# lefser 1.20.0

## Significant user-visible changes

* Removed `blockCol` and `groupCol` arguments in `lefser` function.

# lefser 1.18.0

## Significant user-visible changes

* Removed defunct `expr` argument in `lefser` function.
* Set `blockCol` and `groupCol` arguments to defunct in main `lefser` function.

## Minor improvements and bug fixes

* Added `CITATION` file and section in `README.md`

# lefser 1.15.10

* [Major] Name of the two arguments for `lefser` function is changed from 
`groupCol` and `blockCol` to `classCol` and `subclassCol`, respectively.
* [Major] Defunct `expr` argument in `lefser`
* [New function] `lefserPlotFeat` plots the histogram of relative abundance 
(in the (0,1) interval) of the selected features
* [New function] `lefserPlotClad` draws the cladogram of the significantly 
more abundant taxa and their LDA scores
* [New function] `lefserClades` runs the `lefser`, returning additional 
information (e.g., agglomerates the features abundance at different taxonomic
ranks) required for `lefserPlotClad`.
* [New feature] Visualization functions are using a color-blind friendly color
palette by default. 

# lefser 1.15.7 
* [Major algorithm update] We remove the step (`createUniqueValues`) in the 
`lefser` function, which used to add small random numbers to make all the 
values unique. Potential issues (e.g., LDA) due to excess 0s should be managed 
by filtering out low abundant features from the input. 

# lefser 1.15.3

* The column names of `lefser` output is changed to `c("features", "scores")`
from `c("Names", "scores")`
* [New feature] The `get_terminal_nodes` function to select only the terminal
nodes of the hierarchical features (e.g., taxonomic data).
* [Major algorithm update] Add an option for adjusting the first Kruskal-Wallis 
Rank Sum Test and Wilcoxon-Rank Sum test for multiple hypothesis testing 
through the new argument `method` in the `lefser` function.

# lefser 1.14.0

* [Error fix] The `lefserPlot` function merged the duplicated labels when the 
truncated name of the feature is used. Now those are plotted separately.
* [New feature] The `lefserPlot` function accepts the `title` argument that 
adds the barplot title.
* [Update] The feature names of the `lefserPlot` outputs are re-positioned 
for the improved readability.
* [Major algorithm update] Sub-sampling and bootstrap for LDA step in the 
`lefser` function is removed. Now the LDA score is calculated directly from
the whole samples.


# lefser 1.12.0

## Significant user-visible changes

* The `checkAbundances` argument in `lefser()` checks that data are as relative
abundances and warns if otherwise (@LiNk-NY @sdgamboa, #28)
* `relativeAb` helper function available to convert data (@LiNk-NY)
* Deprecate the `expr` argument and use `relab` (short for relative abundances)
* Add group labels to `lefserPlot` (@LiNk-NY #25, @asyakhl #31)
* 'Interoperating with `phyloseq`' section added to the vignette (#16)

# lefser 1.0.0

* `lefser` is an R/Bioconductor implementation of the `LEfSe` method for microbiome marker
discovery (https://doi.org/10.1186/gb-2011-12-6-r60)
* LEfSe uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear
Discriminant Analysis to find biomarkers in groups and sub-group blocks.
* `lefser` also implements the format of the LEfSe barplot of results
