# NEWS

myTAI 2.3.5
===========
- added functions `get_strata_legend` and `get_phylomap`
- removed faulty dynamic links from documentation

myTAI 2.3.4
===========
Patches:
- taxid now throws warning instead of error and returns NULL if no internet is available
- taxonomy.Rmd vignetter now builds even with no internet
- fixed plot_contribution failing when some of the stratas have no genes

myTAI 2.3.0.9006
===========

This update has focused on improving the single-cell phyloset functionality.

The single-cell phylo expression object no longer depends on Seurat. You can construct the ScPhyloExpressionSet either from a count matrix (sparse or dense), using `ScPhyloExpressionSet_from_matrix`, or from a Seurat object, using `ScPhyloExpressionSet_from_seurat`. For consistency, one can use `BulkPhyloExpressionSet_from_df` instead of `as_BulkPhyloExpressionSet`.

One key functionality of the single-cell object is the ability to switch between different identities when plotting (equivalent to the `Seurat::Idents` functionality). This is done by setting the `::identities_label` property of the object. The `::available_idents` property can be used to see what options the user has in setting the current identity. By setting `::idents_colours[[]]`, the user can choose a colour pallette for the different identities when plotting, which are saved across different plotting calls. 

The computation of TAI values for single cell is now cached. Moreover, we have readded the C++ accelerated code for the computation of TAI, which upon profiling shows to be faster than the R version when handling more than 100000 cells (an adaptive function chooses the appropriate implementation for the object size). 

Some of the plotting functionality had been improved and more options were added for plotting (e.g. plot_gene_heatmap now allows for passing a custom colour mapping for the rows (genes), instead of colouring them by their strata; plot_signature for single cell should be more readable).

Bug fixes:
- validation of S7 objects now works properly
- printing of object information now works properly (instead of dumping all the properties information)




myTAI 2.2.0.9006
===========

Most importantly, new vignettes were added and the website has been updated. Many thanks to @LotharukpongJS

Functionality wise:

- added more input validation across functions
- improved plotting in `destroy_pattern`
- renamed `tfPS` to `tf_PS` and fixed bug which prevented strata transformations from happening (PhyloExpressionSet now has an extra field @strata_values which keeps track of the phylostratum values)
- added back standard deviation ribbon to plot_signature
- finer control over cell identity selection in the sc object
- fixed bugs in some of the plotting functions, such as plot_signature_multiple showing the colours in reverse, plot_genes_heatmap not working when given just one gene etc.

myTAI 2.1.0.9000
===========

## Major Refactoring and New Features
- **Single-cell support:** New `ScPhyloExpressionSet` S7 class for single-cell data, alongside `BulkPhyloExpressionSet` for bulk data.
- **Property renaming:** `conditions` → `identities` (and `conditions_label` → `identities_label`), `counts`/`counts_collapsed` → `expression`/`expression_collapsed`.
- **All core logic and plotting now robust to both bulk and single-cell objects.**

## Function Renaming and Prefixes
- **Statistical tests:** All core test functions now use the `stat_` prefix:
    - `flatline_test()` → `stat_flatline_test()`
    - `early_conservation_test()` → `stat_early_conservation_test()`
    - `late_conservation_test()` → `stat_late_conservation_test()`
    - `reductive_hourglass_test()` → `stat_reductive_hourglass_test()`
    - `reverse_hourglass_test()` → `stat_reverse_hourglass_test()`
    - `pairwise_test()` → `stat_pairwise_test()`
    - `generic_conservation_test()` → `stat_generic_conservation_test()`
    - `generate_conservation_txis()` → `stat_generate_conservation_txis()`
- **Gene selection/filtering:** All gene selection/filtering functions now use the `genes_` prefix:
    - `top_expression_genes()` → `genes_top_mean()`
    - `top_variance_genes()` → `genes_top_variance()`
    - `lowly_expressed_genes()` → `genes_lowly_expressed()`
    - `filter_dyn_expr()` → `genes_filter_dynamic()`

## Other Changes
- Many internal and Rd files renamed for consistency (e.g., `gene_patterns.R` → `genes_patterns.R`, `S7_utils.R` → `utils_S7.R`).
- Deprecated/legacy files removed: `expression_utils.R`, `single_cell.R`.
- All documentation and examples updated to use new function/property names.

myTAI 2.0.0.9000
===========
## Major Changes

### New S7 Class System
- Migrated from traditional R data structures to modern S7 classes
- New `PhyloExpressionSet` S7 class replaces the old data.frame-based format
- New `TestResult` S7 class for standardized storage of statistical test results
- Computed properties automatically calculate derived values like TXI, pTXI, conditions, etc.
- Built-in data validation and type checking through S7 properties
- Improved replicate data handling with automatic collapsing

### Function Name Modernization
Function names have been updated to use snake_case convention:

#### Statistical Tests (old → new)
- `FlatLineTest()` → `flatline_test()`
- `ReductiveHourglassTest()` → `reductive_hourglass_test()`
- `EarlyConservationTest()` → `early_conservation_test()`
- `LateConservationTest()` → `late_conservation_test()`
- `ReverseHourglassTest()` → `reverse_hourglass_test()`
- `PairwiseTest()` → `pairwise_test()`

#### Visualization Functions (old → new)
- `PlotSignature()` → `plot_signature()`
- `PlotPattern()` → `plot_signature()`
- `PlotContribution()` → `plot_contribution()`
- `PlotDistribution()` → `plot_distribution_strata()`
- `PlotCategoryExpr()` → `plot_strata_expression()`
- `PlotRE()` → `plot_relative_expression_line()`
- `PlotBarRE()` → `plot_relative_expression_bar()`
- `PlotGeneSet()` → `plot_gene_profiles()`
- `PlotMeans`, `PlotVars`, `PlotMedians` → `plot_strata_expression(aggregate_FUN="mean"/"var"/"median")
- `PlotSignatureMultiple()` → `plot_signature_multiple()`
- `PlotSignatureTransformed()` → `plot_signature_transformed()`
- `PlotSignatureGeneQuantiles()` → `plot_signature_gene_quantiles()`

#### Utility Functions (old → new)
- `TAI()` → Computed property of PhyloExpressionSet (still accessible via `TAI()`)
- `TDI()` → Computed property of PhyloExpressionSet (still accessible via `TDI()`)
- `TEI()` → Computed property of PhyloExpressionSet (still accessible via `TEI()`)
- `TPI()` → Computed property of PhyloExpressionSet (still accessible via `TPI()`)
- `pTAI()`, `pTDI` → `sTXI()` (generalized for all transcriptomic indices)
- `pMatrix()` → `pTXI()`
- `CollapseReplicates()` → `collapse`, Built into PhyloExpressionSet constructor
- `Expressed()` → `lowly_expressed_genes()`
- `MatchMap()` → `match_map()`
- `SelectGeneSet()` → `select_genes()`
- `TopExpressionGenes()` → `top_expression_genes()`
- `TopVarianceGenes()` → `top_variance_genes()`
- `REMatrix()` → `rel_exp_matrix()`
- `RE()` → `relative_expression()`
- `omitMatrix()` → `omit_matrix()`
- `is.ExpressionSet()` → Built into S7 validation
- `age.apply()` → `age.apply()` (unchanged)
- `tf()` → `tf()` or `transform_counts()`
- `tfPS()` → `tfPS()` (unchanged)
- `tfStability()` → `tf_stability()`
- `taxid()` → `taxid()` (unchanged)

### New Functions
- `destroy_pattern()`: Apply GATAI algorithm to identify pattern-contributing genes
- `plot_signature_multiple()`: Plot multiple signatures on the same plot
- `plot_signature_gene_quantiles()`: Plot signature with gene expression quantiles
- `plot_signature_transformed()`: Plot signatures with different transformations
- `plot_sample_space()`: Visualize sample relationships using PCA or UMAP
- `plot_mean_var()`: Mean-variance relationship plots
- `plot_gene_profiles()`: Individual gene expression profiles
- `plot_distribution_expression()`: Expression distribution plots
- `plot_distribution_pTAI()`: Partial TXI distribution plots
- `plot_distribution_pTAI_qqplot()`: Q-Q plots for pTXI distributions
- `plot_distribution_strata()`: Phylostrata distribution plots
- `plot_gene_heatmap()`: Gene expression heatmaps
- `plot_gene_space()`: Gene space visualization
- `plot_cullen_frey()`: Cullen-Frey plots for distribution assessment
- `plot_null_txi_sample()`: Null TXI sample plots
- `as_PhyloExpressionSet()`: Convert data to PhyloExpressionSet S7 object
- `get_sc_TAI()`: Single-cell TAI computation for Seurat objects=
- `diagnose_test_robustness()`: Diagnose statistical test robustness
- `remove_genes()`: Remove genes from PhyloExpressionSet
- `PS_colours()`: Generate phylostratum color palettes
- `ConservationTestResult()`: S7 class for conservation test results
- `TestResult()`: S7 class for statistical test results

### Enhanced Features
- Improved performance with parallelized C++ functions using RcppArmadillo
- All plots now use ggplot2 with consistent styling
- Comprehensive unit tests
- Updated to use modern R packages (ggplot2, dplyr, etc.)

### Breaking Changes
- Function names have been updated to snake_case convention
- PhyloExpressionSet is now an S7 object instead of a data.frame
- Function signatures have been updated for consistency
- Some deprecated functions have been removed
- New package dependencies: S7, RcppArmadillo

### Migration Guide
To migrate from myTAI 1.x to 2.0:

1. **Convert data format**:
   ```r
   # Old format (data.frame)
   old_phyex <- PhyloExpressionSetExample
   
   # New format (S7 object)
   new_phyex <- as_PhyloExpressionSet(old_phyex)
   ```

2. **Update function calls**:
   ```r
   # Old syntax
   PlotSignature(phyex_set, TestStatistic = "FlatLineTest")
   
   # New syntax
   plot_signature(phyex_set, conservation_test = flatline_test)
   ```

3. **Access computed properties**:
   ```r
   # Old syntax
   tai_values <- TAI(phyex_set)
   
   # New syntax
   tai_values <- phyex_set@TXI
   # or
   tai_values <- TAI(phyex_set)
   ```

myTAI 1.0.2.9000
===========
## New Functions
- New function `tfPS()` : Perform transformation of phylostratum values, analogous to `PS()` which transforms expression levels. Currently, `tfPS()` supports quantile rank transformation.
- New function `PairwiseTest()` : Statistically evaluate the pairwise difference in the phylotranscriptomic pattern between two contrasts based on \code{\link{TAI}} or \code{\link{TDI}} computations.
- New function `pairScore()` : Compute pairwise difference in TAI (or TDI) score.

## Bug and Issue Fixes
- Removed `taxonomy()` and references to it due to the deprecation of `taxize()`. This is needed for CRAN submission.

myTAI 1.0.1.9000
===========
## New Functions
- New function `PlotSignatureTransformed()` : Plot evolutionary signatures across transcriptomes and RNA-seq transformations
- New function `tfStability()`: Perform Permutation Tests Under Different Transformations (to test the robustness of the p-values of a given test (e.g. `FlatLineTest()`, `ReductiveHourglassTest()`, `ReverseHourglassTest()`, `EarlyConservationTest()` and `LateConservationTest()`) to expression data transformations)
- New function `LateConservationTest()` : Perform Reductive Late Conservation Test (to test for a high-mid-low (or high-high-low) TAI or TDI pattern)
- New function `lcScore()` : Compute the Hourglass Score for the LateConservationTest

- internal `rcpp` functions are now using Eigen to automatically enable parallelization

## New Features
- `PlotSignature()` updated to be able to perform the `TestStatistic = "LateConservationTest"`.
- `PlotSignature()` now prints p-value as a subtitle rather than via `ggplot2::annotate()`.
- `tf()` now has a `pseudocount` parameter, which is useful for performing logarithmic transformations when there are genes with 0 counts.
- `tf()` now supports `vst` and `rlog` transformations from [DESeq2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
- `tf()` now has an `intergerise` parameter, which is needed when applying `vst` or `rlog` transformations.
- `tf()` updated documentation for performing rank transformation, which assigns ranks to the gene expression values within each stage, based on their relative positions compared to other values.
- Improvements to existing test functions (`ecScore()`, `rhScore()` and `reversehourglassScore()`) to give a message when the phylotranscriptomic pattern is unlikely to follow the test statistics.

- `FlatLineTest()` - newly returns the ks test statistics for the fitting of gamma
- `FlatLineTest()` - improved fitting
- `FlatLineTest()` - cpp functions are newly parallelized and progress bar is implemented for the computation of permutations
  
## Bug and Issue Fixes
- Some changes to remove errors and warnings from `devtools::test()` and `devtools::check()`, when building this package, which has been accumulated from previous updates.

myTAI 1.0.0
===========
## New Functions
- New function `TEI()`: Compute the Transcriptome Evolutionary Index 
- New function `pMatrixTEI`: Compute Partial Transcriptome Evolutionary Index (TEI) Values 
- New function `pStrataTEI`: Compute Partial Transcriptome Evolutionary Index (TEI) Strata Values
- New function `bootTEI`: Compute a Permutation Matrix of Transcriptome Evolutionary Index (TEI)
- new internal `rcpp` functions to support parallel C++ computations for `TEI()`, `pMatrixTEI()`, `pStrataTEI()`, `bootTEI()`

## New Features
- `CollapseReplicates()` now returns `tibble` objects
- `PlotCategoryExpr()` received a new argument `y.ticks` 

## Bug and Issue Fixes

- `CollapseFromTo()` now has an exception when a replicate number `1` is passed to the function
-> previously this would cause an error to occur


myTAI 0.9.3
===========
- removing the depreciated `std::random_shuffle()` function to sample `plylostratum` or `divergence stratum` columns and replacing it with `std::shuffle()`. See full discussion [here](https://meetingcpp.com/blog/items/stdrandom_shuffle-is-deprecated.html).
- removing depreciated function calls such as `dplyr::funs()` and `tibble::is.tibble()`
- updated unit tests

myTAI 0.9.2
===========
- changing maintainer email-address


myTAI 0.9.1
===========

- fixing a unit test that uses `set.seed(123)` which causes an error in the new
R version `3.6.0` due to the switch from a `non-uniform "Rounding" sampler`
to a `"Rejection" sampler` in the new R version; the corresponding unit test `test-PlotEnrichment.R`
was adjusted accordingly. Here the CRAN statement:

>Note that this ensures using the (old) non-uniform "Rounding" sampler
for all 3.x versions of R, and does not add an R version dependency.
Note also that the new "Rejection" sampler which R will use from 3.6.0
onwards by default is definitely preferable over the old one, so that
the above should really only be used as a temporary measure for
reproduction of the previous behavior (and the run time tests relying on
it).


myTAI 0.9.0
===========

### New Functions

- new function `ReverseHourglassTest()` to perform a `Reverse Hourglass Test`.
The Reverse Hourglass Test aims to statistically evaluate the existence of a reverse hourglass pattern based on TAI or TDI computations. The corresponding p-value quantifies the probability that a given TAI or TDI pattern (or any phylotranscriptomics pattern) does follow an hourglass like shape. A p-value < 0.05 indicates that the corresponding phylotranscriptomics pattern does rather follow a reverse hourglass (low-high-low) shape.

- new function `reversehourglassScore()` for computing the `Reverse Hourglass Score` for the `Reverse Hourglass Test`

### Updated Functionality

- function `PlotSignature()` receives a new `TestStatistic` (`TestStatistic = "ReverseHourglassTest"`) to perform a `revserse hourglass test` (= testing
the significance of a low-high-low pattern) 


myTAI 0.8.0
===========

### Updated Functionality

- fix remaining issues when input is a `tibble` 


myTAI 0.7.0
===========

## Updates

### New Functions

- new function `PlotCIRatio()` to compute and visualize TAI/TDI etc patters using bootstrapping and confidence intervals (contributed by @ljljolinq1010)


### Update Functionality

- all functions can now handle `tibble` data as input -> before there were errors
thrown when input data wasn't in strict `data.frame` format

myTAI 0.6.0
===========

### Updates

- `is.ExpressionSet()` now prints out more detailed error messages when ExpressionSet is violated

- adapt `PlotContribution()` to new version of `dplyr` where `summarise_each()` is deprecated.

Error message occurring after new `dplyr` release was:

2. Failure: `PlotContribution()` works properly with DivergenceExpressionSet input... (@test-PlotContribution.R#16) 
  PlotContribution(DivergenceExpressionSetExample, legendName = "DS") produced messages.
  
  
  `summarise_each()` is deprecated.
  Use `summarise_all()`, `summarise_at()` or `summarise_if()` instead.
  To map `funs` over all variables, use `summarise_all()`
  `summarise_each()` is deprecated.
  Use `summarise_all()`, `summarise_at()` or `summarise_if()` instead.
  To map `funs` over all variables, use `summarise_all()`
  
Is now fixed.  


myTAI 0.5.0
===========

### New Functions

- new function `PlotSignature()` allows users to plot evolutionary signatures across transcriptomes (based on ggplot2 -> new main visualization function aiming to replace the `PlotPattern()` function)

- new function `TPI()` allows users to compute the Transcriptome Polymorphism Index introduced by `Gossmann et al., 2015`.

- new function `PlotMedians()` allows users to compute and visualize the median expression of all age categories

- new function `PlotVars()` allows users to compute and visualize the expression variance of all age categories

### Updates

- `PlotContribution()` is now based on ggplot2 and loses base graphics arguments

- now R/RcppExports.R and src/rcpp_funcs.cpp are included in the package due to previous compilation problems (see also [stackoverflow discussion](https://stackoverflow.com/questions/34585560/travis-ci-r-package-error-in-documentation))

- `MatchMap()` is now based on `dplyr::inner_join()` to match age category table with a gene expression dataset

- `PlotCorrelation()` has been extended and optimized for producing high publication quality plots 

- `PlotMeans()` is now based on ggplot2 and lost all base graphics arguments.

- `PlotRE()` is now based on ggplot2 and lost all base graphics arguments.

### Vignettes

- In `Introduction` vignette: complete restructuring of the Introduction 
- In `Introduction` vignette: add new ggplot2 based examples

 
 
myTAI 0.4.0
===========

### New Functions

- a new function `PlotSelectedAgeDistr()` allowing unsers to visualize the PS or DS gene distribution of a subset of genes stored in the input ExpressionSet object
- a new function `PlotGroupDiffs()` allowing users to plot the significant differences between gene expression distributions of PS or DS groups
- a new function `GroupDiffs()` allowing users to perform statistical tests to quantify the gene expression level differences between all genes of defined PS or DS groups 

### Updates

- `PlotDistribution()` now uses ggplot2 to visualize the PS or DS distribution and
is also based on the new function `PlotSelectedAgeDistr()`; furthermore it loses arguments `plotText` and `...` and gains a new argument `legendName`

- remove arguments 'main.text' and '...' from `PlotCorrelation()`
- `PlotCorrelation()` is now based on ggplot2
- `PlotGroupDiffs()` receives a new argument `gene.set` allowing users to statistically quantify the group specific PS/DS differences of a selected set of genes
- analogously to `PlotGroupDiffs()` the function `GroupDiffs()` also receives a new argument `gene.set` allowing users to statistically quantify the group specific PS/DS differences of a selected set of genes
- Fixing wrong x-axis labeling in `PlotCategoryExpr()` when `type = "stage-centered"` is specified
- `PlotCategoryExpr()` now also prints out the PS/DS absolute frequency distribution of the selected `gene.set`

myTAI 0.3.0
===========

### Vignettes

- adding examples for `PlotCategoryExpr()` to `Advanced` Vignette
- adding examples for `PlotReplicateQuality()` to `Expression`
 vignette
 
### New Functions

- a new function `PlotCategoryExpr()` allowing users to plot the expression levels of each age or divergence category as boxplot, dot plot or violin plot
- a new function `PlotReplicateQuality()` allowing users to visualize the quality of biological replicates


myTAI 0.2.1
===========

### Vignettes

- fixed a wrong example in the Enrichment vignette (https://github.com/HajkD/myTAI/commit/8d52fd60c274361dc9028dec3409abf60a738d8a)


### Updates

- `PlotGeneSet()` and `SelectGeneSet()` now have a new argument `use.only.map` specifying whether or not instead of using a standard `ExpressionSet` a `Phylostratigraphic Map` or `Divergene Map` is passed to the function.
- a wrong version of the edgeR Bioconductor package was imported causing version 0.2.0 to fail R CMD Check on unix based systems


myTAI 0.2.0
===========

### Vignettes

- adding new vignette __Taxonomy__ providing spep by step instructions on retrieving taxonomic information for any organism of interest

- adding new vignette __Expression Analysis__ providing use cases to perform gene expression
data analysis with `myTAI`

- adding new vignette __Enrichment__ providing step-by-step instructions on how to perform PS and DS enrichment analyses with `PlotEnrichment()`

- adding examples for `pStrata()`, `pMatrix()`, `pTAI()`, `pTDI()`, and `PlotContribution()`
to the __Introduction__ Vignette

### New Functions

- a new function `taxonomy()` allows users to retrieve taxonomic information for any organism of interest; this function has been taken from the [biomartr](https://github.com/ropensci/biomartr) package and was removed from `biomartr` afterwards. Please notice, that in myTAI version 0.1.0 the Introduction vignette referenced to the `taxonomy()` function in `biomartr`. This is no longer the case (since myTAI version 0.2.0), because now `taxonomy()` is implemented in myTAI. 

- the new `taxonomy()` function is based on the powerful R package [taxize](https://github.com/ropensci/taxize).

- a new function `SelectGeneSet()` allows users to fastly select a subset of genes in an ExpressionSet

- a new function `DiffGenes()` allows users to perform differential gene expression analysis with ExpressionSet objects

- a new function `EnrichmentTest()` allows users to perform a Fisher's exact test based enrichment analysis of over or underrepresented Phylostrata or Divergence Strata within a given gene set without having to plot the result

- a new function `PlotGeneSet()` allows users to visualize the expression profiles of a given gene set

- a new function `PlotEnrichment()` allows users to visualize the Phylostratum or Divergence Stratum enrichment of a given Gene Set as well as computing Fisher's exact test to quantify the statistical significance of enrichment

- a new function `PlotContribution()` allows users to visualize the Phylostratum or Divergence Stratum contribution to the global TAI/TDI pattern

- a new function `pTAI()` allows users to compute the phylostratum contribution to the global TAI pattern

- a new function `pTDI()` allows users to compute the divergence stratum contribution to the global TDI pattern

### Updates

- `FilterRNASeqCT()` has been renamed to `Expressed()` allowing users to apply this filter function
to RNA-Seq data as well as to microarray data 
- `PlotRE()` and `PlotMeans()` are now based on colors from the RColorBrewer package (default)
- `PlotRE()` and `PlotMeans()` now have a new argument `colors` allowing unsers to choose custom colors for the visualized relative or mean expression profiles 
- `geom.mean()` and `harm.mean()` now are external functions accessible to the `myTAI` user

myTAI 0.1.0
===========

### Main News

- now all functions have unit tests

### New Functions

- a new function `pStrata()` allows users to compute partial TAI/TDI values for all Phylostrata or Divergence Strata

- a new function `CollapseReplicates()` allows users to combine replicate expression levels in ExpressionSet objects

- a new function `FilterRNASeqCT()` allows users to filter expression levels of `ExpressionSet` objects deriving from RNA-Seq count tables  

### Updates

- function `MatchMap()` now receives a new argument `remove.duplicates` allowing users to delete
duplicate gene ids (that might be stored in the input PhyoMap or DivergenceMap) during the process of matching a Map with an ExpressionSet

- `FlatLineTest()`, `ReductiveHourglassTest()`, `EarlyConservationTest()`, and `PlotPattern()` implement a new argument `custom.perm.matrix` allowing users to pass their own (custom) permutation matrix to the corresponding function. All subsequent test statistics and p-value/std.dev computations are then based on this custom permutation matrix

- `EarlyConservationTest()` and `ReductiveHourglassTest()` now have a new parameter `gof.warning` allowing users to choose whether or not non significant goodness of fit results should be printed as warning

- now when specifying `TestStatistic = NULL` in `PlotPattern()` only the TAI/TDI profile is drawn (without performing any test statistics); this is equavalent to performing: `plot(TAI(PhyloExpressionSetExample)`

- function `combinatorialSignificance()` is now named `CombinatorialSignificance()`

- changing the title and description of the `myTAI` package 

- some minor changes in vignettes and within the documentation of functions


myTAI 0.0.2
===========

## New Features in v. 0.0.2

- `combinatorialSignificance()`, `FlatLineTest()`, `ReductiveHourglassTest()`, and `EarlyConservationTest()`
now support multicore processing

- `MatchMap()` has been entirely rewritten and is now based on [dplyr](https://github.com/tidyverse/dplyr); additionally
it now has a new argument `accumulate` that allows you to accumulate multiple expression levels to a unique expressiion level for a unique gene id

### Vignettes

All three Vignettes: `Introduction`, `Intermediate`, and `Advanced` have been updated and extended.

### Bug Fixes

- two small bugs in `ReductiveHourglassTest()` and `EarlyConservationTest()` have been fixed that caused
that instead of displaying 3 or 4 plots (`par(mfrow=c(1,3))` or `par(mfrow=c(2,2))`) only 1 plot has been generated

- a small bug in `PlotMeans()` that caused the visualization of a wrong y-axis label
when plotting only one group of Phylostrata or Divergence Strata


myTAI 0.0.1
===========

Introducing myTAI 0.0.1:

A framework to perform phylotranscriptomics analyses for Evolutionary Developmental Biology research.
