Treatment of Zeros, Left-Censored and Missing Values in Compositional Data Sets

Principled methods for the imputation of zeros, left-censored and missing data in compositional data sets.


Imputation of Zeros, Nondetects and Missing Data in Compositional Data Sets

News

RELEASE HISTORY OF THE "zCompositions" PACKAGE

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.

Reference manual

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install.packages("zCompositions")

1.2.0 by Javier Palarea-Albaladejo, a month ago


Browse source code at https://github.com/cran/zCompositions


Authors: Javier Palarea-Albaladejo and Josep Antoni Martin-Fernandez


Documentation:   PDF Manual  


Task views: Missing Data


GPL (>= 2) license


Depends on MASS, NADA, truncnorm


Imported by baytrends, robCompositions.


See at CRAN