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Changes and developments in the difNLR package

Changes in version 1.4.3 (2023-05-03)

MAJOR UPDATES

  • "likelihood" option for maximum likelihood estimation in the estimNLR() function was renamed to "mle".
  • S3 methods for the estimNLR() function were extended and improved.

Changes in version 1.4.2-1 (2023-05-03)

THIS IS A CRAN VERSION

MINOR UPDATES

  • CITATION file was updated.

Changes in version 1.4.2 (2023-05-02)

BUGFIXING

  • plot.ddfMLR() now correctly plots ordinal data.
  • Option test = "W" was fixed for the difNLR() and NLR() functions.
  • Constraints handling was fixed for the difNLR() and NLR() functions.

MINOR UPDATES

  • startNLR now handles missing values. Returns error when not enough complete observations are provided.
  • Arguments in ggplot2 plotting methods were updated to follow changes in the ggplot2 package.
  • Linetype and its legend appearance in ggplot2 plotting methods were updated.
  • ggplot2 v.3.4.0 is now imported.
  • Examples for the difORD() and ORD() functions were updated. Now using the Anxiety dataset from the ShinyItemAnalysis package.

Changes in version 1.4.1 (2022-04-18)

MINOR UPDATES

  • Some typos fixed.
  • class handling was updated.

Changes in version 1.4.0 (2022-04-16)

It includes versions 1.3.7-1 - 1.3.7-3

Changes in version 1.3.7-3 (2022-02-11)

BUGFIXING

  • Option parameterization = "logistic" was fixed in formulaNLR() function.

MAJOR UPDATES

  • First version of iteratively reweighted least squares algorithm was implemented in difNLR(), NLR(), and estimNLR() functions.
  • coef.difNLR(), coef.difORD(), and coef.ddfMLR() methods now include delta method for IRT and logistic parameterizations.
  • coef.difNLR(), coef.difORD(), and coef.ddfMLR() methods now include calculation of confidence intervals.

MINOR UPDATES

  • Some typos fixed.
  • Examples in functions were updated.
  • References were updated.
  • Output of estimNLR() function is now unified via print() method.
  • Packages CTT, grDevices, methods are no longer imported.

Changes in version 1.3.7-2 (2021-10-05)

MAJOR UPDATES

  • First version of predicted.difORD() to compute predicted values for difORD object was implemented.

Changes in version 1.3.7-1 (2021-02-16)

BUGFIXING

  • Bug in plotting empirical probabilities in plot.difNLR() fixed.

Changes in version 1.3.6/1.3.7 (2021-01-07)

THIS IS A CRAN VERSION

MINOR UPDATES

  • doi in DESCRIPTION file updated.
  • doi in help pages were updated.
  • CITATION file updated.
  • References were updated.

Changes in version 1.3.5-2 (2020-11-24)

BUGFIXING

  • Empty factor levels were removed from Data in ddfMLR() to fix bug when plotting.

Changes in version 1.3.5-1 (2020-09-03)

MAJOR UPDATES

  • Sandwich estimator for covariance matrix in case that method = "nls" was implemented into the vcov() method for the output of the estimNLR() function.
  • Wald test for implemented for the difNLR() function.
  • Sandwich estimator for covariance matrix in case that method = "nls" was implemented into the difNLR() function via an argument sandwich = TRUE.

Changes in version 1.3.4/1.3.5 (2020-08-24)

THIS IS A CRAN VERSION

BUGFIXING

  • Error when covariance matrix cannot be computed for some items in difNLR() function was fixed.

DOCUMENTATION

  • URLs for GH were updated.

Changes in version 1.3.3 (2020-04-29)

THIS IS A CRAN VERSION

BUGFIXING

  • Bug in calculation of standard errors for estimates of difNLR() was fixed.
  • Bug in coefficients of difNLR() for non-converged items including naming of parameters was fixed (Reported by Jan Netik).
  • In case that covariance matrix cannot be computed in NLR(), function gives warning and NA values for covariance matrix and vector of standard errors are returned.

MAJOR UPDATES

  • Confidence intervals were added into predict.difNLR() method.
  • Delta method for alternative parametrization is now applied for whole covariance matrix in difNLR().
  • Unnecessary arguments of plot.difNLR(), plot.difORD() and plot.ddfMLR() were removed. Change of colours/linetypes/shapes/title can be managed using standard ggplot2 syntax.
  • plot.difNLR() now offers possibility to turn off drawing of empirical probabilities using argument draw.empirical = FALSE.
  • plot.difNLR() now offers possibility to plot confidence intervals for predicted values as offered in predict.difNLR() using argument draw.CI = TRUE.
  • Starting values calculated via startNLR() were improved for score as matching criterion using argument match.

DOCUMENTATION

  • Documentation of the package was updated.
  • Some typos were fixed.
  • Documentation of main functions was updated:
    • S3 methods are now referenced in See Also sections.
    • S3 methods are now documented in seperate files.
  • CITATION file was updated.
  • Formatting was improved.

MINOR UPDATES

  • Legends in plot.difNLR(), plot.difORD() and plot.ddfMLR() were unified.
  • Colors in plot.difORD() and plot.ddfMLR() were changed to blind-color friendly palettes.

Changes in version 1.3.2 (2020-01-28)

THIS IS A CRAN VERSION

BUGFIXING

  • Bug in plot.difNLR() was fixed.

Changes in version 1.3.1 (2020-01-27)

THIS IS A CRAN VERSION

It includes versions 1.3.0-1 - 1.3.0-6 and following changes:

BUGFIXING

  • Method plot.difNLR() now correctly uses matching criterion when item purification is applied.

DOCUMENTATION

  • Documentation of the package was updated.
  • Some typos were fixed.

MINOR UPDATES

  • NEWS file is now generated using markdown.
  • README file was updated.

Changes in version 1.3.0-6 (2020-01-22)

BUGFIXING

  • Mismatch in null and alternative models was fixed for all functions.
  • MLR() function now returns correct value of log-likelihood for alternative model.

MAJOR UPDATES

  • Default option of argument type in NLR() function was set to "all" instead of "both".
  • Input Data in difNLR() function can be also a vector now.

Changes in version 1.3.0-5 (2020-01-20)

BUGFIXING

  • Function MLR() was fixed for binary data and IRT parametrization.
  • Typo fixed in print.difORD() method.
  • Method plot.ddfMLR() was fixed for binary data.

Changes in version 1.3.0-4 (2020-01-17)

MAJOR UPDATES

  • Function ddfORD() was renamed to difORD().

MINOR UPDATES

  • Function genNLR() with an option itemtype = "nominal" returns nominal items as factors with levels presented by capital letters.
  • Legend for plot.ddfMLR() was updated to show P(Y = option) instead of option alone.
  • README file updated.
  • Typos fixed.

Changes in version 1.3.0-3 (2020-01-07)

DOCUMENTATION

  • Documentation was updated.
  • Authors' details were updated.

MAJOR UPDATES

  • Seed was added for re-calculation of bootstrapped initial values in NLR() estimation.

MINOR UPDATES

  • Argument item for S3 methods of difNLR class can be now name of the column in Data.
  • Legends in plot.ddfMLR() and plot.ddfORD() were updated.
  • Some typos were fixed.

Changes in version 1.3.0-2 (2020-01-03)

MAJOR UPDATES

  • Default option of argument type in difNLR() function was set to "all" instead of "both".

MINOR UPDATES

  • Package styler was used to improve formatting of the code.
  • Package ShinyItemAnalysis was added into Suggests.
  • Figures for README were updated.

DOCUMENTATION

  • Documentation for all data was updated. Format of data was fixed.
  • Documentation of estimNLR() was improved.

Changes in version 1.3.0-1 (2019-12-16)

BUGFIXING

  • Legend in plot.ddfORD() is now correctly displayed.

Changes in version 1.3.0 (2019-08-19)

THIS IS A CRAN VERSION

It includes versions 1.2.3 - 1.2.8-4 and following changes:

MINOR UPDATES

  • Some typos fixed in print.difNLR()
  • Authors' details were updated.
  • CITATION file was updated.

Changes in version 1.2.8-4 (2019-08-09)

MINOR UPDATES

  • Typos fixed in print.ddfORD() and print.ddfMLR().
  • Matching criterion for plot.ddfORD() uses anchor items.

Changes in version 1.2.8-3 (2019-08-08)

BUGFIXING

  • plot.ddfORD() now works when Data is factor.

MINOR UPDATES

  • genNLR() now generates ordinal data using adjacent category logit model with argument itemtype = "ordinal".

Changes in version 1.2.8-2 (2019-08-07)

BUGFIXING

  • plot.ddfORD() now works when items have different scales.
  • Argument anchor is now used for calculation of matching criterion in function ORD().
  • IRT parametrization was fixed for ddfORD().
  • logLik.ddfMLR() now works properly.
  • anchor items are now used for calculation of matching criterion in plot.ddfORD() and plot.ddfMLR().

MAJOR UPDATES

  • Names of reference and focal group in plot.difNLR() can be changed with group.name argument.

MINOR UPDATES

  • Help pages for difNLR(), ddfMLR(), ddfORD(), MLR(), and ORD() functions were updated.

Changes in version 1.2.8-1 (2019-08-06)

MINOR UPDATES

  • IRT parametrization now available in ddfMLR() function with argument parametrization. SE calculated with delta method.
  • Names of reference and focal group in plot.ddfMLR() can be changed with group.name argument.

Changes in version 1.2.8 (2019-08-05)

MAJOR UPDATES

  • ddfORD() function was renamed. Now ddfORD().
  • IRT parametrization now available in ddfORD() function with argument parametrization. SE calculated with delta method.
  • Names of reference and focal group in plot.ddfORD() can be changed with group.name argument.

MINOR UPDATES

  • Help page for ddfORD() was updated.
  • Reference for ddfORD() was added.

Changes in version 1.2.7 (2019-07-04)

BUGFIXING

  • Check for input item in S3 methods for difNLR(), ddfMLR(), and ddfORD() was fixed.

MAJOR UDPATES

  • S3 methods plot() outputs for difNLR(), ddfMLR(), and ddfORD() functions were unified.

MINOR UPDATES

  • Help pages were updated.
  • README file was updated.

Changes in version 1.2.6 (2019-07-03)

MAJOR UDPATES

  • S3 method plot() for ddfORD() was implemented.

Changes in version 1.2.5 (2019-07-02)

MAJOR UPDATES

  • S3 methods AIC(), BIC(), logLik(), coef() for ddfORD() were implemented.
  • S3 methods AIC(), BIC(), logLik(), residuals() for difNLR() and ddfMLR() objects now handle column names as item argument.
  • S3 method coef() for difNLR and ddfMLR objects were updated. Their now includes arguments SE (logical) to print standard errors and simplify (logical) whether list of estimates should be simplified into a matrix.

MINOR UPDATES

  • CITATION was updated.
  • All static DOI links were updated.

Changes in version 1.2.4 (2019-07-02)

MAJOR UPDATES

  • New functions ddfORD() and ORD() for DDF detection for ordinal data with adjacent and cumulative logistic regression models were added. Output is displayed via S3 method print.ddfORD()

MINOR UPDATES

  • Authors' details were updated.
  • Some typos were fixed.
  • Helps for ddfMLR(), MLR(), and difNLR() were updated.

Changes in version 1.2.3 (2019-06-20)

BUGFIXING

  • plot.ddfMLR() now handles also binary data.
  • ddfMLR() returns consistently "No DDF item detected" when no DDF item was detected.

MAJOR UPDATES

  • Matching criterion for plot.ddfMLR() was improved for displaying more smooth curves.

MINOR UPDATES

  • Authors' details were updated.

Changes in version 1.2.2 (2018-05-03)

THIS IS A CRAN VERSION

It includes versions 1.2.1-1 - 1.2.1-3

Changes in version 1.2.1-3 (2018-04-26)

MINOR UPDATES

  • S3 methods AIC(), BIC(), logLik() of ddfMLR() are now item specific.

Changes in version 1.2.1-2 (2018-03-19)

BUGFIXING

  • difNLR()
    • Check for constraints was fixed.
  • NLR()
    • initboot = FALSE now works properly.

Changes in version 1.2.1-1 (2018-03-16)

BUGFIXING

  • difNLR():
    • P-value adjustment is now performed in the last iteration of purification as described.
    • In difPur output columns are properly named.
  • ddfMLR():
    • P-value adjustment is now performed in the last iteration of purification as described.
    • In difPur output columns are properly named.

MINOR UPDATES

  • Warning messages do not include the call.

Changes in version 1.2.1 (2018-03-01)

THIS IS A CRAN VERSION

It includes versions 1.2.0-1 - 1.2.0-7

Changes in version 1.2.0-7 (2018-02-27)

MAJOR UPDATES

  • Argument start in difNLR() function is now item-specific. The input is correctly checked.
  • In case that some items do not converge, starting values are recalculated from bootstraped sample and problematic models are fitted again. This is done 20 times at most. The options were added into difNLR() and NLR() functions.
  • Argument constraints in difNLR() function is now item-specific.

MINOR UPDATES

  • Minor typos were fixed in print() method for difNLR class.
  • Title was shorten.
  • Description of package was updated.
  • Description file was updated, reference was added.
  • README file was updated.
  • CITATION file was updated.

Changes in version 1.2.0-6 (2018-02-26)

MAJOR UPDATES

  • S3 methods for difNLR class are now properly described, especially, plot.difNLR() and predict.difNLR().
  • difNLR() documentation was improved.

BUGFIXING

  • S3 methods for class difNLR can now properly handle items with convergence issues.
  • NLR() now detects DIF correctly with F test.

MINOR UPDATES

  • Typos were fixed.

Changes in version 1.2.0-5 (2018-02-20)

MAJOR UPDATES

  • print(), plot(),fitted(), predict(), logLik(), AIC(), BIC() and residuals() for difNLR class now handles item specific arguments (model, type and constraints).
  • residuals for difNLR class now uses argument item.

BUGFIXING

  • Checking inputs in difNLR was fixed and improved.
  • Fixing degrees of freedom and p-values calculations in NLR().
  • Fixing parameters, SE and covariances calculations in NLR().
  • S3 methods for difNLR class can now handle convergence issues.

MINOR UPDATES

  • Documentation of difNLR-package was updated.
  • Syntax in plot() and residuals() for difNLR was slightly improved.
  • logLik() for difNLR now returns list of logLik class values.

Changes in version 1.2.0-4 (2018-02-19)

MAJOR UPDATES

  • Function startNLR() now handles item-specific arguments (model and parameterization). Its output is now in the form of list. It can be simplified with argument simplify into table when all parameterizations are the same.
  • Function NLR() now handles item-specific arguments (model, type and constraints).
  • Function difNLR() now handles item-specific arguments (model, type and constraints).

MINOR UPDATES

  • README file was updated.

Changes in version 1.2.0-3 (2018-02-19)

BUGFIXING

  • Starting values in input of estimNLR() in NLR() are now properly named.
  • Bug in alternative parameterization for testing differences in parameters c and d in function formulaNLR() was fixed.

MINOR UPDATES

  • Descriptions of formulaNLR() and estimNLR() were improved.

Changes in version 1.2.0-2 (2018-02-15)

MAJOR UPDATES

  • Function genNLR() can now also generate nominal data based on model specified in ddfMLR().
  • Argument parameters in genNLR() is no longer applicable.
  • Arguments a, b, c, d were added into genNLR() as parameters - discrimination, difficulty, guessing, inattention
  • Function genNLR() can now also generate different underlying distributions for reference and focal group with arguments mu and sigma.

MINOR UPDATES

  • Email address of maintainer was changed.

Changes in version 1.2.0-1 (2018-02-14)

MAJOR UPDATES

  • New function estimNLR() to estimate parameters of NLR models was added. This function uses non-linear least squares or maximum likelihood method.
  • Function NLR() now uses estimNLR() for estimation of models parameters.
  • Function difNLR() can now estimate models parameters with also maximum likelihood method.
  • Iteratively reweighted least squares (IRLS) method was added into estimNLR() function. This option is not fully functional.

BUGFIXING

  • Bug in plot() for ddfMLR class in matching criterion was fixed.
  • Bug in NLR() was fixed. User-specified starting values are now available.
  • Bug in startNLR() was fixed. Function runs even if there are not unique cuts for total scores/match.
  • Bug in log-likelihood calculation in estimNLR() was fixed.

MINOR UPDATES

  • Some preparation for new estimation methods for F test in NLR() was done.
  • Convergence failure warning is now item specific.
  • Warning and error messages were improved.

Changes in version 1.1.3 (2018-02-06)

BUGFIXING

  • Bug in delta method in NLR() function was fixed.
  • Bug in match argument in difNLR() function was fixed.
  • Bug in one dimensional Data in difNLR() function was fixed.

MAJOR UPDATES

  • Specification of upper and lower asymptotes in startNLR() function was improved.
  • Functions ddfMLR() and MLR() can now handle also total score or other user-specified matching criterion.
  • S3 functions plot() for class ddfMLR can also handle total score or other user-specified matching criterion.

MINOR UPDATES

  • New auxiliary function checkInterval() was added.
  • Size of labs and title was unified in graphical outputs of functions difNLR() and ddfMLR().

Changes in version 1.1.2 (2017-12-12)

MAJOR UPDATES

  • CITATION file was added with reference to relevant paper.
  • Bug when loading group by group identificator was fixed.
  • Condition to check dimension of complete cases data was added.
  • Function residuals.difNLR() was added.
  • S3 functions AIC() and BIC() for difNLR class were updated.
  • S3 functions plot(), fitted() and predict() for difNLR class can now handle also other matching criteria than zscore.

MINOR UPDATES

  • Reference lists were updated.
  • README file was updated.

Changes in version 1.1.1 (2017-08-28)

THIS IS A CRAN VERSION

MAJOR UPDATES

  • Bug in startNLR() function for missing values was fixed.

MINOR UPDATES

  • Graphical representation for difNLR() and ddfMLR() functions was mildly updated and unified.

Changes in version 1.1.0 (2017-08-21)

THIS IS A CRAN VERSION

MINOR UPDATES

  • Bug in plot.difNLR() was fixed.
  • README file was updated.
  • Package documentation was updated.
  • Default value for constraints arguments in NLR() and formulaNLR() functions were set to NULL.
  • Default starting values were added into NLR() function by startNLR() function.

Changes in version 1.0.8 (2017-08-14)

BUGFIXING

  • Several bugs were fixed:
    • difNLR() function can handle Data with one column.
    • startNLR() now works when match argument is set.
    • Check input condition was fixed in formulaNLR() function.
    • Delta method in NLR() function.

MINOR UPDATES

  • Function startNLR() was mildly updated.

Changes in version 1.0.7 (2017-08-10)

MAJOR UPDATES

  • Item purification was implemented into ddfMLR() function.
  • Anchor items were implemented into ddfMLR() function.
  • Anchor items were implemented into MLR() function.

MINOR UPDATES

  • Minor bug in logLik.ddfMLR() function was fixed.
  • Documentation of difNLR() was updated.

Changes in version 1.0.6 (2017-08-09)

MAJOR UPDATES

  • Item purification was implemented into difNLR() function.
  • Anchor items were implemented into difNLR() function.
  • Anchor items were implemented into NLR() function.

MINOR UPDATES

  • README file was updated.

Changes in version 1.0.5 (2017-08-09)

MAJOR UPDATES

  • Datasets difMedical, difMedicaltest, and difMedicalkey were renamed. Now they are MSATB, MSATBtest, and MSATBkey. from Medical School Admission Test in Biology.

MINOR UPDATES

  • LazyData is now available.
  • References were updated.
  • README file updated.

Changes in version 1.0.4 (2017-08-08)

MAJOR UPDATES

  • New function formulaNLR() was implemented. Function returns formula for NLR model for 11 predefined models and 4 predefined DIF types to test. Model and DIF type can be also specified with constraints on parameters a, b, c and d.
  • Function NLR() now handles 11 predefined models and 4 predefined DIF types to test. Model and DIF type can be also specified with constraints on parameters a, b, c and d.
  • Function startNLR() was edited to return starting parameters with different parameterization. It was also mildly changed to correspond to new version of NLR() function.
  • Function difNLR() can now handle also total score or other user-specified matching score.
  • Function constrNLR() is no longer part of the difNLR package.

MINOR UPDATES

  • References were updated.
  • Some minor bugs were fixed:
    • Items are no longer renamed by difNLR() and ddfMLR() functions.
    • Starting values are now correctly checked in difNLR() function.
  • msm package is now used for delta method in difNLR() function.

Changes in version 1.0.3 (2017-06-15)

THIS IS A CRAN VERSION

MAJOR UPDATES

  • Bug of plot.ddfMLR() for non-uniform DDF was fixed.
  • References were updated.

Changes in version 1.0.2 (2017-06-06)

THIS IS A CRAN VERSION

MAJOR UPDATES

  • Bug of dimensions for parameter estimates of difNLR() function was fixed.
  • Datasets GMAT and GMATtest were extended by criterion variable which is intended to be predicted by test.
  • coef, logLik, AIC and BIC S3 methods were added for class ddfMLR.

MINOR UPDATES

  • Functions plot.ddfMLR() and plot.difNLR() were slightly improved.
  • Updated error and warning handling in difNLR() and ddfMLR() functions.
  • Description file was updated.
  • Item names are now the same as in original data set.
  • README file updated.

Changes in version 1.0.0 (2017-01-10)

THIS IS A CRAN VERSION

MAJOR UPDATES

  • New function ddfMLR() to detect Differential Distractor Functioning (DDF) with Multinomial Log-linear Regression (MLR) model. S3 methods for class ddfMLR also added - print and plot.
  • New function MLR() to calculate likelihood ratio statistic for detecting DDF with MLR model.
  • The difNLR() function can handle 6 generalized logistic regression models with option model.
  • Functions startNLR(), genNLR() ans S3 methods for class difNLR were changed according difNLR() function. S3 method coef was created.
  • New functions NLR() and constrNLR() can now calculates DIF detection statistics and specify constraints for generalized logistic regression model.
  • Function difNLR() was edited to response to difR package and its DIF detection functions.
  • Function genNLR() was changed to generate dataset from generalized logistic regression model with 8 parameters.

MINOR UPDATES

  • The CITATION file was updated.
  • Several typos were fixed.
  • Some default options of input were changed.
  • AIC(), BIC(), and logLik() S3 methods added to difNLR().

Changes in version 0.2.0 (2016-11-09)

THIS IS A CRAN VERSION

MAJOR UPDATES

  • S3 method plot for class difNLR was updated.
  • New option of test in difNLR() function was added. Possible choices are now F for F-test and LR for likelihood ratio test.
  • Choice of significant level alpha was added into difNLR() function with default option 0.05.
  • Six new data sets were added - scored GMAT data, its unscored version GMATtest and its key GMATkey. Scored difMedical data set, its unscored version difMedicaltest and key difMedicalkey.
  • New function genNLR() was added to generate scored (binary) data with model by difNLR.

MINOR UPDATES

  • Several typos were fixed.