v0.7.0

Unfold v0.7.0

Diff since v0.6.10

This is a bigger release 🎉 with some clearly breaking changes. For most users, those breaking changes should be near "invisible", but we can't promise it. Update as always without warranty.

Breaking:

• New major types:
  • all UnfoldModel-types are now parametric types with e.g. Float64 or Missing,Float64, which will make specializations in fitting much easier in the future (e.g. no missing values => faster fit!)
  • Internal: New Trait ContinuousTimeTrait making it easier to specify custom types
  • UnfoldModel now takes a vector of AbstractDesignMatrices, where each AbstractDesignMatrix holds only one formula, one table and one modelmatrix. If you used accessorfunctions like events and formulas not much should change. Those accessor functions were harmonized to produce vectors of content.
• FIR by default does not linearly interpolate anymore. This will help throughout the toolbox with minimal consequences on model-accuracy. That is, if an event-latency is in between two datasamples, it used to be linearly "split up". This now needs to manually activated using interpolate=true in firbasis. In the case of interpolate=false only integer event-latencies are allowed. In practice, this should have little impact, but it will change your numbers slightly.
• Dict(:A=>(formula,times)) from dict to vector of pairs [:A=>(formula,times]
• coeftable column basisname renamed to eventname, basisfunctions now need to have the same name as the event in the Design-specification

Public renaming (breaking)

old	new
predict	predicttable (predict now returns a vector of arrays
formula	formulas (now returns a vector of StatsFormulas for all models)

Internal renaming

old	new
combineDesignmatrices	combine_designmatrices
equalizeLengths	equalize_lengths
zeropad	equalize_size
shiftOnset	shift_onset
get_modelmatrix	modelmatrices
randomeffectgroupings	random_effect_groupings
changeMatSize!	change_modelmatrix_size!
equalizeReMatlengths!	equalize_ReMat_lengths!
changeReMatSize!	change_ReMat_size!
lmm_combineMats!	lmm_combine_modelmatrix!
extract_symbol	termname
dropMissingEpcohs	drop_missing_epochs
DesignMatrix.Xs	DesignMatrix.modelmatrix

New functions & features:

• BasisFunction now has a method height, in addition to it's StatsModels.width
• pretty Term.jl output for models and designmatrices
• massunivariate models by default calculate SE now
• many more docstrings
• documentation fixes @vladdez
• residual(uf,data) function
• fit/solver show_progress controls output

Closes: #192 #161 #52 #189 #155

Merged pull requests:

• readability - index.md (#187) (@vladdez)
• readability - tutorials/howto (#188) (@vladdez)
• readability - howto/lmm_pvalues (#191) (@vladdez)
• unfold breaking 0.7 (#192) (@behinger)

Closed issues:

• Documentation improvement suggestions (#189)
• FileIO.load does not work (#194)

v0.6.10

Unfold v0.6.10

Diff since v0.6.9

speed up effects
load older JLD2 files

Merged pull requests:

• backward compatible loading of JLD2 files (#176) (@behinger)
• betterBackwardJLD2 (#177) (@behinger)
• Update effects.jl (#179) (@behinger)
• docs: add vladdez as a contributor for bug (#180) (@allcontributors[bot])
• Update basisfunctions.md - readability (#184) (@vladdez)

Closed issues:

• Confusing documentation about Effects (#178)
• Confusing usage of acronyms (#181)
• firbasis shows error when name is not specified (#183)
• Better error (message) when swapping basisfunction and formula in the event dict tuple (#186)

v0.6.9

Unfold v0.6.9

Diff since v0.6.8

• stderror was wrongly forced to type of data, but should be type of coefficients. This lead to very rare problem (introduced in 0.6.6) thanks @vladdez for reporting
• LMMs had a major bug #175. If you had a model of type 0~ [...] + (1|item) + (1+A|subject) where the first term had fewer random slopes than the second, then the coeftable(model) had wrongly ordered coefnames for the random effects. This is fixed now
• fixed LMM bugs in the tutorial (following from UnfoldSim major v0.4).

Merged pull requests:

• Fix LMM, Fix STDerror bug (#174) (@behinger)
• Fix LMM Reorder bug (#175) (@behinger)

v0.6.8

Unfold v0.6.8

Diff since v0.6.7

• bugfix: stderror threw a typeerror
• benchmarks are back

Merged pull requests:

• benchmark2 (#172) (@behinger)
• Benchmark Test (#173) (@behinger)

v0.6.7

Unfold v0.6.7

Diff since v0.6.6

• fixed speed issue with new effects fix in 0.6.6
• added Tullio.jl to speed up calculations

Merged pull requests:

• tullioEffects (#171) (@behinger)

v0.6.6

Unfold v0.6.6

Diff since v0.6.5

• greatly improved speed of effects calculation
• fixed tests & documentation with UnfoldSim major 0.4

Merged pull requests:

• effectsSpeedup (#170) (@behinger)

v0.6.5

Unfold v0.6.5

Diff since v0.6.4

• JuliaFormatter on everything
• added Effects for UnfoldLinearMixedModels
• updated docs & docstrings

Merged pull requests:

• Create darus-dataverse.yml (#158) (@behinger)
• UnfoldMakie0.4 (#159) (@behinger)
• effects for LMMs (#160) (@behinger)
• Update CITATION.cff (#162) (@jschepers)
• fix for SE calculation breaking CI (#163) (@behinger)
• fix #124, assert min number of spines; compat 0.17 BSplineKit (#164) (@behinger)
• added docstrings for types fix #133 (#165) (@behinger)
• JuliaFormatter (#166) (@behinger)

Closed issues:

• 2nd level tools / plots / stats (#13)
• [docs] Timebasis is empty? (#102)
• Krylov + multithreading crashed (#122)
• add errormessage if n_spl = 3 is used (#124)
• Missing doc strings and types & functions in the Unfold documentation (#133)

v0.6.4

Unfold v0.6.4

Diff since v0.6.3

• Fix bug with multi-channel mixed models extension reshaping
• greatly enhanced documentation

Merged pull requests:

• Update julia_call HowTo (#132) (@jschepers)
• Updated "Adding documentation" section in the README (#134) (@jschepers)
• Update README.md (#135) (@jschepers)
• Update README.md (#136) (@jschepers)
• added the @all-contributors functionality to the toolbox and added the emoji key (#142) (@ReboreExplore)
• docs: add ReboreExplore as a contributor for infra (#143) (@allcontributors[bot])
• docs: add jschepers as a contributor for bug, code, and 5 more (#144) (@allcontributors[bot])
• docs: add behinger as a contributor for bug, code, and 9 more (#145) (@allcontributors[bot])
• docs: add ReneSkukies as a contributor for bug, and doc (#146) (@allcontributors[bot])
• docs: add palday as a contributor for code, and infra (#147) (@allcontributors[bot])
• docs: add kleinschmidt as a contributor for doc (#148) (@allcontributors[bot])
• docs: add ssaket as a contributor for bug (#149) (@allcontributors[bot])
• docs: add suddha-bpn as a contributor for bug (#150) (@allcontributors[bot])
• Add window length explanation to Docs (#151) (@ReneSkukies)
• How to save and load unfold models (#152) (@jschepers)
• docs: add ReneSkukies as a contributor for tutorial (#153) (@allcontributors[bot])
• update autoformat test (#156) (@behinger)

Closed issues:

• Missing information about Extensions? (#138)
• Outdated information in "Traditional Mass Univariate Analysis" tutorial (#139)

v0.6.3

Unfold v0.6.3

Diff since v0.6.2

Fixes Packagextensionbug for Unfold versions with julia <1.9 #131

Merged pull requests:

• Update README.md (#128) (@behinger)
• Create CITATION.cff (#130) (@vladdez)

v0.6.2

Unfold v0.6.2

Diff since v0.6.1

• added rePCA for LMMs
  • some minor bugfixes
  • greatly improved type-stability, especially for time_expand
  • potentially breaking: starting to deprecate FIRbasis.kernel field. kernel(firbasis) does not return the kernelfunction anylonger, which was required to be an anonymous function. Rather, it is replaced by kernel(firbasis,e) to directly calculate the kernel at e. While the FIRBasis Type changed, we have a @deprecate in place that should catch the old access.

Merged pull requests:

• faster timeexpand (#127) (@behinger)