NEWS
zCompositions 1.5.0-4 (2024-06-19)
MODIFICATIONS
- Fix small bug in mult- functions when using labelled rows.
zCompositions 1.5.0-3 (2024-03-13)
MODIFICATIONS
- Fix z.warning behaviour and messages.
zCompositions 1.5.0-1 (2024-01-09)
MODIFICATIONS
- Error when all columns contain more zeros/unobs values than threshold set by z.warning controlled.
zCompositions 1.5.0
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.
zCompositions 1.4.1 (2023-08-23)
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.
zCompositions 1.4.0-1 (2022-03-26)
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.
zCompositions 1.3.4 (2020-03-04)
MODIFICATIONS
- Minor fix to meet upcoming R version requirement.
- Bug found in lrDA fixed.
zCompositions 1.3.3-1 (2019-12-08)
MODIFICATIONS
- Minor fix to meet upcoming R version requirement.
zCompositions 1.3.3 (2019-11-17)
NEW FEATURES
- zPatterns allows to personalise display of patterns (see new bar.ordered argument).
MODIFICATIONS
- zPatterns: internal optimisation.
- Updated documentation.
zCompositions 1.3.2-2 (2019-11-13)
MODIFICATIONS
- lrDA: external dependence on miscF and related removed.
- multKM: minor bug related to dependency on NADA smashed.
zCompositions 1.3.2 (2019-06-02)
NEW FEATURES
- lrDA allows to impute missing data.
MODIFICATIONS
zCompositions 1.3.1 (2019-05-27)
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.
zCompositions 1.2.0 (2019-02-18)
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.
zCompositions 1.1.2 (2018-11-06)
MODIFICATIONS
- Minor bug fixed.
- Updated documentation.
zCompositions 1.1.1 (2017-08-09)
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.
zCompositions 1.0.3-1 (2016-04-14)
MODIFICATIONS
- References updated and adaptation to new CRAN policies.
zCompositions 1.0.3 (2014-09-12)
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.
zCompositions 1.0.1 (2014-06-03)
- Minor bugs in error messages fixed.
- cmultRepl: label argument added (default label = 0).
zCompositions 1.0.0 (2014-05-20)
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.