# PyDDM Cookbook¶

Here are a list of examples of common model features and how to
implement them in PyDDM. **If you created an example or model in
PyDDM and would like it to be added to the cookbook, please** send
it to us **so we can add it**.
Include the author(s) of the example or model and optionally a
literature reference so that we can give you proper credit and direct
users to your paper!

`Download cookbook.py (all models in the cookbook)`

## Task paradigms¶

Here are some examples of potential task paradigms that can be simulated with PyDDM.

## Drift and noise¶

I want:

- A drift rate which changes over time (see “task paradigms” section above)
- Leaky or unstable integration
`A general Ornstein-Uhlenbeck process`

- A drift rate which depends linearly on a task parameter (e.g. coherence)
- A biased drift dependent on a task condition (e.g. reward or choice history)
- A leaky integrator with a drift rate which depends linearly on a task parameter (e.g. coherence)
- An urgency gain function
- Drift rate variability (uniform distribution)
- Drift rate or noise which depends on a moment-to-moment signal, unique to each trial
- Something else (Write your own, using these as a guide.)

## Collapsing bounds (or time-varying bounds)¶

I instead want bounds which:

`Are constant over time`

`Collapse linearly`

`Collapse exponentially`

- Collapse exponentially after a delay
- Collapse according to a Weibull CDF
- Collapse according to a step function
- Vary based on task conditions, e.g. for a speed vs accuracy task
- Increase over time
- Something else (Write your own, using these as a guide)

## Initial conditions¶

I don’t want my initial conditions to be ```
A single point
positioned in the middle of the bounds
```

(the
default). Instead, I want my initial conditions to be:

- A single point
- A uniform distribution
`A Gaussian distribution centered in the middle of the bounds`

- A Cauchy distribution
`A specific distribution which does not change based on task parameters`

- Something else (Write your own, using these as a guide)

## Non-decision time¶

I want to use a non-decision time which is:

## Mixture models (Contaminant RTs)¶

I want to fit a distribution which has contaminant RTs distributed according to:

`A uniform distribution`

`An exponential distribution (corresponding to a Poisson process)`

- Something else (Write your own)

## Objective functions¶

I don’t want to use the default recommended objective function
(`negative log likelihood`

) but would rather
use:

`Squared error`

`BIC`

- Mean RT and P(correct)
- Something which takes undecided trials into account
- Something else (Write your own, using these as a guide)

(Note that changing the objective function to something other than likelihood will not speed up model fitting.)

## Fitting methods¶

I don’t want to fit using the default recommended method (differential evolution), but would rather fit using:

(While using a fitting method other than differential evolution will likely reduce the time needed for fitting models, other methods may not offer robust parameter estimation for high-dimensional models.)

## Models from specific papers¶

*If you have a paper which used PyDDM, please* send us your model *so we can include them here!*

- Shinn et al. (2020) - Confluence of timing and reward biases in perceptual decision-making dynamics
- De Gee et al (2020) - Pupil-linked phasic arousal predicts a reduction of choice bias across species and decision domains
- Shinn et al. (2021) - Transient neuronal suppression for exploitation of new sensory evidence

## Other recipes¶

I want to: