OLDNEWS.md

In tpq/propr: An R package to calculate proportionality and other measures for compositional data

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• Deprecate outdated C++ code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

tpq/propr documentation built on April 21, 2024, 12:50 p.m.