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Change log

v0.2.8

  • Removed central estimation in curveball.models.*_ci functions.
  • Build with conda-build version 1; version 2 caused problems on travis-ci (see PR #1342).
  • Removed python-dateutil dependency.

v0.2.7

  • Fixed bug: find_K_ci was called with wrong args in cli.py.
  • Added --nsamples to CLI
  • Test with CLI with --ci
  • Adjusted to seaborn API change: sns.Grid->sns.axisgrid.Grid

v0.2.6

  • added tests for competitions.py
  • fixed bad docstrings
  • avoid loading qt
  • add y0 arg to competition CI function
  • update to lmfit 0.9.3 to solve bug
  • confidence interval version for fit_and_compete
  • fix bootstrap bug
  • raise dev status to alpha in PyPI identifiers
  • plot sampled curves and sampled model fits
  • small bug fixes

See commit log for more details

v0.2.5

  • When using a find_*_ci function, it now also returns an estimate - the average of all samples (bug fix).
  • Added find_K_ci to find the confidence interval of the K parameter (closes #131)

v0.2.4

  • Bug fixes
  • Fit and compete - fit total OD to total of competition model (699f8b6)
  • Lotka Volterra competition models (started at fbc6dc8)
  • New competitions model based on resource consumption (22d949c)
  • Smoothing is more stable and doesn't require parameters (97c64d4)
  • Fix definition of q0 in docs
  • Measure minimal doubling time (7ffdd24; suggested by Idan Frumkin)
  • Measure confidence interval for max growth rate, lag, and min doubling time and report in CLI (d95bf3d and further commits afterwards)
  • Improved parameter guess functions (97c64d4, 0cecfaf)
  • Fit exponential model (523b30270ff6cd95d6702ed1b497e3f12655129b)
  • Support for Python 3.5 (4a1c5b8)
  • Moved docs from divshot to netlify (fbe022d)

v0.2.3

  • each growth model is now a separate class
  • new growth model: Baranyi-Roberts with v=r (nu is free)
  • fit to full data instead of just weights
  • quantifiedcode integration
  • guessing nu gives false results, set it to 1
  • fix D calculation in lrtest to be numerically stable
  • refactor calc_weights
  • added more competition models
  • residuals plots much improved, added model residuals plot
  • sample y0 in compete
  • bootstrap sampling of model parameters
  • fit_model accepts name of fitting method
  • new module for likelihood analysis
  • read and write csv files in Curveball format
  • allow none blank in CLI - this avoids subtracting the OD of the blank well from the other wells
  • added weighted AIC and BIC to model attributes
  • docs improved
  • removed some tests: tests should check that code works, not that it gives positive results

v0.2.2

  • warning when number of samples from sample_params is lower than requested
  • added Baranyi-Roberts model with nu=1 and v=r (see Baty & Delignette-Muller, 2004)
  • reorganized parameter guessing and setting - closes #35
  • v=inf when there is no lag phase
  • added arguments to override parameters in competitions
  • plot_residuals to plot the residuals of a model fit
  • added arguments to fit_model and options to the CLI to control minimal values for parameters and to fix parameters to initial guess.

v0.2.1

  • added guess, param_max, and weights/no-weights as options to curveball analyse - closes #76
  • fix max param settings in curveball.models.fit_model.
  • hide future warnings in CLI when verbose is off - closes #100
  • output RMSD, NRMSD, CV(RMSD) from curveball analyse - closes #94
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