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Changelog

Source: NEWS.md

rTASSEL 0.13.0

  • Added installation of TASSEL from the standalone archives published on GitHub, which is the only source of nightly builds:
    • setupTASSEL(source = "github") installs the newest nightly build cut from TASSEL’s develop branch
    • A specific build can be pinned by version ("5.2.98-dev.20260801") or by release tag ("dev-20260801"), and tagged releases can be installed the same way with "latest" or "v5.2.97"
    • Archives bundle every dependency, so no dependency resolution is needed, and each download is verified against its published SHA-256 checksum
    • Nightly builds are cached beside released versions under their full version, so both can be installed at once and switched between with options(rTASSEL.tassel.version = ...)
    • GITHUB_PAT or GITHUB_TOKEN is used for release lookups when set, which avoids the anonymous GitHub rate limit
  • The startup message now names which channel the loaded JARs came from, distinguishing a nightly build from a released version
  • Update checks follow the installed channel: a nightly install is checked against the newest nightly build rather than Maven Central, so it is never prompted to “upgrade” to an older release. The channel can also be queried directly with checkForTASSELUpdate(channel = "nightly")
  • Added automatic TASSEL update checks:
    • library(rTASSEL) now checks Maven Central for a newer TASSEL release and reports it in the startup message
    • The check runs at most once per day and caches its result on disk
    • Only versions that rTASSEL can actually install are reported, so an incomplete upload upstream will not prompt an unusable upgrade
    • Skipped in non-interactive sessions, during R CMD check, and on CI; network failures are ignored
    • Disable with options(rTASSEL.check.updates = FALSE) or the RTASSEL_NO_VERSION_CHECK environment variable
  • Added new function checkForTASSELUpdate() to run the check on demand
  • Added Maven dependency resolution so setupTASSEL() can install TASSEL releases published without a bundled dependency JAR:
    • Detects whether a release ships a fat JAR or a thin JAR plus a POM
    • Resolves the transitive dependency tree from the POM, honoring parent inheritance, dependency management, BOM imports, scopes, optional dependencies, exclusions, and nearest-wins version conflicts
    • Fetches artifacts from Maven Central, SciJava, and JBoss, matching the repositories used by TASSEL’s own build
    • Drops artifacts superseded by a newer coordinate under a different name, such as google-collections alongside guava, which would otherwise shadow each other on the classpath
  • The startup message now reports the TASSEL version the JVM actually loaded rather than the version rTASSEL expected, which differed when JARs came from a user-supplied rTASSEL.java.path
  • Added tracking of the active TASSEL version:
    • setupTASSEL() records the version it installs, so a newly installed version is loaded on the next library(rTASSEL)
    • Override with options(rTASSEL.tassel.version = ...)
    • Fixes a bug where installing any version other than the pinned default left rTASSEL reporting “TASSEL JARs not found”
  • Every downloaded artifact is now verified against its published SHA-1 checksum, rather than only the pinned default version
  • setupTASSEL(force = TRUE) now clears the cached version first, so stale dependency JARs cannot linger on the classpath
  • Moved digest from Suggests to Imports and added jsonlite to Imports

rTASSEL 0.12.0

  • Added new LDResults class:
    • Stores pairwise LD statistics and analysis parameters from linkageDiseq()
  • Added new LDRegion class:
    • Defines genomic regions for highlighting LD blocks on plotLD() plots
  • Added new function plotLD():
    • Replaces deprecated ldPlot() with a redesigned LD heatmap
    • Supports Haploview and viridis-family color schemes
    • LD block highlighting via LDRegion objects
    • Optional genomic position track above the heatmap
    • Toggleable site index labels along the diagonal
  • Added new function plotSnpDensity():
    • Generates heatmap-style SNP density plots across chromosomes
    • Configurable window size, viridis color palettes, and log-scaled counts
  • Removed deprecated ldPlot() and ldJavaApp() functions
  • Removed deprecated interactive Java visualizations section from vignette
  • Updated vignette with new LD and SNP density visualization sections

rTASSEL 0.11.0

  • Add fixes to possible issues related to ggplot2 v4.0
  • Bug fixes for filterGenotypeTableSites():
    • Fixed error “missing value where TRUE/FALSE needed” when filtering by position with matching start/end chromosomes and NULL position values
    • Added input validation for negative startSite and endSite values
    • Added input validation for negative startPos and endPos values
  • Removed bundled JAR files from inst/java/ to reduce package size
  • Added setupTASSEL() function to download TASSEL JARs from Maven Central and cache them locally
  • Added JAR resolution system with priority: user option, Maven cache, then bundled (legacy fallback)
  • Replaced all class() == checks with inherits() for proper S4 class handling
  • Fixed implicit S4 generic imports from BiocGenerics (colnames, rownames, ncol, nrow)
  • Improved package startup messages using cli formatting
  • Consolidated GitHub Actions workflows into a single ci.yaml
  • Added unit tests for setup, constants, and package loading
  • Added BiocGenerics to Imports; digest and withr to Suggests

rTASSEL 0.10.0

rTASSEL 0.9.33

rTASSEL 0.9.32

  • Updated tableReport() method dispatch for all AssociationResults objects:
    • Will now return default statistics output for all association results when running tableReport(assocObj) where assocObj is an object of type AssociationResults
  • Removed HDF5 file export support
  • Improved logic support for plotPCA()

rTASSEL 0.9.31

  • Added new PCAResults class
    • Allows for more controlled access of data and simplified downstream functions for end users
  • Add new function plotScree():
    • Generates quick scree plots from PCAResults objects
  • Add new function plotPCA():
    • Generates quick PCA plots from PCAResults objects
    • Allows for grouping from generated hierarchical clustering or grouping from metadata via the metadata parameter and subsequent mCol parameters.

rTASSEL 0.9.30

  • Added new AssociationResults class
    • Allows for more controlled access of data and simplified downstream functions for end users
  • Added new function plotManhattan():
    • Supercedes older Manhattan plotting methods to work with new AssociationResults class.
  • Added new function plotQQ():
    • Plotting function for QQ results from AssociationResults class
  • Added new function plotManhattanQC():
    • Plotting function and QC method for zoomed in regions of interest across genome
  • Prior 3 functions also include interactive component that wraps ggplot2 objects with PlotlyJS components

rTASSEL 0.9.29

  • Added genotype table summary methods:
  • TasselGenotypePhenotype objects containing genotype table data can now be coerced into R matrix objects using the function as.matrix()
    • This will return a taxa x site matrix where taxa is the number of rows and sites is the number of columns.
  • Added generalized join methods:
  • Added read method for importing GIGWA data through QBMS:

rTASSEL 0.9.28

  • Fixed log4j warning issue
    • This removes log4j warning messages when the startLogger() function is called.
  • Removed useRef parameter from getSumExpFromGenotypeTable() function.
    • This is now automatically detected from the file input.
    • This fixes ref/alt allele vs major/minor allele encoding issues.
  • Added Journal of Open Source Software citation for the rTASSEL package.
    • For citation information, use utils::citation("rTASSEL")
  • Added data object, rtPaths
    • Includes paths to external toy data for rTASSEL

rTASSEL 0.9.27

  • No significant updates in this version. This version is virtually identical to 0.9.26 and is for linking to Zenodo for archival purposes.

rTASSEL 0.9.26

  • Bug fixes:
    • Fixed r2 parameter bug in ldPlot()
    • Fixed space bugs in certain column names of data frame objects. _ values now replace spaces.
    • Fixed show() method for TasselDistanceMatrix objects.
  • Add new function:
    • seqDiversity()
    • Calculates diversity basic diversity metrics on genetic data.

rTASSEL 0.9.25

  • Bug fixes:
    • Fixed character conversion bug in DataFrame object returns.
  • pca() can optionally report eigenvalues and eigenvectors as a list object.
  • Added new function:
  • Added new function:
    • imputLDKNNi()
    • Allows for LD KNNi imputation of GenotypeTable objects.

rTASSEL 0.9.24

  • Added new function:
    • pca()
    • Allows for user to run PCA on rTASSEL objects containing a GenotypeTable object.
  • Added new function:
    • mds()
    • Allows for user to run MDS on TasselDistanceMatrix objects.
  • Enhancements:
    • New summary print output for TasselDistanceMatrix objects.

rTASSEL 0.9.23

  • Added new TasselDistanceMatrix class
    • Specified function (kinshipMatrix() and distanceMatrix()) now return an object of type TasselDistanceMatrix.
    • Prevents console overload and freezing as seen with large distance matrix objects.
    • Now shows summary overview of matrix instead of Java object reference.
    • Generic functions colnames(), rownames(), ncol(), and nrow() will return relative information similar to how these operate with matrix type objects.
    • Primitive function as.matrix() now supersedes deprecated functions kinshipToRMatrix() and distanceToRMatrix().
    • Prior functions that take in a kinship object will now take in this new class.
  • Added new function:
  • Added new function:
    • asTasselDistanceMatrix()
    • Coerces a pairwise matrix (e.g. m x m dimensions) with the same column and row names of type matrix to an object of type TasselDistanceMatrix.
  • Added new function:
    • createTree()
    • interface to TASSEL’s tree creation methods
    • Allows for Neighbor_Joining and UPGMA methods
  • Added new function:
    • treeJavaApp()
    • wrapper for TASSEL’s interface to the Archaeopteryx Java tree Viewer
    • Implements same methods for tree creation as createTree()

rTASSEL 0.9.22

  • Fix manhattanPlot() aesthetics:
    • Remove redundant marker labels from x-axis
    • Change x-axis label to SNP Positions

rTASSEL 0.9.21

rTASSEL 0.9.20

rTASSEL 0.9.19

  • Added two new parameters to filterGenotypeTableSites()
    • removeMinorSNPStates: Boolean; removes minor SNP states.
    • removeSitesWithIndels: Boolean; removes sites with indels.
  • Added better descriptive error handling for filterGenotypeTableSites()
  • Fixed siteRangeFilterType parameter bug in filterGenotypeTableSites(). Now defaults to none when user does not specify filter type.
  • Added two new parameters to getSumExpFromGenotypeTable()
    • coerceDosageToInt: Returns raw byte dosage array instead of integer from Java.
    • verbose: Display console messages for large “memory-intensive” datasets.

rTASSEL 0.9.18

  • Added functions to calculate linkage disequilibrium (LD)
  • Proposed LD functions:
    • linkageDiseq() - Returns TASSEL LD table report as data frame
    • ldPlot() - Returns static ggplot2 plot
    • ldJavaApp() - Initiates TASSEL’s interactive LD viewer

rTASSEL 0.9.17

  • Added new function:
    • manhattanPlot()
  • Removed tidyverse dependencies

rTASSEL 0.9.16

  • Added write to file parameters for:
    • assocModelFitter()
  • Added p-value threshold parameters for:
    • assocModelFitter()
  • Added thread usage paramters for:
    • assocModelFitter()
  • Optimized table report to data frame generation
  • Added new filtration features for genotype tables via filterGenotypeTableSites()
    • parameters for variant sites
    • parameters for physical positions
    • filtration via chromsomome position files
    • filtration via BED file formats

rTASSEL 0.9.13

  • Added error checks for catching C stack usage errors for the following functions:
    • filterGenotypeTableSites()
    • filterGenotypeTableTaxa()
  • Added NEWS file for tracking version updates.

rTASSEL 0.9.12

  • Added new functions:
    • leaveOneFamilyOut()
    • genomicPredction()
  • Fixed a bug where tibbles when passed through readPhenotypeFromDataFrame(), would cause errors.