Changes in version 1.2.0 (2025-10-28)                  

    o   
	New function readFragPipe() to read FragPipe output.

    o   
	New function readMaxQuant() to read MaxQuant output.

    o   
	readDIANN() now allows user-specified input column names and
	"parquet" is now the default format.

    o   
	Bug fixes to readSpectronaut() when `sep` is other than a tab
	or when there is only one peptide annotation column.

    o   
	Revisions to all the read functions. readDIANN(),
	readFragPipe(), readMaxQuant(), and readSpectronaut() all use
	`fread()` with `data.table=FALSE` now to read ascii delimited
	files.

    o   
	New argument `logit.p` for dztbinom(), which allows the
	function to avoid subtractive cancellation for success
	probabilities close to 1. dpc() now uses the new argument when
	calling dztbinom().

    o   
	New function dpcON() to estimate the DPC assuming the
	oberved-normal model. Should give same output as dpc() but is
	somewhat faster. dpcON() calls a new function,
	pztbinomSameSizeLogitPBothTails(), which computes left and
	right tail p-values for zero-truncated binomial quantiles.

    o   
	Revisions to dpcCN() to improve convergence. To improve speed,
	the function now randomly selects a subset of rows of data to
	process, with the number of rows given by the new argument
	`subset`. The default number of outer iterations is decreased
	to 2.

    o   
	dpcImpute() now sets row.names. Sections on dpcImpute() and
	imputeByExpTilt() have been added to the package vignette.

    o   
	dpcQuant() now calls dpcImpute() automatically when all
	proteins have just one peptide.

    o   
	New function plotPeptides() to plot the peptide-level
	log-intensities for one protein.

    o   
	Fix simProteinDataSet() processing of `prop.missing` argument.

    o   
	Cite the limpa bioRxiv preprint (Li et al, bioRxiv 2025) in the
	vignette and help pages.

    o   
	Expand Quantification section in the vignette to give more math
	details.

                 Changes in version 1.0.0 (2025-04-16)                  

    o   
	dpcQuant() and peptides2Proteins() now return essentially equal
	values if there are multiple entirely imputed values for the
	same protein.

    o   
	Update readSpectronaut() to allow more flexibility regarding
	which columns are read.

    o   
	Remove reference to DIA in vignette, because limpa works for
	both DIA and DDA.

    o   
	New function plotMDSUsingSEs(), which accounts for standard
	errors when computing between-sample distances for the plot.

    o   
	New argument `chunk` for dpcQuant() and dpcImpute().

    o   
	dpcImpute() now passes the `verbose` argument to
	peptides2Proteins().

    o   
	Add more background information to the vignette, including
	references for DIA-NN, Spectronaut and MaxQuant. Add mention of
	voomaLmFitWithImputation().

    o   
	Bug fix to starting values in peptides2Proteins() for
	single-peptide proteins.

    o   
	expTiltByColumns() is now more robust for datasets with very
	few rows, especially when the column variance is exactly zero
	by chance. It originally assumed that the number of rows would
	always be large. This also improves the robustness of
	imputeByExpTilt().

    o   
	peptides2Proteins() now runs imputeByExpTilt() on the whole
	dataset in order to get starting values for each protein. This
	improves speed slightly and makes the starting values more
	robust for large datasets with many NAs.

    o   
	readDIANN() now supports DIA-NN output in either tsv or Parquet
	formats.

    o   
	New functions dpcImpute() and dpcImputeHyperparam() to
	facilitate imputation and differential expression analysis at
	the peptide level. This may be needed for phosphoproteomics and
	analogous applications.

    o   
	Package title changed to "Quantification and Differential
	Analysis of Proteomics Data", and package description expanded.

    o   
	New function plotProtein(), to plot the quantifications for a
	given protein with error bars.

    o   
	Cleanup annotation output from dpcQuant() to remove
	peptide-level annotation columns

    o   
	dpc() now outputs `n.detected` for each peptide.

    o   
	dpc() now checks for peptides that are entirely missing.

    o   
	plotDPC() now accepts input from either dpc() or dpcCN(). It
	now estimates the jittering amount automatically.

    o   
	Add readDIANN() code to vignette.

    o   
	Add peptide filtering to vignette.

    o   
	New function voomaLmFitWithImputation(), which is the same as
	limma::voomaLmFit() except that it allows for loss of degrees
	of freedom when all the values for a particular protein in a
	particular group are imputed. dpcDE() now calls this new
	function instead of limma::voomaLmFit(), making the
	differential expression analysis more robust to high rates of
	missing values.

    o   
	Fix dpcQuant() `genes` output when the input `y` is a plain
	matrix instead of an `EList` object.

    o   
	New argument `dpc.slope` for dpcQuant(), to allow the use of a
	preset DPC slope.

    o   
	estimateDPCIntercept() now allows `dpc.slope=0`, corresponding
	to the case that missing values are uninformative.

                 Changes in version 0.99.0 (2025-01-03)                 

    o   
	Initial public release of the limpa package ("Linear Models for
	Proteomics Data") at <https://github.com/SmythLab/limpa> with
	the following exported functions: completeMomentsON, dpc,
	dpcCN, dpcDE, dpcQuant, dpcQuant.default, dpcQuant.EList,
	dpcQuantHyperparam, dztbinom, estimateDPCIntercept,
	expTiltByColumns, expTiltByRows, filterCompoundProteins,
	filterCompoundProteins.default, filterCompoundProteins.EList,
	filterCompoundProteins.EListRaw, filterNonProteotypicPeptides,
	filterNonProteotypicPeptides.default,
	filterNonProteotypicPeptides.EList,
	filterNonProteotypicPeptides.EListRaw, filterSingletonPeptides,
	filterSingletonPeptides.default, filterSingletonPeptides.EList,
	filterSingletonPeptides.EListRaw, fitZTLogit, imputeByExpTilt,
	imputeByExpTilt.default, imputeByExpTilt.EList,
	imputeByExpTilt.EListRaw, observedMomentsCN,
	peptides2ProteinBFGS, peptides2ProteinNewton,
	peptides2Proteins, peptides2ProteinWithoutNAs, plotDPC,
	proteinResVarFromCompletePeptideData, pztbinom, readDIANN,
	readSpectronaut, removeNARows, removeNARows.default,
	removeNARows.EList, simCompleteDataCN, simCompleteDataON,
	simProteinDataSet.