Code

WIP: Rv restructure#1

Code

Draft

RivkadeVries wants to merge 149 commits intorv_test_functionsroqua/ShadowCAT:rv_test_functionsfrom rv_restructureroqua/ShadowCAT:rv_restructureCopy head branch name to clipboard

+8,024-7,766

Commits

Commits on Nov 30, 2015

• createConstraints() restructured, n added to stop argument in tests

  RivkadeVries

  committed
  2a086f8

  Copy full SHA for 2a086f8

• stop_test() renamed and restructured

  RivkadeVries

  committed
  bf30ba1

  Copy full SHA for bf30ba1

• File name test_must_stop adapted

  RivkadeVries

  committed
  f9a9af6

  Copy full SHA for f9a9af6

Commits on Dec 1, 2015

• prob restructured and renamed into probabilities_and_likelihoods

  RivkadeVries

  committed
  d4f6231

  Copy full SHA for d4f6231

Commits on Dec 2, 2015

• get_ll_in_nlm_format() removed

  RivkadeVries

  committed
  fb85c16

  Copy full SHA for fb85c16

• get_fisher_information restructured

  RivkadeVries

  committed
  0da37a5

  Copy full SHA for 0da37a5

Commits on Dec 3, 2015

• Some bugs fixed

  RivkadeVries

  committed
  5b132e4

  Copy full SHA for 5b132e4

• Bugs fixed

  RivkadeVries

  committed
  7841373

  Copy full SHA for 7841373

• estimate_latent_trait restructured

  RivkadeVries

  committed
  d49b6d8

  Copy full SHA for d49b6d8

• test_must_stop simplified

  RivkadeVries

  committed
  5d78600

  Copy full SHA for 5d78600

• get_item_index_max_information restructured

  RivkadeVries

  committed
  f942610

  Copy full SHA for f942610

Commits on Dec 6, 2015

• get_item_index_max_information_constrained(), get_item_information(), and get_posterior_expected_kl_information() restructured

  RivkadeVries

  committed
  2d2317d

  Copy full SHA for 2d2317d

• test_must_stop() simplified

  RivkadeVries

  committed
  1eba517

  Copy full SHA for 1eba517

Commits on Dec 7, 2015

• get_best_item(), get_next_item(), ShadowCAT(), and simulate_answer() restructured

  RivkadeVries

  committed
  2d495f9

  Copy full SHA for 2d495f9

Commits on Dec 8, 2015

• Documentation ShadowCAT adapted, initial estimate and variance in test function as arguments

  RivkadeVries

  committed
  7eab1c5

  Copy full SHA for 7eab1c5

• Prior <- NULL removed from probabilities_and_likelihoods()

  RivkadeVries

  committed
  ab8dd73

  Copy full SHA for ab8dd73

• Prior, eta, guessing arguments moved to different place

  RivkadeVries

  committed
  d5c4b63

  Copy full SHA for d5c4b63

• Documentation: prior does not need to be defined anymore when not required for computations

  RivkadeVries

  committed
  d696fd3

  Copy full SHA for d696fd3

• Some documentation changed, initTest() and initPerson() removed, output constraints_correct_format simplified

  RivkadeVries

  committed
  b29d6ca

  Copy full SHA for b29d6ca

• file constraints_correct_format renamed into constraints_lp_format

  RivkadeVries

  committed
  86e4aff

  Copy full SHA for 86e4aff

• subset.ShadowCAT.items removed, file names ShadowCAT in lowercase

  RivkadeVries

  committed
  e1f7a6c

  Copy full SHA for e1f7a6c

• simulate functions moved to testthat folder

  RivkadeVries

  committed
  d19e646

  Copy full SHA for d19e646

• Documentation and wording improved in simulate functions

  RivkadeVries

  committed
  ce766a2

  Copy full SHA for ce766a2

• simulate_answer() simplified

  RivkadeVries

  committed
  a095656

  Copy full SHA for a095656

• Uppercase X into lowercase x

  RivkadeVries

  committed
  6ee5ca0

  Copy full SHA for 6ee5ca0

Commits on Dec 9, 2015

• In test probabilities_and_likelihoods changed theta values in non zero values

  RivkadeVries

  committed
  f45f3a1

  Copy full SHA for f45f3a1

• In tests get_fisher_information changed theta values into nonzero values

  RivkadeVries

  committed
  a41185f

  Copy full SHA for a41185f

• Unused test files removed

  RivkadeVries

  committed
  ad6089c

  Copy full SHA for ad6089c

• Test functions in estimate_latend_trait() with EAP estimate un-commented

  RivkadeVries

  committed
  1b7e922

  Copy full SHA for 1b7e922

• Tests with EAP uncommented for get_posterior_expected_l_information and get_item_information

  RivkadeVries

  committed
  8b8fc62

  Copy full SHA for 8b8fc62

• Two EAP estimates added to test shadowcat_roqua

  RivkadeVries

  committed
  6e5ee3d

  Copy full SHA for 6e5ee3d

• First few EAP simulations. PEKL does not seem to work well yet

  RivkadeVries

  committed
  a04d524

  Copy full SHA for a04d524

Commits on Dec 10, 2015

• EAP example uncommented in estimate_latent_trait file

  RivkadeVries

  committed
  ec67933

  Copy full SHA for ec67933

• Bug posterior_expected_kl_information (PEKL) solved, some simulations for EAP and PEKL added

  RivkadeVries

  committed
  ee2197a

  Copy full SHA for ee2197a

• ML in test that title

  RivkadeVries

  committed
  d1a5be3

  Copy full SHA for d1a5be3

• Safe_ml now uses EAP instead of MAP. Need to run new simulations with EAP and new safe_ml yet

  RivkadeVries

  committed
  7bba862

  Copy full SHA for 7bba862

• Argument estimator in sub functions estimate_latent_trait() removed

  RivkadeVries

  committed
  ec6a1f4

  Copy full SHA for ec6a1f4

• Safe_ml changed into safe_nlm, that is, there is now a safe option for both ML and MAP

  RivkadeVries

  committed
  74679bd

  Copy full SHA for 74679bd

• Option added to simulate varying number of item steps

  RivkadeVries

  committed
  766b2d9

  Copy full SHA for 766b2d9

Commits on Dec 11, 2015

• Simulation results added for one dimension, estimators ML and MAP

  RivkadeVries

  committed
  ae8469d

  Copy full SHA for ae8469d

• Simulation results one dimension, EAP estimate added

  RivkadeVries

  committed
  8322547

  Copy full SHA for 8322547

Commits on Dec 14, 2015

• Simulations 3 dimensions ML and MAP added

  RivkadeVries

  committed
  3fa241b

  Copy full SHA for 3fa241b

Commits on Dec 15, 2015

• Small documentation changes

  RivkadeVries

  committed
  a8b222c

  Copy full SHA for a8b222c

Commits on Dec 16, 2015

• simulate_testbank restructured

  RivkadeVries

  committed
  7ef3876

  Copy full SHA for 7ef3876

• Bugs fixed in simulate_testbank()

  RivkadeVries

  committed
  470c161

  Copy full SHA for 470c161

• Option added for minimum number of items to be administered

  RivkadeVries

  committed
  c5ebbe0

  Copy full SHA for c5ebbe0

• Tests added for zero start items

  RivkadeVries

  committed
  d72426c

  Copy full SHA for d72426c

Commits on Dec 17, 2015

• Useless prior definition removed

  RivkadeVries

  committed
  aa2b76c

  Copy full SHA for aa2b76c

• Separate code for first iteration removed in shadowcat_roqua()

  RivkadeVries

  committed
  ed49c00

  Copy full SHA for ed49c00

• cutoff criterion added in test_must_stop()

  RivkadeVries

  committed
  d429606

  Copy full SHA for d429606

• randomByDimension and nByDimension in lowercase

  RivkadeVries

  committed
  b54cbee

  Copy full SHA for b54cbee

Commits on Jan 4, 2016

• Documentation added for test_shadowcat_roqua()

  RivkadeVries

  committed
  0716313

  Copy full SHA for 0716313

Commits on Jan 6, 2016

• Docker- and guard file removed

  RivkadeVries

  committed
  f53fed6

  Copy full SHA for f53fed6

• instakk-package-dependencies fixed

  RivkadeVries

  committed
  3826428

  Copy full SHA for 3826428

Commits on Jan 12, 2016

• Documentation added for simulation functions

  RivkadeVries

  committed
  27f5974

  Copy full SHA for 27f5974

• constraints argument changed into constraints_and_characts

  RivkadeVries

  committed
  b471b54

  Copy full SHA for b471b54

Commits on Jan 13, 2016

• objective changed into information summary

  RivkadeVries

  committed
  db52454

  Copy full SHA for db52454

• In documentation: get_item_information instead of objective

  RivkadeVries

  committed
  fb61891

  Copy full SHA for fb61891

• objective should information summary in test

  RivkadeVries

  committed
  33a7267

  Copy full SHA for 33a7267

Commits on Jan 18, 2016

• Bug fixed in computation of Fisher information for GRM and SM model

  RivkadeVries

  committed
  e50616f

  Copy full SHA for e50616f

Commits on Jan 28, 2016

• superfluous item_selection arg removed

  RivkadeVries

  committed
  b6c209e

  Copy full SHA for b6c209e

Commits on Feb 1, 2016

• get_D_GRM and get_D_GPCM with sapply()

  RivkadeVries

  committed
  f359716

  Copy full SHA for f359716

• Capitals removed in get_fisher_information()

  RivkadeVries

  committed
  a280ddc

  Copy full SHA for a280ddc

• name change and sm information with sapply

  RivkadeVries

  committed
  12ba9d6

  Copy full SHA for 12ba9d6

• constraints_lp_format slightly formatted

  RivkadeVries

  committed
  1e001a7

  Copy full SHA for 1e001a7

Commits on Feb 2, 2016

• Documentation improved, likelihoods should be likelihood

  RivkadeVries

  committed
  74ff08a

  Copy full SHA for 74ff08a

• indices changed into indeces

  RivkadeVries

  committed
  0c80efa

  Copy full SHA for 0c80efa

• information_summary options with full names rather than abbreviations

  RivkadeVries

  committed
  55cea23

  Copy full SHA for 55cea23

• estimator options in lower case and no abbreviation

  RivkadeVries

  committed
  717e3ec

  Copy full SHA for 717e3ec

Commits on Feb 4, 2016

• Small renames in probabilities_and_likelihood, some comments removed

  RivkadeVries

  committed
  e0642df

  Copy full SHA for e0642df

• probabilities_and_likelihoods() split up into three functions

  RivkadeVries

  committed
  4199af6

  Copy full SHA for 4199af6

• Default for responses in get_probs_and_likelihoods_per_item()

  RivkadeVries

  committed
  9235fd7

  Copy full SHA for 9235fd7

• get_probabilities() removed

  RivkadeVries

  committed
  347d5ef

  Copy full SHA for 347d5ef

Commits on Feb 8, 2016

• shadowcat_roqua now returns list with next item key, estimate, and named list of responses

  RivkadeVries

  committed
  019a27a

  Copy full SHA for 019a27a

• shadowcat_roqua restructured a bit, bug in test-get_probs_and_likelihoods_per_item solved

  RivkadeVries

  committed
  a3498b5

  Copy full SHA for a3498b5

• if (is.null(beta)) removed in get_guessing()

  RivkadeVries

  committed
  0c3d6b8

  Copy full SHA for 0c3d6b8

Commits on Feb 9, 2016

• Comment stringr removed

  RivkadeVries

  committed
  664cfcc

  Copy full SHA for 664cfcc

• Unnecessary random seeds removed, second bug in test-get_probs_and_likelihoods_per_item fixed

  RivkadeVries

  committed
  e273cfa

  Copy full SHA for e273cfa

Commits on Feb 11, 2016

• Shadowcat returns error in case of missing or all zero item information values

  RivkadeVries

  committed
  8065124

  Copy full SHA for 8065124

• Tests added for validate, some bugs in validate fixed

  RivkadeVries

  committed
  329a496

  Copy full SHA for 329a496

Commits on Feb 15, 2016

• Small changes in documentation

  RivkadeVries

  committed
  db6d221

  Copy full SHA for db6d221

• exposure() removed, some comments changed or removed

  RivkadeVries

  committed
  abe7e3f

  Copy full SHA for abe7e3f

• get_posterior_expected_kl_information() made more efficient

  RivkadeVries

  committed
  ea8fc54

  Copy full SHA for ea8fc54

• shadowcat_roqua renamed into shadowcat

  RivkadeVries

  committed
  aaec541

  Copy full SHA for aaec541

• file names changed

  RivkadeVries

  committed
  95870ed

  Copy full SHA for 95870ed

• shadowcat_roqua() removed

  RivkadeVries

  committed
  e671efa

  Copy full SHA for e671efa

Commits on Feb 16, 2016

• Documentation and validate extended for constraints_lp_format()

  RivkadeVries

  committed
  6c578ad

  Copy full SHA for 6c578ad

• Documentation improved

  RivkadeVries

  committed
  64aa72c

  Copy full SHA for 64aa72c

• Extra tests for random by dimension sampling

  RivkadeVries

  committed
  ba6e9bc

  Copy full SHA for ba6e9bc

• Comments for random_by_dimension adapted

  RivkadeVries

  committed
  98b81be

  Copy full SHA for 98b81be

• get_fisher_informaton() without estimator argument

  RivkadeVries

  committed
  5d0c4cc

  Copy full SHA for 5d0c4cc

Commits on Feb 17, 2016

• Temporary init_quad added, which should be a correct version of the init.quad from the MultiGHQuad package. eval.quad now correctly uses the likelihood instead of posterior probability.

  RivkadeVries

  committed
  58e5da9

  Copy full SHA for 58e5da9

Commits on Feb 18, 2016

• Faster eval_quad()

  RivkadeVries

  committed
  6b169b0

  Copy full SHA for 6b169b0

• Temporarily eval_quad added

  RivkadeVries

  committed
  7a2acb9

  Copy full SHA for 7a2acb9

• In 3 dim test voor EAP: "AEP" should be expected_aposteriori; error fix not needed anymore

  RivkadeVries

  committed
  da01fd3

  Copy full SHA for da01fd3

• Comment added regarding negative likelihoods

  RivkadeVries

  committed
  764f291

  Copy full SHA for 764f291

• Simulations added for Jan Bebber

  RivkadeVries

  committed
  f8a48d5

  Copy full SHA for f8a48d5

• Comment added to simulations for Jan Bebber

  RivkadeVries

  committed
  ee20e5c

  Copy full SHA for ee20e5c

Commits on Feb 19, 2016

• max_n defined outside arguments line

  RivkadeVries

  committed
  521e7e8

  Copy full SHA for 521e7e8

Commits on Feb 20, 2016

• eval_quad only adds a number to f if values in f are small

  RivkadeVries

  committed
  5622b82

  Copy full SHA for 5622b82

• m in eval_quad() adapted

  RivkadeVries

  committed
  61270cd

  Copy full SHA for 61270cd

• Simulation results EAP, one dimension, one replication per condition

  RivkadeVries

  committed
  b981c03

  Copy full SHA for b981c03

• Simulations redone for "one dimension, no constraints on item selection, one replication per condition, expected_aposteriori

  RivkadeVries

  committed
  98ef5bb

  Copy full SHA for 98ef5bb

Commits on Feb 22, 2016

• Simulations for Jan Bebber adapted, eval_quad back to old version

  RivkadeVries

  committed
  bcd733d

  Copy full SHA for bcd733d

Commits on Feb 23, 2016

• eval.quad and init.quad used from MultiGHQuad package

  RivkadeVries

  committed
  1b81ed1

  Copy full SHA for 1b81ed1

• Option for minimum n added to simulation function

  RivkadeVries

  committed
  7a72da9

  Copy full SHA for 7a72da9

• Simulations added with empirical item bank of Jan Bebber

  RivkadeVries

  committed
  06d94d4

  Copy full SHA for 06d94d4

• Simulations with empirical item bank with true theta = 3 added

  RivkadeVries

  committed
  ba33da2

  Copy full SHA for ba33da2

• Simulation results one iteration per condition added for Bayesian estimators

  RivkadeVries

  committed
  a0950c0

  Copy full SHA for a0950c0

• Simulation results one replication per condition for maximum likelihood

  RivkadeVries

  committed
  785399e

  Copy full SHA for 785399e

• Comment removed

  RivkadeVries

  committed
  85dfa6a

  Copy full SHA for 85dfa6a

Commits on Feb 24, 2016

• Simulation results added for one dimension, ML estimator

  RivkadeVries

  committed
  29ee631

  Copy full SHA for 29ee631

• Remove empirical itembank from package

  RivkadeVries

  committed
  56933f8

  Copy full SHA for 56933f8

• Merge branch 'rv_restructure' of github.com:roqua/ShadowCAT into rv_restructure; more extended simulation results for one dimension, ML estimator

  RivkadeVries

  committed
  e79c025

  Copy full SHA for e79c025

• More detailed simulation results for one dimension, ML estimator

  RivkadeVries

  committed
  7fc1c01

  Copy full SHA for 7fc1c01

Commits on Feb 25, 2016

• Simulations for one dimension and maximum likelihood estimator now really with bounds -6 and 6

  RivkadeVries

  committed
  c05c8a0

  Copy full SHA for c05c8a0

• Last test line for one dimension, ML estimator

  RivkadeVries

  committed
  3f5930d

  Copy full SHA for 3f5930d

• Conditions for simulations MAP one dimension set

  RivkadeVries

  committed
  b5cef36

  Copy full SHA for b5cef36

Commits on Feb 26, 2016

• Simulation results added for MAP estimator, one dimension

  RivkadeVries

  committed
  a5fd2fd

  Copy full SHA for a5fd2fd

Commits on Feb 28, 2016

• Simulation results added for EAP estimator, one dimension

  RivkadeVries

  committed
  296fc7a

  Copy full SHA for 296fc7a

Commits on Mar 1, 2016

• variance as separate parameter rather than as attribute in shadowcat() and as vector, key_new_item returned as scalar

  RivkadeVries

  committed
  81cdc10

  Copy full SHA for 81cdc10

Commits on Mar 8, 2016

• Simulation results added for three dimensions, EAP estimator

  RivkadeVries

  committed
  184624d

  Copy full SHA for 184624d

Commits on Mar 17, 2016

• Extra checks added

  RivkadeVries

  committed
  e86ba01

  Copy full SHA for e86ba01

• continue_test element added to shadowcat output

  RivkadeVries

  committed
  b8ee710

  Copy full SHA for b8ee710

Commits on Mar 29, 2016

• Documentation item_information improved

  RivkadeVries

  committed
  9d22c1b

  Copy full SHA for 9d22c1b

• Name change: get_item_information changed into get_summarized_information

  RivkadeVries

  committed
  002c1b0

  Copy full SHA for 002c1b0

• number grid points also defined for > 5 dimensions

  RivkadeVries

  committed
  405f892

  Copy full SHA for 405f892

Commits on Apr 5, 2016

• Validate checks added

  RivkadeVries

  committed
  d6484c7

  Copy full SHA for d6484c7

Commits on Apr 6, 2016

• get_eap_estimate_riemannsum() added

  RivkadeVries

  committed
  734e552

  Copy full SHA for 734e552

• Shadow cat now allows choice between gauss hermite quadrature and riemannsum as integration method for the eap estimate. Need to incorporate this in PEKL function yet

  RivkadeVries

  committed
  1d1a85b

  Copy full SHA for 1d1a85b

Commits on Apr 7, 2016

• get_eap_estimate_riemannsum() now allows choice between riemannsum or gaussian hermit quadrature. get_eap_estimate_riemannsum() now allows adapt = NULL for uniform prior

  RivkadeVries

  committed
  57d0901

  Copy full SHA for 57d0901

• Small change in documentation for get_eap_estimate_riemannsum()

  RivkadeVries

  committed
  2c3068e

  Copy full SHA for 2c3068e

Commits on Apr 11, 2016

• responses changed into answers

  RivkadeVries

  committed
  45edffa

  Copy full SHA for 45edffa

Commits on Apr 12, 2016

• In PEKL likelihood_or_post_density_theta estimator should be EAP

  RivkadeVries

  committed
  a45a477

  Copy full SHA for a45a477

• My name added to authors

  RivkadeVries

  committed
  6fc748d

  Copy full SHA for 6fc748d

Commits on Apr 13, 2016

• Bug cutoffs fixed

  RivkadeVries

  committed
  39abc91

  Copy full SHA for 39abc91

• Test for test_must_stop slightly changed

  RivkadeVries

  committed
  dd4425d

  Copy full SHA for dd4425d

Commits on Apr 20, 2016

• Shadow cat can now handle uniform prior, and the mean of the normal prior can be any value

  RivkadeVries

  committed
  c8ce42f

  Copy full SHA for c8ce42f

Commits on Apr 22, 2016

• Tests added for uniform prior and non zero prior mean, safe_maximum replaced by safe_ml, nearPD added to trans(),

  RivkadeVries

  committed
  62e391a

  Copy full SHA for 62e391a

• MAP should be maximum a posteriori in documentation

  RivkadeVries

  committed
  0687fda

  Copy full SHA for 0687fda

• Comment added in estimate_latent_trait example

  RivkadeVries

  committed
  65ae263

  Copy full SHA for 65ae263

Commits on Apr 26, 2016

• get_item_index_max_information() takes finished dimensions into account

  RivkadeVries

  committed
  9144e2d

  Copy full SHA for 9144e2d

• Simulations rerun for one repetition per condition

  RivkadeVries

  committed
  8219930

  Copy full SHA for 8219930

Commits on May 21, 2016

• Simulations added for uniform prior one dimension

  RivkadeVries

  committed
  312c317

  Copy full SHA for 312c317

Commits on May 25, 2016

• Safer grid point transformation with uniform prior, simulations added for 3 dims uniform prior maximum aposteriori estimation

  RivkadeVries

  committed
  23c7df0

  Copy full SHA for 23c7df0

Commits on May 31, 2016

• Simulations added 3 dim EAP estimator uniform prior; better definition of grid points in PEKL function

  RivkadeVries

  committed
  79831f7

  Copy full SHA for 79831f7

Commits on Jun 1, 2016

• Better tests characteristics and constraints added

  RivkadeVries

  committed
  2d5a067

  Copy full SHA for 2d5a067

• Checks NA patterns beta and eta added; indeces corrected as indices

  RivkadeVries

  committed
  d8ce30d

  Copy full SHA for d8ce30d

• init.quad with forcePD

  RivkadeVries

  committed
  66b901d

  Copy full SHA for 66b901d