RELEASE HISTORY OF THE "zCompositions" PACKAGE
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CHANGES IN zCompositions VERSION 1.6.1 [2026-04]:
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* Bug fixes and code optimisation.

CHANGES IN zCompositions VERSION 1.6.0 [2026-01]:
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NEW FEATURES

* perLog: new implementation of test of differences in mean/location for compositional data based on pairwise logratios.

CHANGES IN zCompositions VERSION 1.5.0-5 [2025-06]:
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MODIFICATIONS

* multLN, multKM, splineKM: revised versions to remove dependence on the NADA package.
* lcTest and related functions removed: to be replaced by updated procedure soon.

CHANGES IN zCompositions VERSION 1.5.0-4 [2024-06]:
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MODIFICATIONS

* Fix small bug in mult- functions when using labelled rows.

CHANGES IN zCompositions VERSION 1.5.0-3 [2024-03]:
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MODIFICATIONS

* Fix z.warning behaviour and messages.

CHANGES IN zCompositions VERSION 1.5.0-1 [2023-12]:
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MODIFICATIONS

* Error when all columns contain more zeros/unobs values than threshold set by z.warning controlled.

CHANGES IN zCompositions VERSION 1.5.0 [2023-12]:
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MODIFICATIONS

* Parametric methods requiring regular data sets (no. obs > no. vars) now warn the user about this and stop.
* When no dl vector/matrix provided then column minima used automatically as thresholds and a warning message is shown.
* Handling excess of zeros/unobs modified: new logical argument z.delete allows the user to decide what to do with columns/rows containing zero/unobs values over the threshold set by z.warning.

CHANGES IN zCompositions VERSION 1.4.1 [2023-08]:
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MODIFICATIONS

* Handling excess of zeros/unobs (z.warning argument): columns/rows individually exceeding the given zero/unobserved values proportion threshold are now automatically deleted. A warning message details the particular columns/rows involved.
* Minor bugs fixed and edits to the documentation.

CHANGES IN zCompositions VERSION 1.4.0-1 [2022-03]:
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NEW FEATURES

* lrSVD and lrSVDplus: imputation algorithm based on singular value decomposition for censored, missing data, or both simultaneously. Particularly thought for wide data sets (no. obs < no. vars).

MODIFICATIONS

* Error control: dl argument checked for unique vector or matrix internally and converted if possible.
* Error control: error thrown when GBM method not applicable due to only one positive value in variable.
* New argument added throughout to warn about excess of zeros/unobserved values per column/row.
* multRepl & others: previous parameter 'delta' is deprecated and replaced by 'frac' to avoid confusion with original notation used in multiplicative replacement method's literature.
* Minor bugs fixed and edits to the documentation.

CHANGES IN zCompositions VERSION 1.3.4 [2020-03]:
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MODIFICATIONS

* Minor fix to meet upcoming R version requirement.
* Bug found in lrDA fixed.

CHANGES IN zCompositions VERSION 1.3.3-1 [2019-12]:
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MODIFICATIONS

* Minor fix to meet upcoming R version requirement.

CHANGES IN zCompositions VERSION 1.3.3 [2019-11]:
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NEW FEATURES

* zPatterns allows to personalise display of patterns (see new bar.ordered argument).

MODIFICATIONS

* zPatterns: internal optimisation.
* Updated documentation.

CHANGES IN zCompositions VERSION 1.3.2-2 [2019-11]:
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MODIFICATIONS

* lrDA: external dependence on miscF and related removed.
* multKM: minor bug related to dependency on NADA smashed.

CHANGES IN zCompositions VERSION 1.3.2 [2019-06]:
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NEW FEATURES

* lrDA allows to impute missing data.

MODIFICATIONS

* Updated documentation.

CHANGES IN zCompositions VERSION 1.3.1 [2019-05]:
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NEW FEATURES

* multRepl allows to impute missing data (BETA).
* multReplus: new function to simultaneously deal with zeros and missing data by multiplicative simple replacement (BETA).

MODIFICATIONS

* lrEM: multiplicative simple replacement can be also used to initiate the EM algorithm for missing data imputation.
* Minor bugs fixed.
* Updated documentation.

CHANGES IN zCompositions VERSION 1.2.0 [2019-02]:
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NEW FEATURES

* lrEMplus: new function to simultaneously deal with zeros and missing data based on the EM algorithm.

MODIFICATIONS

* zPatterns able to separate zero and missingness patterns. New warnings about either zeros or NAs not identified by the label argument.
* Updated documentation.

CHANGES IN zCompositions VERSION 1.1.2 [2018-11]:
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MODIFICATIONS

* Minor bug fixed.
* Updated documentation.

CHANGES IN zCompositions VERSION 1.1.1 [2017-08]:
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NEW FEATURES

* lrEM now allows to impute missing data.
* zVarArray: variation arrays by zero/unobserved data patterns or groups.
* zVarArrayError: squared relative errors in variation arrays across groups.
* zVarArrayTest: homogeneity test of variation arrays across groups.
* lcTest: homogeneity test of log-contrast across groups.

MODIFICATIONS

* Improved documentation.
* Verbosity controlled throughout by suppress.print argument.
* zPatterns: argument to show means (geometric or arithmetic) by pattern included.


CHANGES IN zCompositions VERSION 1.0.3-1 [2016-04]:
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MODIFICATIONS

* References updated and adaptation to new CRAN policies.

CHANGES IN zCompositions VERSION 1.0.3 [2014-09]:
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NEW FEATURES

* Support for multiple limits of detection/threshold values by component.
* Choice for storing multiply imputed data sets in lrDA function.
* multKM: new non-parametric imputation method added.
* splineKM: visualisation of Kaplan-Meier and cubic spline smoothed empirical cumulative distribution function (helper function for multKM).
* New example data set included (Water).

MODIFICATIONS

* Alternative imputation by multRepl in lrEM and lrDA of censoring patterns with only one observed component.

* Fixed problem that caused error when a censoring pattern consisted of a single sample.

* Improved documentation.

CHANGES IN zCompositions VERSION 1.0.1 [2014-06]:
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* Minor bugs in error messages fixed.

* cmultRepl: label argument added (default label = 0).

CHANGES IN zCompositions VERSION 1.0.0 [2014-05]:
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NEW FEATURES

* cmultRepl function: bayesian-multiplicative replacement of compositional count zeros included.

* lrDA function: data augmentation algorithm, including multiple imputation, to replace left-censored values.

* zPatterns function: summarises the patterns of unobserved values (censored, nondetects, ...) in a data set and generates a vector of labels.

MODIFICATIONS

* General revision and optimisation. Documentation improvements.

* multLN: parameter estimates based on the normal distribution on the positive real line. Random imputation based on truncated normal instead of rejection method.

* Re-scaling to preserve ratios that leaves absolute observed values unaltered when working with non-closed data now implemented for all the methods (continuous data). 

* The replacement methods include an argument 'label' allowing the user to enter the label (special character, number, ...) denoting unobserved value in a data set.

* Error handling introduced.

* New lrEM function: replaces previous alrEM function and implements both ordinary and robust EM-based imputation methods. New arguments allow to specify the method to obtain initial estimates and the convergence criterion.



