Tutorials

This part of the documentation guides you through all of the library’s usage patterns.

Automatic generation from .ipynb files requires:

• pandoc

And documentation development in .org files requires:

• emacs with org babel

• jupyter (and kernel e.g. cloph-310)

• r

• 1. Fitting
  • 1.1. Conventions and best approaches
  • 1.2. Initial imports
  • 1.3. Single Cl titration.
    • 1.3.1. Using R
    • 1.3.2. using rpy2
    • 1.3.3. lmfit
  • 1.4. Notes
• 2. Fit titration with multiple ts
  • 2.1. lmfit of single y1 using analytical Jacobian
    • 2.1.1. emcee
  • 2.2. global
    • 2.2.1. using lmfit with np.r_ trick
    • 2.2.2. lmfit constraints aiming for generality
      • 2.2.2.1. emcee
    • 2.2.3. bootstrap con pandas
    • 2.2.4. using R
    • 2.2.5. lmfit.Model
  • 2.3. TODO See also this tutorial
    • 2.3.1. TODO jackknife to auto-reject
    • 2.3.2. TODO uncertainty estimate
• 3. Example 2P Cl–ratio
  • 3.1. using lmfit.model
  • 3.2. using R
• 4. Old scripts
  • 4.1. fit_titration.py
  • 4.2. fit_titration_global.py
  • 4.3. IBF database uses
• 5. Getting started with prtecan
  • 5.1. To parse a Tecan file
  • 5.2. To group list of files into a titration
  • 5.3. pH titration analysis
  • 5.4. Cl titration analysis
  • 5.5. Fitting
    • 5.5.1. selection
    • 5.5.2. combining
• 6. Getting started with prenspire