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Recent Releases of https://github.com/openthermochronology/thermochron.jl

https://github.com/openthermochronology/thermochron.jl - v0.16.3

Thermochron v0.16.3

Diff since v0.16.2

  • Fix typo in uaftm input when parsing chronometers

- Julia
Published by github-actions[bot] 7 months ago

https://github.com/openthermochronology/thermochron.jl - v0.16.2

Thermochron v0.16.2

Diff since v0.16.1

  • Add live t-T path plotting functionality during both burn-in and collection

Merged pull requests: - Update tTinversion.jl (#26) (@kmcdannell) - Add example of saving results in front-end script (#27) (@kmcdannell) - Optional live t-T path plotting during inversion (#28) (@brenhinkeller)

Closed issues: - Live t-T path plotting (#24)

- Julia
Published by github-actions[bot] 7 months ago

https://github.com/openthermochronology/thermochron.jl - v0.16.1

Thermochron v0.16.1

Diff since v0.15.8

  • Accelerate track length calculations by reusing r and pr where possible (#23)

Merged pull requests: - Update tTinversion.jl (#19) (@kmcdannell) - Reuse r and pr in equivalent FissionTrackLength chronometers (#23) (@brenhinkeller)

Closed issues: - Logarithmic timesteps (#12)

- Julia
Published by github-actions[bot] 7 months ago

https://github.com/openthermochronology/thermochron.jl - v0.15.8

Thermochron v0.15.8

Diff since v0.15.7

*Plot both ApatiteTrackLength and ApatiteTrackLengthOriented in tTinversion.jl * Update PlotsExt to account for val and err deprecation

- Julia
Published by github-actions[bot] 7 months ago

https://github.com/openthermochronology/thermochron.jl - v0.15.7

Thermochron v0.15.7

Diff since v0.15.6

  • Allow un-oriented apatite fission track lengths to use a different annealing model that does not assume c-axis projection
  • Oriented and un-oriented apatite fission tracks are now stored using separate ApatiteTrackLength vs ApatiteTrackLengthOriented types
  • Store initial (zero-age) fission track length (l0) and uncertainty (l0_sigma) in FissionTrackLength structs rather than AnnealingModel structs
  • Allow user-specified l0 and l0_sigma for each track length object
  • Infer apatite l0 and l0_sigma from dpar, if not otherwise specified
  • Expand documentation

Merged pull requests: - Update tTinversion.jl (#15) (@kmcdannell) - Allow user-specified initial fission track length (l0) and uncertainty for each chronometer (#16) (@brenhinkeller) - Allow unoriented apatite fission track lengths to use a different annealing model (#17) (@brenhinkeller) - Account for variable offsets in empiricaluncertainty! estimation (#18) (@brenhinkeller)

Closed issues: - Ability to empirically resample He-date uncertainties per sample (#7) - Predicted apatite track length distribution for multiple samples (#8) - Add method for user-normalized fission tracks (#13) - Model conventional [unprojected] measured track lengths (#14)

- Julia
Published by github-actions[bot] 7 months ago

https://github.com/openthermochronology/thermochron.jl - v0.15.6

Thermochron v0.15.6

Diff since v0.15.5

  • Fix bug caused by split line in rmr0model, for calculation of rmr0 from F,Cl,OH (report courtesy of @isaacstential)

Merged pull requests: - Fix bug at line break in rmr0model function (#10) (@brenhinkeller)

Closed issues: - Potential bug in calculating Ketcham et al. 2007 rmr0 (#9)

- Julia
Published by github-actions[bot] 8 months ago

https://github.com/openthermochronology/thermochron.jl - v0.15.5

Thermochron v0.15.5

Diff since v0.15.4

  • Consider temperature offset in FT too
  • Get ApatiteFT rmr0 from Cl when possible

- Julia
Published by github-actions[bot] 9 months ago

https://github.com/openthermochronology/thermochron.jl - v0.15.4

Thermochron v0.15.4

Diff since v0.15.3

  • Add rmr0fromcl function

- Julia
Published by github-actions[bot] 11 months ago

https://github.com/openthermochronology/thermochron.jl - v0.15.3

Thermochron v0.15.3

Diff since v0.15.2

  • Rescale MDD chronometers by default

- Julia
Published by github-actions[bot] 11 months ago

https://github.com/openthermochronology/thermochron.jl - v0.15.2

Thermochron v0.15.2

Diff since v0.15.1

  • Fit to midpoint of each degassing step, rather than end

- Julia
Published by github-actions[bot] 12 months ago

https://github.com/openthermochronology/thermochron.jl - v0.15.1

Thermochron v0.15.1

Diff since v0.15.0

  • Individual Ea for each domain in MDD, smaller default Ea uncertainties
  • Recalculate degassing schedule at every step in varkinetics inversions
  • Compare model and observed degassing schedules in varkinetics inversions

- Julia
Published by github-actions[bot] 12 months ago

https://github.com/openthermochronology/thermochron.jl - v0.15.0

Thermochron v0.15.0

Diff since v0.13.0

  • Consistent framework for kinetic uncertainty resampling
  • Breaking: to allow that, chronometers now returns two vectors (one for chronometers and one for models)
  • Allow independent control of volume weighting for spherical diffusion chronometers

Merged pull requests: - Update documentation CI (#4) (@brenhinkeller) - CompatHelper: add new compat entry for Plots in [weakdeps] at version 1, (keep existing compat) (#5) (@github-actions[bot]) - CompatHelper: add new compat entry for Statistics at version 1, (keep existing compat) (#6) (@github-actions[bot])

- Julia
Published by github-actions[bot] about 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.13.0

Thermochron v0.13.0

Diff since v0.12.1

  • Breaking: empiricaluncertainty! now adds to σcalc rather than modifying the chronometers themselves
  • Switch to more traditional simulated annealing approach where log likelihoods are scaled by a unitless annealing "temperature"; ensures that all chronometers (including track lengths) are included in simulated annealing
  • Linearly interpolate initial path proposal between boundaries and constraints
  • Ensure initial proposals satisfy detail interval
  • Refactor inversion to use new TtPath struct internally
  • Calculate log likelihood for ApatiteTrackLength samples based on the full distribution of model tracks (rather than just mean and standard deviation)
  • Record calculated track lengths pulled randomly from this full distribution in the stationary distribution (instead of just means)
  • Optional additional (likely redundant) overall track histogram comparison likelihood
  • Add initial implementation of MonaziteFT
  • Add example plots for most all chronometers in TtInversion.jl

- Julia
Published by github-actions[bot] about 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.12.1

Thermochron v0.12.1

Diff since v0.12.0

  • Randomize initial proposal subject to max reheating rate
  • Add optional alpha injection correction, if matrix U-Th-Sm is specified
  • Make GenericHe alpha stopping distances mineral-specific by scaling Farley et al. 1996 decay-specific distances by relative stopping power as calculated from Ketcham et al. 2011 average distances
  • Update @info statements about chronometers under inversion in MCMC functions

- Julia
Published by github-actions[bot] about 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.12.0

Thermochron v0.12.0

Diff since v0.11.3

  • Add zircon fission track! Yamada et al. 2007 model.
  • [breaking]: rename annealing model structs to refer to the paper from which they are derived, to avoid ambiguity

- Julia
Published by github-actions[bot] about 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.11.3

Thermochron v0.11.3

Diff since v0.11.2

  • Add GenericHe and GenericAr chronometers

- Julia
Published by github-actions[bot] about 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.11.2

Thermochron v0.11.2

Diff since v0.11.1

  • Add image_from_paths/image_from_paths!

- Julia
Published by github-actions[bot] about 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.11.1

Thermochron v0.11.1

Diff since v0.11.0

  • Add empiricaluncertainty! function
  • Add Plots extension
  • Update simulated annealing approach, using σmodel as default calculated uncertainty
  • Add dynamicsigma option to freely resample model uncertainties for each chronometer
  • Switch to more traditional version of equivalent time approach
  • Make annealing models @kwdef structs, update Ketcham 1999 coeffs
  • Various internal updates

- Julia
Published by github-actions[bot] about 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.11.0

Thermochron v0.11.0

Diff since v0.10.5

  • Add apatite fission track age and apatite fission track length thermochornology!
  • Input a data to MCMC function as a vector of chronometer objects

- Julia
Published by github-actions[bot] about 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.10.5

Thermochron v0.10.5

Diff since v0.10.4

  • Vary rmr0 throughout inversion in _varkinetics option
  • Changes to handling of point-specific jumping distributions
  • Ensure full non-allocation of lu! from linear algebra
  • Change default Temperature boundary to :reflecting
  • Update example scripts

- Julia
Published by github-actions[bot] over 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.10.4

Thermochron v0.10.4

Diff since v0.10.3

  • Move adm and zdm rdaam/zrdaam damage models into model tuple
  • Move addpoint! to separate function

- Julia
Published by github-actions[bot] over 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.10.3

Thermochron v0.10.3

Diff since v0.10.2

  • Switch from VectorizedStatistics to NaNStatistics

- Julia
Published by github-actions[bot] over 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.10.2

Thermochron v0.10.2

Diff since v0.10.1

  • Allow separate boundary condition types for temperature and time
  • Move boundary types inside Boundary struct
  • Reexport StatGeochemBase

- Julia
Published by github-actions[bot] over 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.10.1

Thermochron v0.10.1

Diff since v0.10.0

  • Make σⱼt and σⱼT point-specific

- Julia
Published by github-actions[bot] over 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.10.0

Thermochron v0.10.0

Diff since v0.9.4

  • Move npoints, agepoints, and Tpoints inside MCMC function (breaking)

- Julia
Published by github-actions[bot] over 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.9.4

Thermochron v0.9.4

Diff since v0.9.3

  • Generalize Unconformity type to Constraint

- Julia
Published by github-actions[bot] over 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.9.3

Thermochron v0.9.3

Diff since v0.9.2

  • Refactor, add options for different boundary condition types

- Julia
Published by github-actions[bot] over 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.9.2

Thermochron v0.9.2

Diff since v0.9.1

  • Update to new fully-in-place tridiagonal lu! solve
  • Simplify construction of Unconformity objects

- Julia
Published by github-actions[bot] over 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.9.1

Thermochron v0.9.1

Diff since v0.9.0

  • Expand compat on StatGeochemBase to v0.6

- Julia
Published by github-actions[bot] over 1 year ago

https://github.com/openthermochronology/thermochron.jl - v0.9.0

Thermochron v0.9.0

Diff since v0.8.0

  • Incorporate reheating rate limit into log likelihood

- Julia
Published by github-actions[bot] almost 2 years ago

https://github.com/openthermochronology/thermochron.jl - v0.8.0

Thermochron v0.8.0

Diff since v0.7.0

  • Handle max reheating rate rejection by restarting proposal process, rather than with individual loops

- Julia
Published by github-actions[bot] almost 2 years ago

https://github.com/openthermochronology/thermochron.jl - v0.7.0

Thermochron v0.7.0

Diff since v0.6.0

  • Enable incorporation of kinetic uncertainties (MCMC_varkinetics)

- Julia
Published by github-actions[bot] almost 2 years ago

https://github.com/openthermochronology/thermochron.jl - v0.6.0

Thermochron v0.6.0

Diff since v0.5.1

  • Add support for apatite helium data

- Julia
Published by github-actions[bot] almost 2 years ago

https://github.com/openthermochronology/thermochron.jl - v0.5.1

Thermochron v0.5.1

Diff since v0.5.0

  • Bump compat on VectorizedStatistics to 0.5.0
  • Slightly higher minimum dynamicjumping temperature sigma

- Julia
Published by github-actions[bot] about 3 years ago

https://github.com/openthermochronology/thermochron.jl - v0.5.0

Thermochron v0.5.0

Diff since v0.4.7

  • The stationary distribution is now recorded as t-T points (tpointdist and Tpointdist) rather than as an already-interpolated Tstepdist)
  • Information about boundaries, unconformities, and detail intervals are now passed using custom Boundary, Unconformity, and DetailInterval types, rather than as NamedTuples
  • Capitalizationocalpyse! Variables now follow more Julian capitalization rules, except for uppercase T denoting temperature (as in t-T), and elements like U,Th, and He.
  • A bugfix to point removal conditions
  • Updated examples

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/openthermochronology/thermochron.jl - v0.4.7

Thermochron v0.4.7

Diff since v0.4.6

  • Numerous bugfixes
  • Add the ability to specify a "detail interval" – a period of time with a minimum number of t-T points

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/openthermochronology/thermochron.jl - v0.4.6

Thermochron v0.4.6

Diff since v0.4.5

  • Fix major bug in recording of stationary distribution
  • Various minor bugfixes and type stability improvements

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/openthermochronology/thermochron.jl - v0.4.5

Thermochron v0.4.5

Diff since v0.4.4

  • Use more efficient in-place linterp1s! in MCMC_vartcryst
  • More efficient alpha deposition and damage when constructing Zircon objects
  • Use ProgressMeter.update! interface in place of @showprogress
  • Dispatch damage model on struct instead of Val(symbol) (i.e., ZRDAAM instead of Val(:zrdaam)) for flexibility in future implementation
  • Add DOI and citation

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/openthermochronology/thermochron.jl - v0.4.4

Thermochron v0.4.4

Diff since v0.4.3

  • Store and reuse du2 and ipiv vecotrs in lu!
  • Store and reuse Dz and DN17 vectors for zircon diffusivities at each timestep
  • Store and reuse Teq vector in anneal!
  • Additional unit tests for Zircon constructor
  • Let model minimum temperature extend to model.Tnow rather than hard-coding it at 0C
  • Remove allocations in return coordinate-transform in HeAgeSpeherical and max reheating rate check in MCMC_vartcryst
  • Relicense as plain GPL3 instead of AGPL3

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/openthermochronology/thermochron.jl - v0.4.3

Thermochron v0.4.3

Diff since v0.4.2

  • Use in-place interpolation of TSteps in MCMC_vartcryst

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/openthermochronology/thermochron.jl - v0.4.2

Thermochron v0.4.2

Diff since v0.4.1

  • More @turbo in HeAgeSpherical
  • Flip orientation of u for better memory access given column-major

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/openthermochronology/thermochron.jl - v0.4.1

Thermochron v0.4.1

Diff since v0.4.0

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/openthermochronology/thermochron.jl - v0.4.0

Thermochron v0.4.0

Diff since v0.3.1

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/openthermochronology/thermochron.jl - v0.3.1

Thermochron v0.3.1

Diff since v0.3.0

  • Move agePoints and tPoints into model tuple too

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/openthermochronology/thermochron.jl - v0.3.0

Thermochron v0.3.0

Diff since v0.2.0

  • Add custom types to store reusable information about individual chronometers
  • Add in-place damageannealing! function
  • Refactor ZrnHeAgeSpherical (now HeAgeSpherical) to store and reuse damage matrices, etc.
  • Refactor how model parameters are stored and passed around
  • Rename various things to be closer in line with Julia naming conventions

- Julia
Published by github-actions[bot] over 3 years ago

https://github.com/openthermochronology/thermochron.jl - v0.2.0

Thermochron v0.2.0

  • Refactor MCMC_vartcryst, ZrnHeAgeSpherical, and several internal functions to dramatically reduce allocations

Closed issues: - TagBot trigger issue (#3)

Merged pull requests: - Create LICENSE (#1) (@brenhinkeller) - CompatHelper: add new compat entry for LoopVectorization at version 0.12, (keep existing compat) (#2) (@github-actions[bot])

- Julia
Published by github-actions[bot] over 3 years ago