bamdit ChangeLog

Version 3.4.3 -- November 2024

  * Further checks and corrections: I changed

  "if(any(tp>n1) || any(fp>n2))stop("the data is inconsistent")"

  in all functions.

Version 3.4.2 -- September 2024

 * Data checks in bsroc() function: I changed
  "if(any(tp>n1) || any(fp>n2))stop("the data is inconsistent")".


Version 3.4.1 -- July 2024

  * Data checks in metadiag() function: I changed
  "if(any(tp>n1) || any(fp>n2))stop("the data is inconsistent")".

   In these changes avoid an error generated for R>= 4.2.0 when comparing
   vectors within the if().

  * Plot function plot.metadiag() allows to plot credibility contours.


Commitments for the next version 3.5.0 -- Summer 2024

 * New function "bforest" for forest plot of posteriors of
  sensitivity and specificity.

 * Modeling function to analyze comparative test

 * Meta-regression for sensitivity and specificity

 * Implement diagnostic function with approximate Bayesian cross-validation

 * Implement diagnostic functions and depreciate the weights plots

Version 3.4.1 -- April 2022

  * Plot function plot.metadiag() allows to plot credibility contours.



Version 3.4.0 -- March 2022

  * New "summary" function for metadiag().

Version 3.3.3 -- August 2021

  * The default option for re.model = "SeSp".
  * New argument "jag.seed" to make results replicable in metadiag().
  * New warning message from "metadiag()" when the number of studies is less than 6.

Version 3.3.2 -- November 2020

  * Function "metadiag()": the argument "r2jags" has been depreciated.
  * Several bugs in ploting functions had been fixed.
  * New data frame "skin" for deep-learning diagnostic tests.

Version 3.3.1 -- July 2019
  * Some keywords are replaced.
  * Groupping variable "group" is the name (as character) of the data frame
    column. This change applies to the following function: plotdata; plotw;
    plotcompare.
  * Bug in the x-y limits in plotdata() function corrected.
  * Bug in the x-y limits in the plot.metadiag() function corrected.
  * The function plotcompare() understands the two.by.two argument from metadiag().
  * Title argument for the function plotw().
  * The metadiag() function returns the posteriors of "se"" and "sp" for each study.
  * The metadiag() function collects the studies' names.
  * The dataframe "ct" has the author and year information.
  * New data frame "diabetes" for comparative studies.
  * New data frame "rapt" for comparative studies.

Version 3.2.1 -- September 2018.
  * The CITATION file corresponds to the JSS paper.

Version 3.2.0 -- August 2018.

  * Corrections in the documentation.
  * Link the package to the JSS paper.
  * Function plotdata(), the argument max.size is active.

Version 3.1.0 -- May 2017

  * In metadiag() and plotdata() we allow that the data format is given
    as 2x2 table with columns' names: TP, FP, TN, FN.
  * A bug is fixed in the calcuation of the posterior distribution of BAUC.
  * The BSROC is calculated for parametrization: re.model = "SeSp".
  * New Summary function for metadiag.
  * New Print function for metadiag.

Version 3.0.0 -- August 2016

  * Implementation of S3 OOP in bamdit.
  * metadiag is now a generic function.
  * The argument re.model in metadiag allows to specify random effects on sensitivities
  and specificities.
  * Priors: hyper parameters mu.S and mu.D based on logistic distributions with
  mean = 0 and scale = 1
  * Priors for the degrees of freedom parameter: df truncated exponential.
  * The function metadiag calculates the posterior probabilities of outliers.
  * New functions: print; summary and plot for metadiag objects.
  * The new plot function summarizes data and model predictions.
  * The BSROC is only displayed in the range of the observed fpr. If this range is less
  than 20% the function gives a warning.
  * We added further documentation and new examples.
  * Further documentation.
  * More validation in input arguments.


Version 2.0.1 -- June 2015
  * minor typos fixed

Version 2.0 -- June 2015
  * The function bsroc() implements te Bayesian SROC curve
  * Bayesian Predictive surface added (BPS)
  * Calculation of the Bayesian area under the curve (BAUC)
  * Migration of all graphical functions, they use ggplot
  * The package "coda" is not required

Version 1.9 -- 2014
  * The function metadiag() has a new implementation with blueprint() function within metadiag()
  * option of using rjags or R2jags in metadiag()
  * conflict of evidence analysis in metadiag() by splitting the variable w in w1 and w2
  * Added a function for simulation of data (sim.meta)

Version 1.4 -- 2014-07-08
  * Improvement in the documentation

Version 1.3 -- 2013-03-15
  * New version of the function metadiag(). This version has main changes:
  * 1) The number of degrees of freedom in the model are fixed to a default value
  * 2) The Wishart prior distribution of the variance covariance matrix is replaced
  * by a conditional model where the priors are given to individual components.
  * 3) The priors of the variance covariance distribution are design to avoid boundary
  * problems in the parameter space.
  * The three adaptation trials are omited in metadiag()

Version 1.2	-- 2012-07-31
  * Added more graphical functions
  * We added meta-analysis examples data.
  * Improved internal model functions

Version 1.1.1 	-- 2011-12-08
  *  Examples do not run during testing.

Version 1.1 	-- 2011-08-30
  * Weights are return from the bamdit function
    when random effects are scale mixed.
  * Change warning messages when model fails to adapt in JAGS.

Version 1.0.1 	-- 2011-08-09
	* Nothing has to be written to disk anymore.
	* Models are compiled / adapted now with "first of three"
	  due to an issue where sometimes models don't adapt.
	* Added ChangeLog
	* Corrected model adaption process from three to two stages

Version 1.0		-- 2011-08-07
	* Initial release