NEWS.md

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

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

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