RELEASE HISTORY OF THE "zCompositions" PACKAGE ============================================== CHANGES IN zCompositions VERSION 1.5.0-4 [2024-06]: ---------------------------------------------------- MODIFICATIONS * Fix small bug in mult- functions when using labelled rows. CHANGES IN zCompositions VERSION 1.5.0-3 [2024-03]: ---------------------------------------------------- MODIFICATIONS * Fix z.warning behaviour and messages. CHANGES IN zCompositions VERSION 1.5.0-1 [2023-12]: ---------------------------------------------------- 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]: ---------------------------------------------------- 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]: ---------------------------------------------------- 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]: ---------------------------------------------------- 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]: ---------------------------------------------------- MODIFICATIONS * Minor fix to meet upcoming R version requirement. * Bug found in lrDA fixed. CHANGES IN zCompositions VERSION 1.3.3-1 [2019-12]: ---------------------------------------------------- MODIFICATIONS * Minor fix to meet upcoming R version requirement. CHANGES IN zCompositions VERSION 1.3.3 [2019-11]: ---------------------------------------------------- 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]: ---------------------------------------------------- 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]: ---------------------------------------------------- NEW FEATURES * lrDA allows to impute missing data. MODIFICATIONS * Updated documentation. CHANGES IN zCompositions VERSION 1.3.1 [2019-05]: ---------------------------------------------------- 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]: ---------------------------------------------------- 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]: ---------------------------------------------------- MODIFICATIONS * Minor bug fixed. * Updated documentation. CHANGES IN zCompositions VERSION 1.1.1 [2017-08]: ---------------------------------------------------- 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]: ---------------------------------------------------- MODIFICATIONS * References updated and adaptation to new CRAN policies. CHANGES IN zCompositions VERSION 1.0.3 [2014-09]: ---------------------------------------------------- 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]: ---------------------------------------------------- * Minor bugs in error messages fixed. * cmultRepl: label argument added (default label = 0). CHANGES IN zCompositions VERSION 1.0.0 [2014-05]: ---------------------------------------------------- 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.