diff --git a/README.md b/README.md index 13e0a95..db8f824 100644 --- a/README.md +++ b/README.md @@ -62,147 +62,7 @@ SOFTWARE. ## NEWS -### CHANGES IN VERSION 0.98.14 - -* Built with R 3.6.1 (2019-07-05) "Action of the Toes" - -#### NEW FEATURES - -* Enhancement https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/issues/6 - "Provide sort options for features and samples" - -#### INTERNAL MODIFICATIONS - -* Support the enhancement - -### CHANGES IN VERSION 0.98.13 - -* Built with R 3.6.1 (2019-07-05) "Action of the Toes" - -#### NEW FEATURES - -* none - -#### INTERNAL MODIFICATIONS - -* Fix https://github.com/HegemanLab/w4mclassfilter/issues/5 - "MAXFEAT does not work for imputation functions that include data transformation" - - -### CHANGES IN VERSION 0.98.12 - -#### NEW FEATURES - -* Enhancement https://github.com/HegemanLab/w4mclassfilter/issues/4 - "add and test no-imputation and centering-imputation functions": - - Support no imputation. - - Support imputating missing feature-intensities as median intensity for the corresponding feature. - -#### INTERNAL MODIFICATIONS - -* Support and tests for new features. -* Built with R 3.6.1 (2019-07-05) "Action of the Toes" -* Version numbers 0.98.10 and 0.98.10 were skipped to synchronize with w4mclassfilter_galaxy_wrapper - - -### CHANGES IN VERSION 0.98.9 - -#### NEW FEATURES - -* none - -#### INTERNAL MODIFICATIONS - -* Fix https://github.com/HegemanLab/w4mclassfilter/issues/3 - "a single column is insufficient to calculate a variance" -* Built with R version 3.4.1 (2017-06-30) "Single Candle" - -### CHANGES IN VERSION 0.98.8 - -#### NEW FEATURES - -* none - -#### INTERNAL MODIFICATIONS - -* Fix https://github.com/HegemanLab/w4mclassfilter/issues/1 - "bad error handling when input file cannot be found" -* Add tests for missing and invalid input files -* Built with R version 3.4.1 (2017-06-30) "Single Candle" - -### CHANGES IN VERSION 0.98.7 - -#### NEW FEATURES - -* First column of sample metadata is by default renamed to "sampleMetadata" unless - argument 'name_smplmetadata_col1' is supplied and set to FALSE. - -#### INTERNAL MODIFICATIONS - -* none - -### CHANGES IN VERSION 0.98.6 - -#### NEW FEATURES - -* Add field filters for variableMetadata as csv; default empty. - - E.g. for mz > 200 and mz < 800 and rt > 150 and rt < 1100, - `mz:200:800,rt:150:1100` - -#### INTERNAL MODIFICATIONS - -* Sort dataMatrix to match order of sampleMetadata and variableMetadata - - -### CHANGES IN VERSION 0.98.3 - -#### NEW FEATURES - -* Galaxy-support unchanged. -* Provide for more flexible input and output from env, list, or matrix/data.frame. - -#### INTERNAL MODIFICATIONS - -* Support and tests for new features. - - -### CHANGES IN VERSION 0.98.2 - -#### NEW FEATURES - -* Added support for R-flavored regular expression pattern matching. -* Empty classes argument or zero-length class\_column result in no samples filtered out. - -#### INTERNAL MODIFICATIONS - -* Support and tests for new features. - -#### BUILD NOTES - -* This package was built from ~/src/w4mclassfilter with R 3.3.1 under bash and miniconda as follows: - -``` - $ ~/miniconda2/bin/conda create -n r3.3.1 r-base=3.3.1 - $ source ~/miniconda2/bin/activate r3.3.1 - (r3.3.1) $ R - > library(devtools) - > document() - > test() - > check() - > build() - > install() - -``` - -Result is at ~/src/w4mclassfilter\_0.98.2.tar.gz - -### CHANGES IN VERSION 0.98.1 - -#### NEW FEATURES - -* First release - Wrap the w4mclassfilter R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample. -* *dataMatrix* *is* modified by the tool, so it *does* appear as an output file -* *sampleMetadata* *is* modified by the tool, so it *does* appear as an output file -* *variableMetadata* *is* modified by the tool, so it *does* appear as an output file - -#### INTERNAL MODIFICATIONS - -* none +See [./inst/NEWS](./inst/NEWS) ## Citations diff --git a/inst/NEWS b/inst/NEWS index 0454d06..e472217 100644 --- a/inst/NEWS +++ b/inst/NEWS @@ -1,112 +1,100 @@ -CHANGES IN VERSION 0.98.14 ------------------------------- +# CHANGES IN VERSION 0.98.14 -SIGNIFICANT USER-VISIBLE CHANGES +## SIGNIFICANT USER-VISIBLE CHANGES * Enhancement https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/issues/6 - "Provide sort options for features and samples" * Built with R 3.6.1 (2019-07-05) "Action of the Toes" -CHANGES IN VERSION 0.98.13 ------------------------------- +# CHANGES IN VERSION 0.98.13 -INTERNAL MODIFICATIONS +## INTERNAL MODIFICATIONS * Fix https://github.com/HegemanLab/w4mclassfilter/issues/5 - "MAXFEAT does not work for imputation functions that include data transformation" * Built with R 3.6.1 (2019-07-05) "Action of the Toes" -CHANGES IN VERSION 0.98.12 ------------------------------- +# CHANGES IN VERSION 0.98.12 -SIGNIFICANT USER-VISIBLE CHANGES +## SIGNIFICANT USER-VISIBLE CHANGES * Enhancement https://github.com/HegemanLab/w4mclassfilter/issues/4 - "add and test no-imputation and centering-imputation functions": - Support no imputation. - Support imputating missing feature-intensities as median intensity for the corresponding feature. -INTERNAL MODIFICATIONS +## INTERNAL MODIFICATIONS * Support and tests for new features. * Built with R 3.6.1 (2019-07-05) "Action of the Toes" * Version numbers 0.98.10 and 0.98.10 were skipped to synchronize with w4mclassfilter_galaxy_wrapper -### CHANGES IN VERSION 0.98.9 ------------------------------- +# CHANGES IN VERSION 0.98.9 -INTERNAL MODIFICATIONS +## INTERNAL MODIFICATIONS * Fix https://github.com/HegemanLab/w4mclassfilter/issues/3 - "a single column is insufficient to calculate a variance" * Built with R version 3.4.1 (2017-06-30) "Single Candle" -### CHANGES IN VERSION 0.98.8 ------------------------------- +# CHANGES IN VERSION 0.98.8 -INTERNAL MODIFICATIONS +## INTERNAL MODIFICATIONS * Fix https://github.com/HegemanLab/w4mclassfilter/issues/1 - "bad error handling when input file cannot be found" * Add tests for missing and invalid input files * Built with R version 3.4.1 (2017-06-30) "Single Candle" -CHANGES IN VERSION 0.98.7 ------------------------------- +# CHANGES IN VERSION 0.98.7 -SIGNIFICANT USER-VISIBLE CHANGES +## SIGNIFICANT USER-VISIBLE CHANGES - o First column of sample metadata is by default renamed to "sampleMetadata" unless argument 'name_smplmetadata_col1' is supplied and set to FALSE. +* First column of sample metadata is by default renamed to "sampleMetadata" unless argument 'name_smplmetadata_col1' is supplied and set to FALSE. -CHANGES IN VERSION 0.98.6 ------------------------------- +# CHANGES IN VERSION 0.98.6 -SIGNIFICANT USER-VISIBLE CHANGES +## SIGNIFICANT USER-VISIBLE CHANGES - o Support eliminating features whose attributes fall outside specified ranges. - o Sort sample names and feature names because some statistical tools expect the same order in dataMatrix row and column names as in the corresponding metadata files. +* Support eliminating features whose attributes fall outside specified ranges. +* Sort sample names and feature names because some statistical tools expect the same order in dataMatrix row and column names as in the corresponding metadata files. -OTHER +## OTHER - o Support and tests for new features. +* Support and tests for new features. -CHANGES IN VERSION 0.98.3 ------------------------------- +# CHANGES IN VERSION 0.98.3 -SIGNIFICANT USER-VISIBLE CHANGES +## SIGNIFICANT USER-VISIBLE CHANGES - o Provide for more flexible input and output from env, list, or matrix/data.frame, +* Provide for more flexible input and output from env, list, or matrix/data.frame, to facilitate use with XCMS outside of the context of Galaxy Workflow4Metabolomics. -OTHER - - o Support and tests for new features. +## OTHER +* Support and tests for new features. -CHANGES IN VERSION 0.98.2 ------------------------------- -SIGNIFICANT USER-VISIBLE CHANGES +# CHANGES IN VERSION 0.98.2 - o Added support for R-flavored regular expression pattern matching. - o Empty classes argument or zero-length class_column result in no samples filtered out. +## SIGNIFICANT USER-VISIBLE CHANGES -OTHER +* Added support for R-flavored regular expression pattern matching. +* Empty classes argument or zero-length class_column result in no samples filtered out. - o Support and tests for new features. +## OTHER +* Support and tests for new features. -CHANGES IN VERSION 0.98.1 ------------------------------- -SIGNIFICANT USER-VISIBLE CHANGES +# CHANGES IN VERSION 0.98.1 - o fixed defects in: w4m_filter_by_sample_class w4m_filter_imputation - o added: test data that exercises changes +## SIGNIFICANT USER-VISIBLE CHANGES +* fixed defects in: w4m_filter_by_sample_class w4m_filter_imputation +* added: test data that exercises changes -CHANGES IN VERSION 0.98.0 ------------------------------- -SIGNIFICANT USER-VISIBLE CHANGES +# CHANGES IN VERSION 0.98.0 - o added: w4m_filter_by_sample_class w4m_filter_imputation +## SIGNIFICANT USER-VISIBLE CHANGES +* added: w4m_filter_by_sample_class w4m_filter_imputation