. data/data/r/man/Titanic.Rd +0 -73
  42. data/data/r/man/ToothGrowth.Rd +0 -40
  43. data/data/r/man/UCBAdmissions.Rd +0 -68
  44. data/data/r/man/UKDriverDeaths.Rd +0 -72
  45. data/data/r/man/UKLungDeaths.Rd +0 -40
  46. data/data/r/man/UKgas.Rd +0 -25
  47. data/data/r/man/USAccDeaths.Rd +0 -23
  48. data/data/r/man/USArrests.Rd +0 -45
  49. data/data/r/man/USJudgeRatings.Rd +0 -38
  50. data/data/r/man/USPersonalExpenditure.Rd +0 -33
  51. data/data/r/man/VADeaths.Rd +0 -51
  52. data/data/r/man/WWWusage.Rd +0 -41
  53. data/data/r/man/WorldPhones.Rd +0 -40
  54. data/data/r/man/ability.cov.Rd +0 -50
  55. data/data/r/man/airmiles.Rd +0 -29
  56. data/data/r/man/airquality.Rd +0 -56
  57. data/data/r/man/anscombe.Rd +0 -62
  58. data/data/r/man/attenu.Rd +0 -66
  59. data/data/r/man/attitude.Rd +0 -48
  60. data/data/r/man/austres.Rd +0 -22
  61. data/data/r/man/beavers.Rd +0 -73
  62. data/data/r/man/cars.Rd +0 -59
  63. data/data/r/man/chickwts.Rd +0 -47
  64. data/data/r/man/co2.Rd +0 -43
  65. data/data/r/man/crimtab.Rd +0 -129
  66. data/data/r/man/datasets-package.Rd +0 -24
  67. data/data/r/man/discoveries.Rd +0 -30
  68. data/data/r/man/esoph.Rd +0 -66
  69. data/data/r/man/euro.Rd +0 -56
  70. data/data/r/man/eurodist.Rd +0 -25
  71. data/data/r/man/faithful.Rd +0 -63
  72. data/data/r/man/freeny.Rd +0 -56
  73. data/data/r/man/infert.Rd +0 -56
  74. data/data/r/man/iris.Rd +0 -62
  75. data/data/r/man/islands.Rd +0 -29
  76. data/data/r/man/lh.Rd +0 -22
  77. data/data/r/man/longley.Rd +0 -56
  78. data/data/r/man/lynx.Rd +0 -33
  79. data/data/r/man/morley.Rd +0 -50
  80. data/data/r/man/mtcars.Rd +0 -44
  81. data/data/r/man/nhtemp.Rd +0 -30
  82. data/data/r/man/nottem.Rd +0 -30
  83. data/data/r/man/occupationalStatus.Rd +0 -44
  84. data/data/r/man/precip.Rd +0 -31
  85. data/data/r/man/presidents.Rd +0 -36
  86. data/data/r/man/pressure.Rd +0 -41
  87. data/data/r/man/quakes.Rd +0 -40
  88. data/data/r/man/randu.Rd +0 -46
  89. data/data/r/man/rivers.Rd +0 -21
  90. data/data/r/man/rock.Rd +0 -34
  91. data/data/r/man/sleep.Rd +0 -51
  92. data/data/r/man/stackloss.Rd +0 -77
  93. data/data/r/man/state.Rd +0 -80
  94. data/data/r/man/sunspot.month.Rd +0 -49
  95. data/data/r/man/sunspot.year.Rd +0 -26
  96. data/data/r/man/sunspots.Rd +0 -33
  97. data/data/r/man/swiss.Rd +0 -79
  98. data/data/r/man/treering.Rd +0 -38
  99. data/data/r/man/trees.Rd +0 -48
  100. data/data/r/man/uspop.Rd +0 -27
  101. data/data/r/man/volcano.Rd +0 -31
  102. data/data/r/man/warpbreaks.Rd +0 -56
  103. data/data/r/man/women.Rd +0 -40
  104. data/data/r/man/zCO2.Rd +0 -81
  105. data/lib/ext/csv.rb +0 -22
  106. data/lib/ext/shoes.rb +0 -131
  107. data/lib/ext/string.rb +0 -39
  108. data/lib/sciruby/analysis/suite.rb +0 -87
  109. data/lib/sciruby/analysis/suite_report_builder.rb +0 -44
  110. data/lib/sciruby/analysis.rb +0 -98
  111. data/lib/sciruby/config.rb +0 -93
  112. data/lib/sciruby/data/guardian.rb +0 -96
  113. data/lib/sciruby/data/r/base.rb +0 -110
  114. data/lib/sciruby/data/r/data_frame.rb +0 -24
  115. data/lib/sciruby/data/r/grouped_data.rb +0 -7
  116. data/lib/sciruby/data/r/list.rb +0 -20
  117. data/lib/sciruby/data/r/multi_time_series.rb +0 -24
  118. data/lib/sciruby/data/r/r_matrix.rb +0 -7
  119. data/lib/sciruby/data/r/time_series.rb +0 -19
  120. data/lib/sciruby/data/r/time_series_base.rb +0 -40
  121. data/lib/sciruby/data/r/vector.rb +0 -125
  122. data/lib/sciruby/data/r.rb +0 -155
  123. data/lib/sciruby/data.rb +0 -168
  124. data/lib/sciruby/editor.rb +0 -82
  125. data/lib/sciruby/plotter.rb +0 -128
  126. data/lib/sciruby/recommend.rb +0 -70
  127. data/lib/sciruby/validation.rb +0 -368
  128. data/readme.md +0 -75
  129. data/static/sciruby-icon.png +0 -0
  130. data/test/helpers_tests.rb +0 -58
  131. data/test/test_recommend.rb +0 -16
data/Rakefile DELETED
@@ -1,178 +0,0 @@
1
- #!/usr/bin/ruby
2
- # -*- ruby -*-
3
- # -*- coding: utf-8 -*-
4
- $:.unshift(File.dirname(__FILE__)+'/lib/')
5
-
6
- require 'rubygems'
7
- require 'rdoc/task'
8
- require 'sciruby'
9
- require 'hoe'
10
-
11
- # Hoe.plugin :compiler
12
- # Hoe.plugin :cucumberfeatures
13
- # Hoe.plugin :gem_prelude_sucks
14
- Hoe.plugin :git
15
- Hoe.plugin :gemspec
16
- Hoe.plugin :bundler
17
- # Hoe.plugin :inline
18
- # Hoe.plugin :manifest
19
- # Hoe.plugin :newgem
20
- # Hoe.plugin :racc
21
- # Hoe.plugin :rubyforge
22
- # Hoe.plugin :website
23
-
24
- desc "Ruby Lint"
25
- task :lint do
26
- executable=Config::CONFIG['RUBY_INSTALL_NAME']
27
- Dir.glob("lib/**/*.rb") {|f|
28
- if !system %{#{executable} -w -c "#{f}"}
29
- puts "Error on: #{f}"
30
- end
31
- }
32
- end
33
-
34
- desc "Open an irb session preloaded with sciruby"
35
- task :console do
36
- sh "irb -rubygems -I lib -r sciruby.rb"
37
- end
38
-
39
- desc "Start the plotter without the console"
40
- task :plotter, [:script] => [] do |t,args|
41
- if args.script.empty?
42
- raise ArgumentError, "Need a script, e.g.: rake plotter[script.rb]"
43
- else
44
- sh "ruby -rubygems -I lib -r sciruby.rb -e 'SciRuby::Plotter.new(\"#{args.script}\")'"
45
- end
46
- end
47
-
48
- desc "Start the plotter without the console"
49
- task :editor do
50
- sh "ruby -rubygems -I lib -r sciruby.rb -e 'SciRuby::Editor.new'"
51
- end
52
-
53
- task :release do
54
- system %{git push origin master}
55
- end
56
-
57
- h = Hoe.spec 'sciruby' do
58
- self.version = SciRuby::VERSION
59
- self.require_ruby_version ">=1.9"
60
- self.developer('SciRuby Development Team', 'sciruby-dev@googlegroups.com')
61
- self.extra_deps = {'distribution' => ">=0.4.0",
62
- 'green_shoes' => ">=1.0.282",
63
- 'statsample' => ">=1.1.0",
64
- 'integration' => ">= 0",
65
- 'minimization' => ">= 0",
66
- 'gsl' => "~> 1.14.5",
67
- 'rsvg2' => '~> 1.0.0',
68
- 'simpler' => '>=0.1.0',
69
- 'rubyvis' => '>=0.4.0' }.to_a
70
-
71
-
72
- self.extra_dev_deps = {'hoe' => "~> 2.12",
73
- 'rdoc' => ">=0",
74
- 'rspec' => ">=2.0",
75
- 'haml' => ">=0", # for Rubyvis
76
- 'coderay' => ">=0", # for Rubyvis
77
- 'nokogiri' => ">=0", # for Rubyvis
78
- 'RedCloth' => ">=0", # for Rubyvis
79
- 'gtksourceview2' => ">=0", # for editor
80
- 'shoulda' => "~> 2.11",
81
- 'hoe-gemspec' => "~> 1.0",
82
- 'hoe-bundler' => "~> 1.1",
83
- 'minitest' => "~> 2.0" }.to_a
84
-
85
- #self.executables = `git ls-files -- bin/*`.split("\n").map { |f| File.basename(f) }
86
-
87
- self.post_install_message = <<-EOF
88
- ***********************************************************
89
- Welcome to SciRuby: Tools for Scientific Computing in Ruby!
90
-
91
- *** WARNING ***
92
- Please be aware that SciRuby is in ALPHA status. If you're
93
- thinking of using SciRuby to write mission critical code,
94
- such as for driving a car or flying a space shuttle, you
95
- may wish to choose other software (for now).
96
-
97
- In order to leverage the GUI features, you will need to
98
- install gtk2 and optionally gtksourceview2:
99
-
100
- $ gem install gtk2 gtksourceview2
101
-
102
- You will probably first need to install the headers for
103
- a number of required packages. In Ubuntu, use:
104
-
105
- $ sudo apt-get install libgtk2.0-dev libgtksourceview2-dev \\
106
- librsvg2-dev libcairo2-dev
107
-
108
- If you have trouble with Green Shoes, you should look at
109
- the Green Shoes wiki:
110
-
111
- * http://github.com/ashbb/green_shoes/wiki
112
-
113
- For Mac OSX Green Shoes:
114
-
115
- * https://github.com/ashbb/green_shoes/wiki/Building-Green-Shoes-on-OSX
116
-
117
- More explicit instructions for SciRuby should be available
118
- at our website, sciruby.com, or through our mailing list
119
- (which can also be found on our website).
120
-
121
- Thanks for installing SciRuby! Happy hypothesis testing!
122
-
123
- ***********************************************************
124
- EOF
125
-
126
- self.need_rdoc = false
127
-
128
- end
129
-
130
- RDoc::Task.new(:docs) do |rd|
131
- rd.main = h.readme_file
132
- rd.options << '-d' if (`which dot` =~ /\/dot/) unless
133
- ENV['NODOT'] || Hoe::WINDOZE
134
- rd.rdoc_dir = 'doc'
135
-
136
- rd.rdoc_files.include("lib/**/*.rb")
137
- rd.rdoc_files += h.spec.extra_rdoc_files
138
- rd.rdoc_files.reject! {|f| f=="Manifest.txt"}
139
- title = h.spec.rdoc_options.grep(/^(-t|--title)=?$/).first
140
- if title then
141
- rd.options << title
142
-
143
- unless title =~ /\=/ then # for ['-t', 'title here']
144
- title_index = spec.rdoc_options.index(title)
145
- rd.options << spec.rdoc_options[title_index + 1]
146
- end
147
- else
148
- title = "#{h.name}-#{h.version} Documentation"
149
- title = "#{h.rubyforge_name}'s " + title if h.rubyforge_name != h.name
150
- rd.options << '--title' << title
151
- end
152
- end
153
-
154
- desc 'Publish rdocs with analytics support'
155
- task :publish_docs => [:clean, :docs] do
156
- ruby %{aggregate_adsense_to_doc.rb}
157
- path = File.expand_path("~/.rubyforge/user-config.yml")
158
- config = YAML.load(File.read(path))
159
- host = "#{config["username"]}@rubyforge.org"
160
-
161
- remote_dir = "/var/www/gforge-projects/#{h.rubyforge_name}/#{h.remote_rdoc_dir
162
- }"
163
- local_dir = h.local_rdoc_dir
164
- Dir.glob(local_dir+"/**/*") {|file|
165
- sh %{chmod 755 #{file}}
166
- }
167
- sh %{rsync #{h.rsync_args} #{local_dir}/ #{host}:#{remote_dir}}
168
- end
169
-
170
- require 'rspec/core/rake_task'
171
- namespace :spec do
172
- desc "Run all specs"
173
- RSpec::Core::RakeTask.new
174
- # options in .rspec in package root
175
- end
176
-
177
-
178
- # vim: syntax=ruby
data/bin/sciruby-plotter DELETED
@@ -1,12 +0,0 @@
1
- #!/usr/bin/env ruby
2
-
3
- require 'rubygems'
4
- require 'sciruby'
5
-
6
- if ARGV.size == 0
7
- STDERR.puts "sciruby-plotter: missing plot script"
8
- STDERR.puts "Usage: sciruby-plotter myscript.rb"
9
- exit false
10
- end
11
-
12
- SciRuby::Plotter.new ARGV.first
@@ -1,51 +0,0 @@
1
- % File src/library/datasets/man/AirPassengers.Rd
2
- % Part of the R package, http://www.R-project.org
3
- % Copyright 1995-2007 R Core Development Team
4
- % Distributed under GPL 2 or later
5
-
6
- \name{AirPassengers}
7
- \docType{data}
8
- \alias{AirPassengers}
9
- \title{Monthly Airline Passenger Numbers 1949-1960}
10
- \description{
11
- The classic Box & Jenkins airline data. Monthly totals of
12
- international airline passengers, 1949 to 1960.
13
- }
14
- \usage{AirPassengers}
15
- \format{
16
- A monthly time series, in thousands.
17
- }
18
- \source{
19
- Box, G. E. P., Jenkins, G. M. and Reinsel, G. C. (1976)
20
- \emph{Time Series Analysis, Forecasting and Control.}
21
- Third Edition. Holden-Day. Series G.
22
- }
23
- \examples{
24
- \dontrun{
25
- ## These are quite slow and so not run by example(AirPassengers)
26
-
27
- ## The classic 'airline model', by full ML
28
- (fit <- arima(log10(AirPassengers), c(0, 1, 1),
29
- seasonal = list(order=c(0, 1 ,1), period=12)))
30
- update(fit, method = "CSS")
31
- update(fit, x=window(log10(AirPassengers), start = 1954))
32
- pred <- predict(fit, n.ahead = 24)
33
- tl <- pred$pred - 1.96 * pred$se
34
- tu <- pred$pred + 1.96 * pred$se
35
- ts.plot(AirPassengers, 10^tl, 10^tu, log = "y", lty = c(1,2,2))
36
-
37
- ## full ML fit is the same if the series is reversed, CSS fit is not
38
- ap0 <- rev(log10(AirPassengers))
39
- attributes(ap0) <- attributes(AirPassengers)
40
- arima(ap0, c(0, 1, 1), seasonal = list(order=c(0, 1 ,1), period=12))
41
- arima(ap0, c(0, 1, 1), seasonal = list(order=c(0, 1 ,1), period=12),
42
- method = "CSS")
43
-
44
- ## Structural Time Series
45
- ap <- log10(AirPassengers) - 2
46
- (fit <- StructTS(ap, type= "BSM"))
47
- par(mfrow=c(1,2))
48
- plot(cbind(ap, fitted(fit)), plot.type = "single")
49
- plot(cbind(ap, tsSmooth(fit)), plot.type = "single")
50
- }}
51
- \keyword{datasets}
@@ -1,34 +0,0 @@
1
- % File src/library/datasets/man/BJsales.Rd
2
- % Part of the R package, http://www.R-project.org
3
- % Copyright 1995-2007 R Core Development Team
4
- % Distributed under GPL 2 or later
5
-
6
- \name{BJsales}
7
- \docType{data}
8
- \alias{BJsales}
9
- \alias{BJsales.lead}
10
- \title{Sales Data with Leading Indicator}
11
- \description{
12
- The sales time series \code{BJsales} and leading indicator
13
- \code{BJsales.lead} each contain 150 observations.
14
- The objects are of class \code{"ts"}.
15
- }
16
- \usage{
17
- BJsales
18
- BJsales.lead
19
- }
20
- \source{
21
- The data are given in Box & Jenkins (1976).
22
- Obtained from the Time Series Data Library at
23
- \url{http://www-personal.buseco.monash.edu.au/~hyndman/TSDL/}
24
- }
25
- \references{
26
- G. E. P. Box and G. M. Jenkins (1976):
27
- \emph{Time Series Analysis, Forecasting and Control},
28
- Holden-Day, San Francisco, p. 537.
29
-
30
- P. J. Brockwell and R. A. Davis (1991):
31
- \emph{Time Series: Theory and Methods},
32
- Second edition, Springer Verlag, NY, pp. 414.
33
- }
34
- \keyword{datasets}
data/data/r/man/BOD.Rd DELETED
@@ -1,53 +0,0 @@
1
- % File src/library/datasets/man/BOD.Rd
2
- % Part of the R package, http://www.R-project.org
3
- % Copyright 1995-2010 R Core Development Team
4
- % Distributed under GPL 2 or later
5
-
6
- \name{BOD}
7
- \docType{data}
8
- \alias{BOD}
9
- \title{ Biochemical Oxygen Demand }
10
- \description{
11
- The \code{BOD} data frame has 6 rows and 2 columns giving the
12
- biochemical oxygen demand versus time in an evaluation of water
13
- quality.
14
- }
15
- \usage{BOD}
16
- \format{
17
- This data frame contains the following columns:
18
- \describe{
19
- \item{Time}{
20
- A numeric vector giving the time of the measurement (days).
21
- }
22
- \item{demand}{
23
- A numeric vector giving the biochemical oxygen demand (mg/l).
24
- }
25
- }
26
- }
27
- \source{
28
- Bates, D.M. and Watts, D.G. (1988),
29
- \emph{Nonlinear Regression Analysis and Its Applications},
30
- Wiley, Appendix A1.4.
31
-
32
- Originally from Marske (1967), \emph{Biochemical
33
- Oxygen Demand Data Interpretation Using Sum of Squares Surface}
34
- M.Sc. Thesis, University of Wisconsin -- Madison.
35
- }
36
- \examples{
37
- \testonly{options(show.nls.convergence=FALSE)
38
- old <- options(digits = 5)}
39
- require(stats)
40
- # simplest form of fitting a first-order model to these data
41
- fm1 <- nls(demand ~ A*(1-exp(-exp(lrc)*Time)), data = BOD,
42
- start = c(A = 20, lrc = log(.35)))
43
- coef(fm1)
44
- fm1
45
- # using the plinear algorithm
46
- fm2 <- nls(demand ~ (1-exp(-exp(lrc)*Time)), data = BOD,
47
- start = c(lrc = log(.35)), algorithm = "plinear", trace = TRUE)
48
- # using a self-starting model
49
- fm3 <- nls(demand ~ SSasympOrig(Time, A, lrc), data = BOD)
50
- summary(fm3)
51
- \testonly{options(old)}
52
- }
53
- \keyword{datasets}
@@ -1,68 +0,0 @@
1
- % File src/library/datasets/man/ChickWeight.Rd
2
- % Part of the R package, http://www.R-project.org
3
- % Copyright 1995-2011 R Core Development Team
4
- % Distributed under GPL 2 or later
5
-
6
- \name{ChickWeight}
7
- \docType{data}
8
- \alias{ChickWeight}
9
- \title{Weight versus age of chicks on different diets}
10
- \description{
11
- The \code{ChickWeight} data frame has 578 rows and 4 columns from an
12
- experiment on the effect of diet on early growth of chicks.
13
- }
14
- \usage{ChickWeight}
15
- \format{
16
- This object of class \code{c("nfnGroupedData", "nfGroupedData",
17
- "groupedData", "data.frame")} containing the following columns:
18
- \describe{
19
- \item{weight}{
20
- a numeric vector giving the body weight of the chick (gm).
21
- }
22
- \item{Time}{
23
- a numeric vector giving the number of days since birth when
24
- the measurement was made.
25
- }
26
- \item{Chick}{
27
- an ordered factor with levels
28
- \code{18} < \dots < \code{48}
29
- giving a unique identifier for the chick. The ordering of
30
- the levels groups chicks on the same diet together and
31
- orders them according to their final weight (lightest to
32
- heaviest) within diet.
33
- }
34
- \item{Diet}{
35
- a factor with levels 1,\dots,4 indicating which
36
- experimental diet the chick received.
37
- }
38
- }
39
- }
40
- \details{
41
- The body weights of the chicks were measured at birth and every
42
- second day thereafter until day 20. They were also measured on day
43
- 21. There were four groups on chicks on different protein diets.
44
-
45
- This dataset was originally part of package \code{nlme}, and that has
46
- methods (including for \code{[}, \code{as.data.frame}, \code{plot} and
47
- \code{print}) for its grouped-data classes.
48
- }
49
- \source{
50
- Crowder, M. and Hand, D. (1990), \emph{Analysis of Repeated Measures},
51
- Chapman and Hall (example 5.3)
52
-
53
- Hand, D. and Crowder, M. (1996), \emph{Practical Longitudinal Data
54
- Analysis}, Chapman and Hall (table A.2)
55
-
56
- Pinheiro, J. C. and Bates, D. M. (2000) \emph{Mixed-effects Models in
57
- S and S-PLUS}, Springer.
58
- }
59
- \seealso{
60
- \code{\link{SSlogis}} for models fitted to this dataset.
61
- }
62
-
63
- \examples{\donttest{
64
- require(graphics)
65
- coplot(weight ~ Time | Chick, data = ChickWeight,
66
- type = "b", show.given = FALSE)
67
- }}
68
- \keyword{datasets}
data/data/r/man/DNase.Rd DELETED
@@ -1,63 +0,0 @@
1
- % File src/library/datasets/man/DNase.Rd
2
- % Part of the R package, http://www.R-project.org
3
- % Copyright 1995-2011 R Core Development Team
4
- % Distributed under GPL 2 or later
5
-
6
- \name{DNase}
7
- \docType{data}
8
- \alias{DNase}
9
- \title{Elisa assay of DNase}
10
- \description{
11
- The \code{DNase} data frame has 176 rows and 3 columns of data
12
- obtained during development of an ELISA assay for the recombinant
13
- protein DNase in rat serum.
14
- }
15
- \usage{DNase}
16
- \format{
17
- This object of class \code{c("nfnGroupedData", "nfGroupedData",
18
- "groupedData", "data.frame")} containing the following columns:
19
- \describe{
20
- \item{Run}{
21
- an ordered factor with levels \code{10} < \dots < \code{3}
22
- indicating the assay run.
23
- }
24
- \item{conc}{
25
- a numeric vector giving the known concentration of the
26
- protein.
27
- }
28
- \item{density}{
29
- a numeric vector giving the measured optical density
30
- (dimensionless) in the assay. Duplicate optical density
31
- measurements were obtained.
32
- }
33
- }
34
- }
35
- \details{
36
- This dataset was originally part of package \code{nlme}, and that has
37
- methods (including for \code{[}, \code{as.data.frame}, \code{plot} and
38
- \code{print}) for its grouped-data classes.
39
- }
40
- \source{
41
- Davidian, M. and Giltinan, D. M. (1995) \emph{Nonlinear Models for
42
- Repeated Measurement Data}, Chapman & Hall (section 5.2.4, p. 134)
43
-
44
- Pinheiro, J. C. and Bates, D. M. (2000) \emph{Mixed-effects Models in
45
- S and S-PLUS}, Springer.
46
- }
47
- \examples{
48
- require(stats); require(graphics)
49
- \testonly{options(show.nls.convergence=FALSE)}
50
- coplot(density ~ conc | Run, data = DNase,
51
- show.given = FALSE, type = "b")
52
- coplot(density ~ log(conc) | Run, data = DNase,
53
- show.given = FALSE, type = "b")
54
- ## fit a representative run
55
- fm1 <- nls(density ~ SSlogis( log(conc), Asym, xmid, scal ),
56
- data = DNase, subset = Run == 1)
57
- ## compare with a four-parameter logistic
58
- fm2 <- nls(density ~ SSfpl( log(conc), A, B, xmid, scal ),
59
- data = DNase, subset = Run == 1)
60
- summary(fm2)
61
- anova(fm1, fm2)
62
- }
63
- \keyword{datasets}
@@ -1,28 +0,0 @@
1
- % File src/library/datasets/man/EuStockMarkets.Rd
2
- % Part of the R package, http://www.R-project.org
3
- % Copyright 1995-2007 R Core Development Team
4
- % Distributed under GPL 2 or later
5
-
6
- \name{EuStockMarkets}
7
- \docType{data}
8
- \alias{EuStockMarkets}
9
- \title{
10
- Daily Closing Prices of Major European Stock Indices, 1991--1998
11
- }
12
- \description{
13
- Contains the daily closing prices of major European stock indices:
14
- Germany DAX (Ibis), Switzerland SMI, France CAC, and UK FTSE. The
15
- data are sampled in business time, i.e., weekends and holidays are
16
- omitted.
17
- }
18
- \usage{
19
- EuStockMarkets
20
- }
21
- \format{
22
- A multivariate time series with 1860 observations on 4 variables.
23
- The object is of class \code{"mts"}.
24
- }
25
- \source{
26
- The data were kindly provided by Erste Bank AG, Vienna, Austria.
27
- }
28
- \keyword{datasets}
@@ -1,44 +0,0 @@
1
- % File src/library/datasets/man/Formaldehyde.Rd
2
- % Part of the R package, http://www.R-project.org
3
- % Copyright 1995-2009 R Core Development Team
4
- % Distributed under GPL 2 or later
5
-
6
- \name{Formaldehyde}
7
- \docType{data}
8
- \alias{Formaldehyde}
9
- \title{Determination of Formaldehyde}
10
- \description{
11
- These data are from a chemical experiment to prepare a standard curve
12
- for the determination of formaldehyde by the addition of chromatropic
13
- acid and concentrated sulphuric acid and the reading of the resulting
14
- purple color on a spectrophotometer.
15
- }
16
- \usage{Formaldehyde}
17
- \format{
18
- A data frame with 6 observations on 2 variables.
19
- \tabular{rlll}{
20
- [,1] \tab carb\tab numeric \tab Carbohydrate (ml) \cr
21
- [,2] \tab optden \tab numeric \tab Optical Density
22
- }
23
- }
24
- \source{
25
- Bennett, N. A. and N. L. Franklin (1954)
26
- \emph{Statistical Analysis in Chemistry and the Chemical Industry}.
27
- New York: Wiley.
28
- }
29
- \references{
30
- McNeil, D. R. (1977) \emph{Interactive Data Analysis.}
31
- New York: Wiley.
32
- }
33
- \examples{
34
- require(stats); require(graphics)
35
- plot(optden ~ carb, data = Formaldehyde,
36
- xlab = "Carbohydrate (ml)", ylab = "Optical Density",
37
- main = "Formaldehyde data", col = 4, las = 1)
38
- abline(fm1 <- lm(optden ~ carb, data = Formaldehyde))
39
- summary(fm1)
40
- opar <- par(mfrow = c(2,2), oma = c(0, 0, 1.1, 0))
41
- plot(fm1)
42
- par(opar)
43
- }
44
- \keyword{datasets}
@@ -1,77 +0,0 @@
1
- % File src/library/datasets/man/HairEyeColor.Rd
2
- % Part of the R package, http://www.R-project.org
3
- % Copyright 1995-2007 R Core Development Team
4
- % Distributed under GPL 2 or later
5
-
6
- \name{HairEyeColor}
7
- \docType{data}
8
- \alias{HairEyeColor}
9
- \title{Hair and Eye Color of Statistics Students}
10
- \description{
11
- Distribution of hair and eye color and sex in 592 statistics students.
12
- }
13
- \usage{HairEyeColor}
14
- \format{
15
- A 3-dimensional array resulting from cross-tabulating 592 observations
16
- on 3 variables. The variables and their levels are as follows:
17
-
18
- \tabular{rll}{
19
- No \tab Name \tab Levels \cr
20
- 1 \tab Hair \tab Black, Brown, Red, Blond \cr
21
- 2 \tab Eye \tab Brown, Blue, Hazel, Green \cr
22
- 3 \tab Sex \tab Male, Female
23
- }
24
- }
25
- \details{
26
- The Hair \eqn{\times}{x} Eye table comes rom a survey of students at
27
- the University of Delaware reported by Snee (1974). The split by
28
- \code{Sex} was added by Friendly (1992a) for didactic purposes.
29
-
30
- This data set is useful for illustrating various techniques for the
31
- analysis of contingency tables, such as the standard chi-squared test
32
- or, more generally, log-linear modelling, and graphical methods such
33
- as mosaic plots, sieve diagrams or association plots.
34
- }
35
- \source{
36
- \url{http://euclid.psych.yorku.ca/ftp/sas/vcd/catdata/haireye.sas}
37
-
38
- Snee (1974) gives the two-way table aggregated over \code{Sex}. The
39
- Sex split of the \sQuote{Brown hair, Brown eye} cell was changed in
40
- \R 2.6.0 to agree with that used by Friendly (2000).
41
- }
42
- \references{
43
- Snee, R. D. (1974)
44
- Graphical display of two-way contingency tables.
45
- \emph{The American Statistician}, \bold{28}, 9--12.
46
-
47
- Friendly, M. (1992a)
48
- Graphical methods for categorical data.
49
- \emph{SAS User Group International Conference Proceedings}, \bold{17},
50
- 190--200.
51
- \url{http://www.math.yorku.ca/SCS/sugi/sugi17-paper.html}
52
-
53
- Friendly, M. (1992b)
54
- Mosaic displays for loglinear models.
55
- \emph{Proceedings of the Statistical Graphics Section},
56
- American Statistical Association, pp. 61--68.
57
- \url{http://www.math.yorku.ca/SCS/Papers/asa92.html}
58
-
59
- Friendly, M. (2000)
60
- \emph{Visualizing Categorical Data.}
61
- SAS Institute, ISBN 1-58025-660-0.
62
- }
63
- \seealso{
64
- \code{\link{chisq.test}},
65
- \code{\link{loglin}},
66
- \code{\link{mosaicplot}}
67
- }
68
- \examples{
69
- require(graphics)
70
- ## Full mosaic
71
- mosaicplot(HairEyeColor)
72
- ## Aggregate over sex (as in Snee's original data)
73
- x <- apply(HairEyeColor, c(1, 2), sum)
74
- x
75
- mosaicplot(x, main = "Relation between hair and eye color")
76
- }
77
- \keyword{datasets}
@@ -1,25 +0,0 @@
1
- % File src/library/datasets/man/Harman23.cor.Rd
2
- % Part of the R package, http://www.R-project.org
3
- % Copyright 1995-2007 R Core Development Team
4
- % Distributed under GPL 2 or later
5
-
6
- \name{Harman23.cor}
7
- \docType{data}
8
- \alias{Harman23.cor}
9
- \title{Harman Example 2.3}
10
- \description{
11
- A correlation matrix of eight physical measurements on 305 girls between
12
- ages seven and seventeen.
13
- }
14
- \usage{Harman23.cor}
15
- \source{
16
- Harman, H. H. (1976)
17
- \emph{Modern Factor Analysis}, Third Edition Revised,
18
- University of Chicago Press, Table 2.3.
19
- }
20
- \examples{
21
- require(stats)
22
- (Harman23.FA <- factanal(factors = 1, covmat = Harman23.cor))
23
- for(factors in 2:4) print(update(Harman23.FA, factors = factors))
24
- }
25
- \keyword{datasets}
@@ -1,28 +0,0 @@
1
- % File src/library/datasets/man/Harman74.cor.Rd
2
- % Part of the R package, http://www.R-project.org
3
- % Copyright 1995-2007 R Core Development Team
4
- % Distributed under GPL 2 or later
5
-
6
- \name{Harman74.cor}
7
- \docType{data}
8
- \alias{Harman74.cor}
9
- \title{Harman Example 7.4}
10
- \description{
11
- A correlation matrix of 24 psychological tests given to 145 seventh and
12
- eight-grade children in a Chicago suburb by Holzinger and Swineford.
13
- }
14
- \usage{Harman74.cor}
15
- \source{
16
- Harman, H. H. (1976)
17
- \emph{Modern Factor Analysis}, Third Edition Revised,
18
- University of Chicago Press, Table 7.4.
19
- }
20
- \examples{
21
- require(stats)
22
- (Harman74.FA <- factanal(factors = 1, covmat = Harman74.cor))
23
- for(factors in 2:5) print(update(Harman74.FA, factors = factors))
24
- Harman74.FA <- factanal(factors = 5, covmat = Harman74.cor,
25
- rotation="promax")
26
- print(Harman74.FA$loadings, sort = TRUE)
27
- }
28
- \keyword{datasets}