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eschen42 committed Oct 23, 2019
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142 changes: 1 addition & 141 deletions README.md
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Expand Up @@ -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

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88 changes: 38 additions & 50 deletions inst/NEWS
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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

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