This class of objects is returned by functions that perform permutation tests. Objects of class "permutationTest" are lists that contain information about the null and alternative hypotheses, the estimated distribution parameters, the test statistic and the p-value. They also contain the permutation distribution of the statistic (or a sample of the permutation distribution).

Details

Objects of S3 class "permutationTest" are returned by any of the EnvStats functions that perform permutation tests. Currently, these are: oneSamplePermutationTest,
twoSamplePermutationTestLocation, and twoSamplePermutationTestProportion.

Methods

Generic functions that have methods for objects of class "permutationTest" include:
print, plot.

Value

A legitimate list of class "permutationTest" includes the components listed in the help file for htest.object. In addition, the following components must be included in a legitimate list of class "permutationTest":

Required Components
The following components must be included in a legitimate list of class "permutationTest".

stat.dist

numeric vector containing values of the statistic for the permutation distribution. When exact=FALSE, the vector is comprised of values sampled from the full permutation distribution.

exact

logical scalar indicating whether the exact permutation distribution was used for the test (exact=TRUE), or if instead the permutation distribution was sampled (exact=FALSE).

Optional Components
The following component may optionally be included in an object of of class "permutationTest":

seed

integer or vector of integers indicating the seed that was used for sampling the permutation distribution. This component is present only if exact=FALSE.

prob.stat.dist

numeric vector containing the probabilities associated with each element of the component stat.dist. This component is only returned by the function twoSamplePermutationTestProportion.

Note

Since objects of class "permutationTest" are lists, you may extract their components with the $ and [[ operators.

Author

Steven P. Millard (EnvStats@ProbStatInfo.com)

Examples

  # Create an object of class "permutationTest", then print it and plot it. 
  #------------------------------------------------------------------------

  set.seed(23) 

  dat <- rlogis(10, location = 7, scale = 2) 

  permutationTest.obj <- oneSamplePermutationTest(dat, mu = 5, 
    alternative = "greater", exact = TRUE) 

  mode(permutationTest.obj) 
#> [1] "list"
  #[1] "list" 

  class(permutationTest.obj) 
#> [1] "permutationTest"
  #[1] "permutationTest" 

  names(permutationTest.obj) 
#>  [1] "statistic"         "parameters"        "p.value"          
#>  [4] "estimate"          "null.value"        "alternative"      
#>  [7] "method"            "estimation.method" "sample.size"      
#> [10] "data.name"         "bad.obs"           "stat.dist"        
#> [13] "exact"            
  # [1] "statistic"         "parameters"        "p.value"          
  # [4] "estimate"          "null.value"        "alternative"      
  # [7] "method"            "estimation.method" "sample.size"      
  #[10] "data.name"         "bad.obs"           "stat.dist"        
  #[13] "exact" 

  #==========

  # Print the results of the test 
  #------------------------------
  permutationTest.obj 
#> $statistic
#> Sum(x - 5) 
#>   49.77294 
#> 
#> $parameters
#> NULL
#> 
#> $p.value
#> [1] 0.001953125
#> 
#> $estimate
#>     Mean 
#> 9.977294 
#> 
#> $null.value
#> Mean (Median) 
#>             5 
#> 
#> $alternative
#> [1] "greater"
#> 
#> $method
#> [1] "One-Sample Permutation Test\n                                 (Exact)"
#> 
#> $estimation.method
#> NULL
#> 
#> $sample.size
#>  n 
#> 10 
#> 
#> $data.name
#> [1] "dat"
#> 
#> $bad.obs
#> [1] 0
#> 
#> $stat.dist
#>    [1] -50.76433285 -45.52894718 -49.77294023 -44.53755456 -49.56281095
#>    [6] -44.32742528 -48.57141833 -43.33603266 -43.16871044 -37.93332477
#>   [11] -42.17731782 -36.94193215 -41.96718854 -36.73180287 -40.97579592
#>   [16] -35.74041025 -40.71385853 -35.47847286 -39.72246591 -34.48708024
#>   [21] -39.51233663 -34.27695096 -38.52094401 -33.28555834 -33.11823612
#>   [26] -27.88285045 -32.12684350 -26.89145783 -31.91671422 -26.68132855
#>   [31] -30.92532160 -25.68993593 -47.99440683 -42.75902117 -47.00301421
#>   [36] -41.76762855 -46.79288494 -41.55749927 -45.80149231 -40.56610665
#>   [41] -40.39878442 -35.16339876 -39.40739180 -34.17200614 -39.19726253
#>   [46] -33.96187686 -38.20586990 -32.97048424 -37.94393251 -32.70854685
#>   [51] -36.95253989 -31.71715423 -36.74241062 -31.50702495 -35.75101800
#>   [56] -30.51563233 -30.34831010 -25.11292444 -29.35691748 -24.12153182
#>   [61] -29.14678821 -23.91140254 -28.15539559 -22.92000992 -33.66622188
#>   [66] -28.43083622 -32.67482926 -27.43944360 -32.46469999 -27.22931432
#>   [71] -31.47330737 -26.23792170 -26.07059947 -20.83521381 -25.07920685
#>   [76] -19.84382119 -24.86907758 -19.63369191 -23.87768495 -18.64229929
#>   [81] -23.61574757 -18.38036190 -22.62435494 -17.38896928 -22.41422567
#>   [86] -17.17884000 -21.42283305 -16.18744738 -16.02012516 -10.78473949
#>   [91] -15.02873253  -9.79334687 -14.81860326  -9.58321759 -13.82721064
#>   [96]  -8.59182497 -30.89629587 -25.66091020 -29.90490325 -24.66951758
#>  [101] -29.69477397 -24.45938830 -28.70338135 -23.46799568 -23.30067346
#>  [106] -18.06528779 -22.30928084 -17.07389517 -22.09915156 -16.86376589
#>  [111] -21.10775894 -15.87237327 -20.84582155 -15.61043588 -19.85442893
#>  [116] -14.61904326 -19.64429965 -14.40891398 -18.65290703 -13.41752136
#>  [121] -13.25019914  -8.01481347 -12.25880652  -7.02342085 -12.04867724
#>  [126]  -6.81329157 -11.05728462  -5.82189895 -31.56214932 -26.32676365
#>  [131] -30.57075670 -25.33537103 -30.36062742 -25.12524175 -29.36923480
#>  [136] -24.13384913 -23.96652691 -18.73114124 -22.97513429 -17.73974862
#>  [141] -22.76500501 -17.52961934 -21.77361239 -16.53822672 -21.51167500
#>  [146] -16.27628933 -20.52028238 -15.28489671 -20.31015310 -15.07476743
#>  [151] -19.31876048 -14.08337481 -13.91605259  -8.68066692 -12.92465997
#>  [156]  -7.68927430 -12.71453069  -7.47914502 -11.72313807  -6.48775240
#>  [161] -28.79222330 -23.55683763 -27.80083068 -22.56544501 -27.59070140
#>  [166] -22.35531574 -26.59930878 -21.36392312 -21.19660089 -15.96121522
#>  [171] -20.20520827 -14.96982260 -19.99507899 -14.75969333 -19.00368637
#>  [176] -13.76830071 -18.74174898 -13.50636332 -17.75035636 -12.51497070
#>  [181] -17.54022708 -12.30484142 -16.54883446 -11.31344880 -11.14612657
#>  [186]  -5.91074091 -10.15473395  -4.91934829  -9.94460467  -4.70921901
#>  [191]  -8.95321205  -3.71782639 -14.46403835  -9.22865269 -13.47264573
#>  [196]  -8.23726006 -13.26251645  -8.02713079 -12.27112383  -7.03573817
#>  [201]  -6.86841594  -1.63303028  -5.87702332  -0.64163765  -5.66689404
#>  [206]  -0.43150838  -4.67550142   0.55988424  -4.41356403   0.82182163
#>  [211]  -3.42217141   1.81321425  -3.21204214   2.02334353  -2.22064951
#>  [216]   3.01473615   3.18205838   8.41744404   4.17345100   9.40883666
#>  [221]   4.38358027   9.61896594   5.37497290  10.61035856 -11.69411234
#>  [226]  -6.45872667 -10.70271972  -5.46733405 -10.49259044  -5.25720477
#>  [231]  -9.50119782  -4.26581215  -4.09848993   1.13689574  -3.10709731
#>  [236]   2.12828836  -2.89696803   2.33841764  -1.90557541   3.32981026
#>  [241]  -1.64363802   3.59174765  -0.65224540   4.58314027  -0.44211612
#>  [246]   4.79326955   0.54927650   5.78466217   5.95198439  11.18737006
#>  [251]   6.94337701  12.17876268   7.15350629  12.38889196   8.14489891
#>  [256]  13.38028458 -40.11586786 -34.88048219 -39.12447524 -33.88908957
#>  [261] -38.91434596 -33.67896029 -37.92295334 -32.68756767 -32.52024545
#>  [266] -27.28485978 -31.52885283 -26.29346716 -31.31872355 -26.08333788
#>  [271] -30.32733093 -25.09194526 -30.06539354 -24.83000787 -29.07400092
#>  [276] -23.83861525 -28.86387164 -23.62848597 -27.87247902 -22.63709335
#>  [281] -22.46977113 -17.23438546 -21.47837851 -16.24299284 -21.26824923
#>  [286] -16.03286356 -20.27685661 -15.04147094 -37.34594185 -32.11055618
#>  [291] -36.35454923 -31.11916356 -36.14441995 -30.90903428 -35.15302733
#>  [296] -29.91764166 -29.75031944 -24.51493377 -28.75892682 -23.52354115
#>  [301] -28.54879754 -23.31341187 -27.55740492 -22.32201925 -27.29546753
#>  [306] -22.06008186 -26.30407491 -21.06868924 -26.09394563 -20.85855996
#>  [311] -25.10255301 -19.86716734 -19.69984512 -14.46445945 -18.70845250
#>  [316] -13.47306683 -18.49832322 -13.26293755 -17.50693060 -12.27154493
#>  [321] -23.01775690 -17.78237123 -22.02636428 -16.79097861 -21.81623500
#>  [326] -16.58084933 -20.82484238 -15.58945671 -15.42213449 -10.18674882
#>  [331] -14.43074187  -9.19535620 -14.22061259  -8.98522692 -13.22921997
#>  [336]  -7.99383430 -12.96728258  -7.73189691 -11.97588996  -6.74050429
#>  [341] -11.76576068  -6.53037501 -10.77436806  -5.53898239  -5.37166017
#>  [346]  -0.13627450  -4.38026755   0.85511812  -4.17013827   1.06524740
#>  [351]  -3.17874565   2.05664002 -20.24783088 -15.01244522 -19.25643826
#>  [356] -14.02105260 -19.04630899 -13.81092332 -18.05491636 -12.81953070
#>  [361] -12.65220847  -7.41682281 -11.66081585  -6.42543019 -11.45068658
#>  [366]  -6.21530091 -10.45929395  -5.22390829 -10.19735656  -4.96197090
#>  [371]  -9.20596394  -3.97057828  -8.99583467  -3.76044900  -8.00444205
#>  [376]  -2.76905638  -2.60173415   2.63365151  -1.61034153   3.62504413
#>  [381]  -1.40021226   3.83517341  -0.40881964   4.82656603 -20.91368433
#>  [386] -15.67829866 -19.92229171 -14.68690604 -19.71216243 -14.47677676
#>  [391] -18.72076981 -13.48538414 -13.31806192  -8.08267625 -12.32666930
#>  [396]  -7.09128363 -12.11654002  -6.88115435 -11.12514740  -5.88976173
#>  [401] -10.86321001  -5.62782434  -9.87181739  -4.63643172  -9.66168811
#>  [406]  -4.42630244  -8.67029549  -3.43490982  -3.26758760   1.96779807
#>  [411]  -2.27619498   2.95919069  -2.06606570   3.16931997  -1.07467308
#>  [416]   4.16071259 -18.14375832 -12.90837265 -17.15236570 -11.91698003
#>  [421] -16.94223642 -11.70685075 -15.95084380 -10.71545813 -10.54813591
#>  [426]  -5.31275024  -9.55674329  -4.32135762  -9.34661401  -4.11122834
#>  [431]  -8.35522139  -3.11983572  -8.09328400  -2.85789833  -7.10189138
#>  [436]  -1.86650571  -6.89176210  -1.65637643  -5.90036948  -0.66498381
#>  [441]  -0.49766159   4.73772408   0.49373103   5.72911670   0.70386031
#>  [446]   5.93924598   1.69525293   6.93063860  -3.81557337   1.41981230
#>  [451]  -2.82418075   2.41120492  -2.61405147   2.62133420  -1.62265885
#>  [456]   3.61272682   3.78004904   9.01543471   4.77144166  10.00682733
#>  [461]   4.98157094  10.21695661   5.97296356  11.20834923   6.23490095
#>  [466]  11.47028662   7.22629357  12.46167924   7.43642285  12.67180852
#>  [471]   8.42781547  13.66320114  13.83052336  19.06590903  14.82191598
#>  [476]  20.05730165  15.03204526  20.26743093  16.02343788  21.25882355
#>  [481]  -1.04564735   4.18973832  -0.05425473   5.18113094   0.15587455
#>  [486]   5.39126021   1.14726717   6.38265283   6.54997506  11.78536073
#>  [491]   7.54136768  12.77675335   7.75149696  12.98688262   8.74288958
#>  [496]  13.97827524   9.00482697  14.24021263   9.99621959  15.23160525
#>  [501]  10.20634887  15.44173453  11.19774149  16.43312715  16.60044938
#>  [506]  21.83583504  17.59184200  22.82722767  17.80197128  23.03735694
#>  [511]  18.79336390  24.02874956 -24.02874956 -18.79336390 -23.03735694
#>  [516] -17.80197128 -22.82722767 -17.59184200 -21.83583504 -16.60044938
#>  [521] -16.43312715 -11.19774149 -15.44173453 -10.20634887 -15.23160525
#>  [526]  -9.99621959 -14.24021263  -9.00482697 -13.97827524  -8.74288958
#>  [531] -12.98688262  -7.75149696 -12.77675335  -7.54136768 -11.78536073
#>  [536]  -6.54997506  -6.38265283  -1.14726717  -5.39126021  -0.15587455
#>  [541]  -5.18113094   0.05425473  -4.18973832   1.04564735 -21.25882355
#>  [546] -16.02343788 -20.26743093 -15.03204526 -20.05730165 -14.82191598
#>  [551] -19.06590903 -13.83052336 -13.66320114  -8.42781547 -12.67180852
#>  [556]  -7.43642285 -12.46167924  -7.22629357 -11.47028662  -6.23490095
#>  [561] -11.20834923  -5.97296356 -10.21695661  -4.98157094 -10.00682733
#>  [566]  -4.77144166  -9.01543471  -3.78004904  -3.61272682   1.62265885
#>  [571]  -2.62133420   2.61405147  -2.41120492   2.82418075  -1.41981230
#>  [576]   3.81557337  -6.93063860  -1.69525293  -5.93924598  -0.70386031
#>  [581]  -5.72911670  -0.49373103  -4.73772408   0.49766159   0.66498381
#>  [586]   5.90036948   1.65637643   6.89176210   1.86650571   7.10189138
#>  [591]   2.85789833   8.09328400   3.11983572   8.35522139   4.11122834
#>  [596]   9.34661401   4.32135762   9.55674329   5.31275024  10.54813591
#>  [601]  10.71545813  15.95084380  11.70685075  16.94223642  11.91698003
#>  [606]  17.15236570  12.90837265  18.14375832  -4.16071259   1.07467308
#>  [611]  -3.16931997   2.06606570  -2.95919069   2.27619498  -1.96779807
#>  [616]   3.26758760   3.43490982   8.67029549   4.42630244   9.66168811
#>  [621]   4.63643172   9.87181739   5.62782434  10.86321001   5.88976173
#>  [626]  11.12514740   6.88115435  12.11654002   7.09128363  12.32666930
#>  [631]   8.08267625  13.31806192  13.48538414  18.72076981  14.47677676
#>  [636]  19.71216243  14.68690604  19.92229171  15.67829866  20.91368433
#>  [641]  -4.82656603   0.40881964  -3.83517341   1.40021226  -3.62504413
#>  [646]   1.61034153  -2.63365151   2.60173415   2.76905638   8.00444205
#>  [651]   3.76044900   8.99583467   3.97057828   9.20596394   4.96197090
#>  [656]  10.19735656   5.22390829  10.45929395   6.21530091  11.45068658
#>  [661]   6.42543019  11.66081585   7.41682281  12.65220847  12.81953070
#>  [666]  18.05491636  13.81092332  19.04630899  14.02105260  19.25643826
#>  [671]  15.01244522  20.24783088  -2.05664002   3.17874565  -1.06524740
#>  [676]   4.17013827  -0.85511812   4.38026755   0.13627450   5.37166017
#>  [681]   5.53898239  10.77436806   6.53037501  11.76576068   6.74050429
#>  [686]  11.97588996   7.73189691  12.96728258   7.99383430  13.22921997
#>  [691]   8.98522692  14.22061259   9.19535620  14.43074187  10.18674882
#>  [696]  15.42213449  15.58945671  20.82484238  16.58084933  21.81623500
#>  [701]  16.79097861  22.02636428  17.78237123  23.01775690  12.27154493
#>  [706]  17.50693060  13.26293755  18.49832322  13.47306683  18.70845250
#>  [711]  14.46445945  19.69984512  19.86716734  25.10255301  20.85855996
#>  [716]  26.09394563  21.06868924  26.30407491  22.06008186  27.29546753
#>  [721]  22.32201925  27.55740492  23.31341187  28.54879754  23.52354115
#>  [726]  28.75892682  24.51493377  29.75031944  29.91764166  35.15302733
#>  [731]  30.90903428  36.14441995  31.11916356  36.35454923  32.11055618
#>  [736]  37.34594185  15.04147094  20.27685661  16.03286356  21.26824923
#>  [741]  16.24299284  21.47837851  17.23438546  22.46977113  22.63709335
#>  [746]  27.87247902  23.62848597  28.86387164  23.83861525  29.07400092
#>  [751]  24.83000787  30.06539354  25.09194526  30.32733093  26.08333788
#>  [756]  31.31872355  26.29346716  31.52885283  27.28485978  32.52024545
#>  [761]  32.68756767  37.92295334  33.67896029  38.91434596  33.88908957
#>  [766]  39.12447524  34.88048219  40.11586786 -13.38028458  -8.14489891
#>  [771] -12.38889196  -7.15350629 -12.17876268  -6.94337701 -11.18737006
#>  [776]  -5.95198439  -5.78466217  -0.54927650  -4.79326955   0.44211612
#>  [781]  -4.58314027   0.65224540  -3.59174765   1.64363802  -3.32981026
#>  [786]   1.90557541  -2.33841764   2.89696803  -2.12828836   3.10709731
#>  [791]  -1.13689574   4.09848993   4.26581215   9.50119782   5.25720477
#>  [796]  10.49259044   5.46733405  10.70271972   6.45872667  11.69411234
#>  [801] -10.61035856  -5.37497290  -9.61896594  -4.38358027  -9.40883666
#>  [806]  -4.17345100  -8.41744404  -3.18205838  -3.01473615   2.22064951
#>  [811]  -2.02334353   3.21204214  -1.81321425   3.42217141  -0.82182163
#>  [816]   4.41356403  -0.55988424   4.67550142   0.43150838   5.66689404
#>  [821]   0.64163765   5.87702332   1.63303028   6.86841594   7.03573817
#>  [826]  12.27112383   8.02713079  13.26251645   8.23726006  13.47264573
#>  [831]   9.22865269  14.46403835   3.71782639   8.95321205   4.70921901
#>  [836]   9.94460467   4.91934829  10.15473395   5.91074091  11.14612657
#>  [841]  11.31344880  16.54883446  12.30484142  17.54022708  12.51497070
#>  [846]  17.75035636  13.50636332  18.74174898  13.76830071  19.00368637
#>  [851]  14.75969333  19.99507899  14.96982260  20.20520827  15.96121522
#>  [856]  21.19660089  21.36392312  26.59930878  22.35531574  27.59070140
#>  [861]  22.56544501  27.80083068  23.55683763  28.79222330   6.48775240
#>  [866]  11.72313807   7.47914502  12.71453069   7.68927430  12.92465997
#>  [871]   8.68066692  13.91605259  14.08337481  19.31876048  15.07476743
#>  [876]  20.31015310  15.28489671  20.52028238  16.27628933  21.51167500
#>  [881]  16.53822672  21.77361239  17.52961934  22.76500501  17.73974862
#>  [886]  22.97513429  18.73114124  23.96652691  24.13384913  29.36923480
#>  [891]  25.12524175  30.36062742  25.33537103  30.57075670  26.32676365
#>  [896]  31.56214932   5.82189895  11.05728462   6.81329157  12.04867724
#>  [901]   7.02342085  12.25880652   8.01481347  13.25019914  13.41752136
#>  [906]  18.65290703  14.40891398  19.64429965  14.61904326  19.85442893
#>  [911]  15.61043588  20.84582155  15.87237327  21.10775894  16.86376589
#>  [916]  22.09915156  17.07389517  22.30928084  18.06528779  23.30067346
#>  [921]  23.46799568  28.70338135  24.45938830  29.69477397  24.66951758
#>  [926]  29.90490325  25.66091020  30.89629587   8.59182497  13.82721064
#>  [931]   9.58321759  14.81860326   9.79334687  15.02873253  10.78473949
#>  [936]  16.02012516  16.18744738  21.42283305  17.17884000  22.41422567
#>  [941]  17.38896928  22.62435494  18.38036190  23.61574757  18.64229929
#>  [946]  23.87768495  19.63369191  24.86907758  19.84382119  25.07920685
#>  [951]  20.83521381  26.07059947  26.23792170  31.47330737  27.22931432
#>  [956]  32.46469999  27.43944360  32.67482926  28.43083622  33.66622188
#>  [961]  22.92000992  28.15539559  23.91140254  29.14678821  24.12153182
#>  [966]  29.35691748  25.11292444  30.34831010  30.51563233  35.75101800
#>  [971]  31.50702495  36.74241062  31.71715423  36.95253989  32.70854685
#>  [976]  37.94393251  32.97048424  38.20586990  33.96187686  39.19726253
#>  [981]  34.17200614  39.40739180  35.16339876  40.39878442  40.56610665
#>  [986]  45.80149231  41.55749927  46.79288494  41.76762855  47.00301421
#>  [991]  42.75902117  47.99440683  25.68993593  30.92532160  26.68132855
#>  [996]  31.91671422  26.89145783  32.12684350  27.88285045  33.11823612
#> [1001]  33.28555834  38.52094401  34.27695096  39.51233663  34.48708024
#> [1006]  39.72246591  35.47847286  40.71385853  35.74041025  40.97579592
#> [1011]  36.73180287  41.96718854  36.94193215  42.17731782  37.93332477
#> [1016]  43.16871044  43.33603266  48.57141833  44.32742528  49.56281095
#> [1021]  44.53755456  49.77294023  45.52894718  50.76433285
#> 
#> $exact
#> [1] TRUE
#> 
#> attr(,"class")
#> [1] "permutationTest"

  #Results of Hypothesis Test
  #--------------------------
  #
  #Null Hypothesis:                 Mean (Median) = 5
  #
  #Alternative Hypothesis:          True Mean (Median) is greater than 5
  #
  #Test Name:                       One-Sample Permutation Test
  #                                 (Exact)
  #
  #Estimated Parameter(s):          Mean = 9.977294
  #
  #Data:                            dat
  #
  #Sample Size:                     10
  #
  #Test Statistic:                  Sum(x - 5) = 49.77294
  #
  #P-value:                         0.001953125

  #==========

  # Plot the results of the test 
  #-----------------------------
  dev.new()
  plot(permutationTest.obj)

  #==========

  # Extract the test statistic
  #---------------------------

  permutationTest.obj$statistic
#> Sum(x - 5) 
#>   49.77294 
  #Sum(x - 5) 
  #  49.77294

  #==========

  # Clean up
  #---------
  rm(permutationTest.obj)
  graphics.off()