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propr 5.1.8

  • Use feature-wise permutation for propr()
  • Fix bug when calling updateCutoffs with func
  • Use harmonic mean when calculating weighted lrv and lrm
  • Add trend=TRUE flag for updateF to use mean-variance trend in limma moderation
  • Use sample weights for limma when calculating weighted theta in propd()

propr 5.1.7

  • Added option to shrink the covariance matrix before computing the propd theta
  • Fix issues when using user provided weights in propd function

propr 5.1.6

  • Added option to use user provided weights in propd function

propr 5.1.5

  • Fixed bug in updateCutoffs related to the use of custom_cutoffs
  • Fixed runNormalization to properly work when theta_mod is used

propr 5.1.4

  • Added results_to_matrix function

propr 5.1.3

  • Corrected tails = 'both' to symmetric two-sided FDR test

propr 5.1.2

  • Restructured graflex to speed up

propr 5.1.1

  • Speed up graflex related functions

propr 5.1.0

  • Allowed updateCutoffs function to compute the FDR values for negative cutoffs
  • Added getCutoffFDR to get a significant cutoff based on the permuted FDR
  • Changed runCutoff into getCutoffFstat
  • Added getSignificantResultsFDR and getSignificantResultsFstat to get the significant pairs as results table
  • Added getAdjacencyFDR and getAdjacencyFstat functions to get the adjacency matrix with the significant pairs
  • Optimized graflex related functions to Rcpp C++
  • Removed fixseed, since setting set.seed() before calling any function is enough to ensure reproducibility
  • Fix bug: when ivar=NA, the already preprocessed data given by the user are replaced when there are zeros, which should not
  • Replaced ppcor::pcor by corpcor::cor2pcor for coherence with the shrunk partial correlations
  • Parallelized propd when ncores > 1

propr 5.0.4

  • Added fixseed option for runGraflex
  • Fix bug: NAs produced by integer overflow in getOR

propr 5.0.3

  • Added fixseed option for updatePermutes

propr 5.0.2

  • Merge parts of graflex package into propr

propr 5.0.1

  • Fix bug: change NA in alr partial correlation to 0 so that FDR can be computed
  • Fix bug: implemented updatePermutes inside propr() and propd()
  • Added corpcor and ppcor in imports
  • Update README and CITATION

propr 5.0.0

  • Merge pull request for new shrinkage method
  • Remove any function that exists only to produce plots
  • Rename functions:
    • Rename pra to selectRatios
    • Rename getReference to selectReference
    • Rename qtheta to runCutoff
    • Rename getNormTheta to runNormalization
    • Rename posthoc to runPostHoc
    • Rename back-end functions

propr 4.3.0

  • Fix bug: partial correlation FDR cutoff checks wrong direction
  • Fix bug: lr2cor saves t-statistic, not r-statistic

propr 4.2.9

  • Accept speed-up pull requests from Ryan Moore
  • Add support for partial correlations
    • ppcor package called by propr(x, metric = "pcor")
    • corpcor package called by propr(x, metric = "pcor.shrink")

propr 4.2.8

  • Add updateCutoffs warning for asymmetric phi FDR call

propr 4.2.7

  • Allow user to skip log-ratio transformation with ivar = NA

propr 4.2.6

  • Fix new R version class bug where matrix is also an array

propr 4.2.5

  • New posthoc method
    • Performs post-hoc testing for an ANOVA of >2 groups

propr 4.2.4

  • Update CITATION and README

propr 4.2.3

  • Update propd method
    • calculateTheta extended to support ANOVA with >2 groups
    • propd updated to allow >2 groups
  • Modified visualization tools
    • Add checks for methods that require 2 groups
    • parallel should support 3 groups

propr 4.2.2

  • Update pra method
    • Fix bug introduced by tryCatch

propr 4.2.1

  • Revise vignettes for thesis publication

propr 4.2.0

  • Update pra method
    • Add tryCatch to handle the Lapack routine 'dgesdd' error
    • This error occurs when the SVD fails to converge

propr 4.1.9

  • Update get methods
    • Pass cutoff and other arguments to getColours
    • Have getColours show which feature is DE

propr 4.1.8

  • New updateCutoffs.propr parallel update
    • Add parallel check and alternate computation for ncores > 1
    • Pass ncores argument from updateCutoffs wrapper

propr 4.1.7

  • New get methods
    • New getNormTheta calculates a per-feature theta against normalization factors
    • New getColour colours pairs based on differential expression results

propr 4.1.6

  • Update propr methods
    • Fix error where select is used in presence of zeros
  • Update propd methods
    • All methods now use N + propd@dfz degrees-of-freedom
    • Omega no longer used for F-statistic by updateF
    • Omega no longer used for cutoff by qtheta

propr 4.1.5

  • Update qtheta methods
    • New fdr argument in qtheta method returns cutoff for FDR-adjusted p-value
    • Remove moderated argument from qtheta method
  • Update get methods
    • New getAdj offers a faster alternative to getAdjacency
    • Have getAdjacency and getMatrix set diagonal to 0

propr 4.1.4

  • Update propd methods
    • Return to using N-K degrees-of-freedom for pf and qf calls
    • Have qtheta still use Omega (biased) to calculate theta from F-stat

propr 4.1.3

  • Update propd methods
    • Now compute F-stat and F-mod using Omega (biased) for weighted thetas
    • Now compute p-value from F-stat and F-mod using Omega (biased) degrees-of-freedom
    • Update qtheta to use Omega (biased) degrees-of-freedom
    • Remove superfluous calculateTheta input checks
    • Stop export of calculateTheta function
  • Update C++ backend
    • Add Omega function to compute population-level pre-factor
    • Remove superfluous first argument to omega function

propr 4.1.2

  • New tests
    • Add getMatrix test

propr 4.1.1

  • New get methods
    • Add getMatrix to return propr or propd object as matrix

propr 4.1.0

  • Update propd methods
    • Have updateF return NA theta_mod when moderated = FALSE
    • Have updateF return BH-adjusted p-values
  • Update get methods
    • Add or argument to getResults, toggles how include works
    • Add or argument to getNetwork, toggles how include works
    • Add or argument to getRatios, toggles how include works
  • Add methods
    • New getAdjacency function returns adjacency matrix
    • Uses include and or arguments

propr 4.0.9

  • Update propd methods
    • Add theta_g routine to calculateTheta

propr 4.0.8

  • Add methods
    • New pra method for principal ratio analysis
    • Add vegan to NAMESPACE

propr 4.0.7

  • General maintenance
    • Fix getResults warning
    • Fix getReference bug

propr 4.0.6

  • Update propr methods
    • Extend propr function and object to support metric = "vlr"
  • Update propd methods
    • Add setEmergent warning for unequal group sizes
    • Extend parallel to replace slice
  • Update get methods
    • Now use only one color for getNetwork of theta_d (cytescape still uses two)
    • New include argument for getResults, getNetwork, and getRatios

propr 4.0.5

  • Add methods
    • New parallel method visualizes sample-wise log-ratios
  • Update getResults method
    • For propd objects, any cutoff > 1 will return top N pairs
    • Now always return data sorted according to outcome
  • Update getRatios method
    • For propd objects, define ratio so Group 1 is at top

propr 4.0.4

  • Add methods
    • Add getReference to find a component proportional to center
  • Update getRatios method
    • Now subsets ratios to include only pairs returned by getResults
  • Update zero handling
    • Package now replaces 0s with next smallest value (instead of 1)
  • General maintenance
    • Stop slate and shale export

propr 4.0.3

  • Update getNetwork method
    • Simplify use by guessing network type based on first argument

propr 4.0.2

  • Update propr method
    • Fix bug where alpha-based method always used ivar = "clr"
  • Update ratios method
    • Add alpha argument to set LR = (partner^alpha - pair^alpha) / alpha
    • Now returns log-ratios instead of ratios
  • Add methods
    • Add wide2long to melt counts and log-ratios for visualization
    • Add getRatios function to retrieve melted log-ratios
  • Add tests
    • Add test for getNetwork
    • Add test for getRatios

propr 4.0.1

  • Add methods
    • Add getResults to retrieve results from a propr or propd object
    • Add getNetwork to build networks from propr and propd objects

propr 4.0.0

  • Update ivar2index method
    • Now replaces zeros with 1 to calculate IQR (fixes "iqlr" bug for alpha > 0)
  • Update propr object backend and API
    • Heavily revise documentation to harmonize propd with propr
    • Create propr function to replace perb, phit, and phis
    • Add @results slot for storing proportionality half-matrix
    • Add @permutes slot for storing reproducible permutations
    • Update subset and [ to disable @results and @permutes
    • Add @fdr slot for storing FDR results
    • Add alpha argument
      • Adjusts alpha-based VLR by var[(component^alpha - reference^alpha)/alpha]
      • Saves alpha to @alpha and alpha-based counts to @logratio
      • Note this is not yet technically equivalent to propd method
    • Add updateCutoffs function to permute FDR for proportionality
      • Add @metric, @ivar and @alpha slots to calculate metric exactly
      • Count rho > cutoff and cor > cutoff as positive results
      • Count phi < cutoff and phs < cutoff as positive results
  • Update propd object backend and API
    • Heavily revise documentation to harmonize propd with propr
    • Fix bug where zeros still get replaced for lrm calculation
    • The updateCutoffs function is now an S4 method
    • Turn @theta slot into @results slot
    • Rebuild pd.d and pd.e objects
  • Update aldex2propr method
    • Update aldex2propr and [ to disable @results and @permutes
    • Add lr2glm and aldex.glm functions
  • Add methods
    • Add qtheta to calculate a cutoff of theta for a given p-value
  • Remove methods
    • Remove differentialCheck
    • Remove prop2prob
    • Remove abstract
    • Remove initialize
    • Remove adjacent
  • Revise vignettes

propr 3.5.1

  • Update CITATION file and README

propr 3.5.0

  • Update alpha-transformation routine
    • Update lrm C++ code
      • Clone Yfull and set to power of alpha
      • Add argument Wfull for complete weights (and check)
      • Update calls to pass Wfull if provided
      • Implement new non-weighted alpha-transformed means
      • Implement new weighted alpha-transformed means
      • Revise alpha-based unit tests
    • Update lrv C++ code
      • Clone Yfull and set to power of alpha
      • Add argument Wfull for complete weights (and check)
      • Update calls to pass Wfull if provided
      • Implement new non-weighed alpha-transformed variances
      • Implement new weighted alpha-transformed variances
      • Revise alpha-based unit tests
    • Remove lrz function

propr 3.2.0

  • Prepare alpha-transformation routine for update
    • Update lrm C++ code
      • Add argument a and prepare code for alpha-based lrm
      • Add argument Yfull for complete data (and check)
      • Update calls to pass Yfull if provided
    • Update lrv C++ code
      • Add argument Yfull for complete data (and check)
      • Update calls to pass Yfull if provided

propr 3.1.9

  • Update C++ code to use && and || instead of & and |

propr 3.1.8

  • Modified propd methods
    • Users can now disable alpha transformation by setting alpha = 0
    • Improve NaN theta value replacement with 1
    • Modified updateF for moderated = TRUE
      • Now offsets counts by 1 to prevent zeros in reference set
      • Now correctly checks for zeros in reference set

propr 3.1.7

  • Check propr and propd input for negative counts
  • Modified propd methods
    • Add dfz slot to the propd class (defaults to 0)
      • Have updateF populate dfz slot if moderated
      • Use dfz to calculate p-value from F-stat
    • Implement revised F-stat moderation
      • Now uses simple moderation term based only on LRV
      • Update test-Fstat.R to reflect changes

propr 3.1.6

  • Modified propd methods
    • Allow p = 0 when initializing propd objects
    • Have calculateTheta compute new weights each permutation

propr 3.1.5

  • Update propr to work with Rcpp >= 0.12.12
  • Modified propd methods
    • All out-of-bounds theta_mod replaced with 1
    • Add @Fivar slot to the propd class
    • Extend updateCutoffs to theta_mod

propr 3.1.4

  • Automatically set @matrix column names when using propr
  • Address notice by CRAN about using Suggests conditionally
    • Vignette will no longer calculate theta when weighted = TRUE
    • Tests for "Fstat" and "theta" now check for limma

propr 3.1.3

  • New ratios and ratiosRcpp functions recast matrix as feature ratios

propr 3.1.2

  • Rename "Calculating Differential Proportionality" vignette
  • Update CITATION file and README
  • Modified propd methods
    • Stop plot functions from creating surplus figure in notebook
    • Use theta_d network method for any non-emergent theta type
    • Add suppressWarnings to compositions::plot call

propr 3.1.1

  • New vignette to discuss F-statistics
  • Modified propd methods
    • Add suppressWarnings to compositions::acomp call

propr 3.1.0

  • Modified propd methods
    • The propd function no longer calls updateCutoffs
    • The calculateTheta function no longer calculates F-statistic
    • Update vignette to reflect these changes
    • Object now stores weights if weighted
  • Modified calculateTheta
    • Added weights argument to pass pre-computed weights
    • Still calculates weights if NA weights argument
    • Consolidated weighted and alpha lrv calls
  • Modified C++ backend
    • Extend lrv to weighted alpha calls
    • Added unit test for weighted alpha calls
    • Merge boxRcpp with lrv and remove boxRcpp
    • Merge lrmRcpp with lrm and remove lrmRcpp
    • Rename lrvMod function to omega
  • New updateF function
    • Added new ivar2index function used by propr and updateF
    • Calculates 4 types of moderated F-statistics
    • Calculates 4 types of non-moderated F-statistics
    • Update propd documentation to reflect change
    • Extend moderation to non-clr references

propr 3.0.7

  • New corr function calculates log-ratio based correlation
  • Fixed mistake with vignette indexing

propr 3.0.6

  • Modified visualization tools
    • Correctly spell geiser function as geyser
    • Allow propd methods to accept 0s
  • Update documentation
    • Finish revision of all vignettes

propr 3.0.5

  • Modified propd Class
    • Now only replaces 0s if alpha is missing or NA
    • Now tabulates 0s whether replaced or not
  • Modified calculateTheta
    • Now replaces 0s to calculate LRM if alpha is provided
    • Now alerts user when using alpha to approximate LRV
  • Update documentation
    • Create new DESCRIPTION that includes differential proportionality
    • Create new README that includes differential proportionality
    • Revise "a_introduction" and move portion to stand-alone critique
    • Revise "b_visualization" and fix co-cluster selection mistake
    • Fork off and revise "d_advanced" as stand-alone critique
    • Spell check and revise other vignettes

propr 3.0.4

  • Modified calculateTheta
    • Now saves log-ratio variance (LRV) modifier in output
  • Modified visualization tools
    • New decomposed function for LRV decomposition
    • Uses LRV modifier for weighted theta types

propr 3.0.3

  • Modified visualization tools
    • Updated plot.propd method to display theta_f

propr 3.0.2

  • Modified propd Class
    • Added @weighted slot now used by updateCutoffs
  • Implement @theta for "weighted theta" calculation
    • Added wtmRcpp for weighted mean calculation
    • Added wtvRcpp for weighted variance calculation
    • Added lrm function with optional weighted calculations
    • Added lrv function with optional weighted calculations
  • Implement "weighted theta" calculation
    • Added calculateThetaW_old for unit testing
    • Added weighted lrv calculation
  • Modified calculateTheta
    • Moved log-ratio mean calculations here
    • Added weighted lrm calculation

propr 3.0.1

  • Modified propd Class
    • Added @active slot now used by updateCutoffs
    • Added setActive method to switch between theta types
  • Modified calculateTheta
    • Added theta_f which equals 1 - theta_e
    • Added only argument to retrieve only one theta type

propr 3.0.0

  • Modified package skeleton
    • Added differential proportionality article to CITATION
    • Added propriety project pre-merger changelog to OLDNEWS.md
  • Manually merged R functions from propriety project
    • New functions: propd and methods, calculateTheta, updateCutoffs
    • Added deprecated functions anticipating unit tests
  • Manually merged C++ functions from propriety project
    • New functions: half2matrix, boxRcpp, ctzRcpp, lrmRcpp
    • Added deprecated functions anticipating unit tests
  • Modified unit tests
    • Added requireNamespace check for ALDEx2 tests
    • Added unit tests from propriety project
  • Modified data
    • Rebuilt pd.d and pd.e data
    • Added top.counts as count data using filtered caneToad.counts
    • Added top.lr as log-ratio data using filtered caneToad.counts
    • Removed top data

propr 2.2.0

  • Modified dataset from Rollins et al. 2015
    • Removed transcripts with < 10 counts in < 10 samples
  • Add dataset from Marguerat et al. 2012
    • Absolute data stored as marg.abs

propr 2.1.9

  • Replace rhoToPhs function with lr2phs
    • Fixed phis bug when using alr-transformation
    • Fixed aldex2propr bug when using alr-transformation
    • Add unit tests for lr2 with ivar
  • Create initialize method to handle ivar and select
    • phit, perb, and phis use new with lr2
    • phit now accepts ivar and select
    • phit now has pca and snapshot
    • Add iqlr and "multi"-alr
  • Updated "Frequently Asked Questions" vignette

propr 2.1.8

  • Modified visualization tools
    • The bucket function now uses non-parametric ANOVA
    • The cytescape function now supports 3D visualization
    • The cytescape function now names columns correctly
  • Add "Frequently Asked Questions" vignette
  • Removed lrmodel module

propr 2.1.7

  • Force column and row names when calculating proportionality
    • Added plotCheck to cytescape function

propr 2.1.6

  • The aldex.cor function now returns average p-value
    • Now uses cor.test as lr2cor foundation instead of cor
  • Modified aldex2propr function
    • Added select argument like in perb function
    • Documented select argument in Details
  • Modified perb function
    • Alerts user when 'ivar' is missing from 'select'
    • Documented select argument in Details

propr 2.1.5

  • Stop exporting progress and migraph functions
  • Color cytescape edges correctly when plotting phi or phs
  • Add progress bar to smear function

propr 2.1.4

  • Add progress bar to aldex2propr and aldex.cor functions
  • Penalize lr2cor and aldex.cor p-values for two-tailed test
  • Add the migraph module to help make igraph networks
  • Modified visualization tools
    • Rebuilt cytescape using migraph module

propr 2.1.3

  • New aldex2propr function convertsaldex.clr object
    • Uses Monte Carlo instances from ALDEx2 package
  • New lr2cor and aldex.cor functions
    • Measures feature associations with continuous variables
  • Modified backend code
    • New backend.h allows import of backend.cpp
    • New lr2 functions calculate proportionality
      • Input log-ratio transformed counts
  • Modified visualization tools
    • Removed minPairs argument from cytescape

propr 2.1.2

  • Modified visualization tools
    • New pca function masks mds function
  • Include inst/CITATION file

propr 2.1.1

  • Modified propr Class
    • Merged propr-class and propr documentation
  • Modified phit, perb functions
    • Merged phit and perb documentation
    • New phis function returns (1 - rho) / (1 + rho)
    • NAs in count matrix now throw error
    • 0s now replaced with 1s
  • Modified visualization tools
    • Merged documentation

propr 2.1.0

  • Modified [ method
    • Now joins newly indexed pairs with any existing index
  • New cytescape function
    • Uses @pairs slot to build an interaction network

propr 2.0.9

  • Modified visualization tools
    • Courtesy prompt argument extended to smear and dendrogram
    • Improved error handling and documentation
  • Modified abstract function
    • New dt argument indexes significant results in @pairs
  • Modified simplify function
    • Now builds index of lower left triangle of matrix
  • New adjacent function
    • Uses @pairs slot to build an adjacency matrix

propr 2.0.8

  • Modified visualization tools
    • bucket now depends on slate function
  • Modified backend code
    • New coordToIndex performs inverse of indexToCoord
  • Modified prop2prob function
    • Return p-values as a sorted data.table
    • Now lets user select method for p-value adjustment
    • New prompt argument turns off big data prompt
    • Fix pass by reference bug in linRcpp
  • New abstract function
    • Combines two propr objects into one

propr 2.0.7

  • New lrmodel class
    • Use modelCLR to capture the clr-transformation rule
    • Use predict to deploy this rule to new data
  • Modified backend code
    • Added corRcpp function from correlateR package
    • Added linRcpp function for Z-transformation
    • Added lltRcpp and urtRcpp to retrieve a half-matrix
    • Added labRcpp to label a half-matrix
  • New prop2prob function
    • Allows hypothesis testing of rho equals naught
    • Tests differential proportionality

propr 2.0.6

  • Modified visualization tools
    • plotCheck extended to all plot functions
    • plot method now calls smear function
    • dendrogram plot now rendered using ggplot2
    • snapshot plot now rendered using ggplot2
    • bokeh plot now on positive log scale
    • plotly support added
  • Modified backend code
    • Temporarily removed a_bool function
  • Modified [ method
    • Removed bool and copy arguments

propr 2.0.5

  • Modified backend code
    • New a_bool function returns thresholded boolean matrix
  • Modified [ method
    • New bool argument toggles whether to use a_bool
    • New tiny argument toggles whether to use simplify
    • New copy argument toggles a_bool copy-on-modify

propr 2.0.4

  • New visualization tools
    • slate returns a table of VLR, VLS, and rho
    • bokeh plots pairs by the individual variances
  • Modified index-naive plot functions
    • Now uses fastcluster::hclust implementation
    • New prompt argument turns off big data prompt
    • prism now depends on slate function
  • Modified dendrogram function
    • Now uses fastcluster::hclust implementation
    • Now returns an hclust object

propr 2.0.3

  • Modified subset method
    • Argument select now correctly rearranges features
  • Modified rhoRcpp function
    • Now accommodates new perb function feature
  • Modified perb function
    • New select argument returns subsetted matrix
    • This subset does not alter values of rho

propr 2.0.2

  • Modified perb function
    • User can now specify name of ivar reference
  • Altered image method
    • Now includes dendrogram with heatmap
    • No longer uses index pairs
    • Now called snapshot
  • New prism function
  • New bucket function
  • New mds function
  • New vignette

propr 2.0.1

  • Modified phit, perb functions
    • These functions now force zero removal
  • New simplify function
    • Subsets propr object based on index in @pairs slot
    • Returns an updated index

propr 2.0.0

  • Modified phit, perb functions
    • Permutation testing removed
    • Added lazyPairs construct
      • Slot @pairs not populated until after [
  • Modified propr Class
    • @pairs slot now integer vector
      • Populated with indexPairs function
      • Translate with indexToCoord function
    • show method updated for lazyPairs construct
    • [ method completely redesigned
      • First argument specifies operation
      • Second argument specifies reference
      • Indexes @matrix based on these
    • subset method revised but still copy-on-modify
      • Resets @pairs when called
    • $ method removed
  • Visualization tools revised
    • plot, image, dendrogram methods
      • Improved performance
      • Compatible with new @pairs indexing
      • No longer requires column names
  • Modified backend code
    • Rephrased code for proprPhit
    • Rephrased code for proprPerb
    • Rephrased code for proprVLR
    • All functions translated into C++
      • Estimated 80% reduction in RAM overhead
      • Estimated 100-fold performance increase
      • ALR methods no longer drop dimension
      • All have modify-in-place behavior

propr 1.1.0

  • New orientation expected for input data
    • Updated backend and vignette accordingly
    • Removed redundant transpositions
  • Fixed rare subsetting errors
  • Tweaked plot methods

propr 1.0.0

  • Introduced phit function
    • Implements Lovell's phi proportionality metric
    • Returns object of class propr
  • Introduced perb function
    • Implements Erb's rho proportionality metric
    • Returns object of class propr
  • Introduced propr Class
    • show method
      • Subsets propr based on @pairs slot
    • subset method
      • Subsets propr based on @matrix slot
    • plot method
      • Plots pairwise lr proportionality
    • dendrogram method
      • Plots clusters of lr-transformed data
    • image method
      • Plots heatmap of lr-transformed data