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OLDNEWS.md

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propriety 1.0.1

  • Replace alphaTheta with improved calculateTheta
    • Now calculates emergent proportionality (theta_e)
    • Now checks for @theta$lrv == 0 (NaN theta)
  • Modified propd function
    • FDR now handled by updateCutoffs function
    • New setDisjointed function makes theta_d active
    • New setEmergent function makes theta_e active
    • Now calculates F from theta_d
  • Modified visualization tools
    • Remove "Bridged" and "Missing" pairs from figures
    • geiser function omits "Bridged" and "Missing" pairs
    • gemini function omits "Bridged" and "Missing" pairs
    • New bowtie function plots log-ratio means by group
  • Modified plot function
    • New plotSkip argument used by pals to skip plot
    • Colors edges by LRM if using theta_d
    • Colors edges by LRV if using theta_e

propriety 1.0.0

  • Include a sample propd object for vignette examples
    • Built using non-zero features with at least 40 counts
  • Add conceptualization and implementation of PAL
    • New pals function computes the popular adjacent ligand
  • Add table and visualization tools
    • New shale function produces table used for graphing
    • New geiser function plots VLR1 vs. VLR2
    • New gemini function plots log-fold VLR vs. LRMs
    • New slice function plots log-ratio abundance
  • Modified plot function
    • Labels disjointedly proportional edges in yellow
    • Now augments graph using an indexed propr object
    • Integer cutoff now selects top N pairs
    • Now supports 3D visualization
  • Add propd vignette

propriety 0.0.7

  • Modified calculateTheta and alphaTheta functions
    • No longer returns a sorted data.table object

propriety 0.0.6

  • Modified calculateTheta and alphaTheta functions
    • Now returns a sorted data.table object
  • Add progress bar and migraph functions
  • New plot method for propd object

propriety 0.0.5

  • New half2mat function builds matrix from half-matrix
  • New propd2propr function converts propd to propr
    • Allows propd to inherit propr methods

propriety 0.0.4

  • Modified propd function
    • Use ctzRcpp to track joint zero frequency
    • Use lrmRcpp to calculate log-ratio mean
    • Help file includes messy LaTeX formulae
  • Update documentation
    • README and vignette outlined with theory
  • Deprecate outdated C++ code

propriety 0.0.3

  • New propd class and function
    • Provides front-end for theta calculation
    • alpha argument toggles theta method
    • Include a unit test for new FDR
  • Extended proportionality statistic theta
    • New alphaTheta function
    • Back-end handled by the boxRcpp function
  • Included slow implementations for testing
    • Deprecated alphaTheta_old
  • All permutation functions now deprecated

propriety 0.0.2

  • Extended proportionality statistic theta
    • New calculateFDR function
  • Removed unused C++ code

propriety 0.0.1

  • Introduced proportionality statistic theta
    • New calculateTheta function
    • New permuteTheta function
  • Included slow implementations for testing
    • Deprecated calculateTheta_old
    • Deprecated permuteTheta_old
  • Added unit tests
    • New and old calculateTheta match
    • New and old permuteTheta match