Codebook reference

The codebook is how you tell Lace about your data. The codebook contains information about

Row names
Column names
The type of data in each column (e.g., continuous, categorical, or count)
The prior on the parameters for each column
The hyperprior on the prior parameters for each column
The prior on the Dirichlet Process alpha parameter

Codebook fields

`table_name`

String name of the table. For your reference.

`state_alpha_prior`

A gamma prior on the Chinese Restaurant Process (CRP) alpha parameter assigning columns to views.

Example with a gamma prior

state_alpha_prior:
  shape: 1.0
  rate: 1.0

`view_alpha_prior`

A gamma prior on the Chinese Restaurant Process (CRP) alpha parameter assigning rows within views to categories.

Example with a gamma prior

view_alpha_prior:
  shape: 1.0
  rate: 1.0

`col_metadata`

A list of columns, ordered by left-to-right occurrence in the data. Contains the following fields:

name: The name of the column
notes: Optional information about the column. Purely for reference
coltype: Contains information about the type type of data, the prior, and the hyper prior. See column metadata for more information
missing_not_at_random: a boolean. If false (default), missing values in the column are assumed to be missing completely at random.

`row_names`

A list of row names in order of top-to-bottom occurrence in the data

Codebook type inference

When you upload your data, Lace will pull the row and column names from the file, infer the data types, and choose and empirical hyperprior from the data.

Type inference works like this:

Categorical if:
- The column contains only string values
  - Lace will assume the categorical variable can take on any of (and only) the existing values in the column
- There are only integers up to a cutoff.
  - If There are only integers in the column x the categorical values will be assumed to take on values 0 to max(x).
Count if:
- There are only integers that exceed the value of the cutoff
Continuous if:
- There are only integers and one or more floats

Column metadata

Either prior or hyper must be defined.
- If prior is defined and hyper is not defined, hyperpriors and hyperparameter inference will be disabled.

It is best to leave the hyperpriors alone. It is difficult to intuit what effect the hyperpriors have on the final distribution. If you have knowledge beyond the vague hyperpriors, null out the `hyper` field with a `~` and set the prior instead. This will disable hyperparameter inference inf favor of the expert knowledge you have provided.

Continuous

The continuous type has the hyper field and the prior field. The prior parameters are those for the Normal Inverse Chi-squared prior on the mean and variance of a normal distribution.

m: the prior mean
k: how strongly (in pseudo observations) that we believe m
s2: the prior variance
v: how strongly (is pseudo observations) that we believe s2

To have widely dispersed components with small variances you would set k very low and very high.

FIXME: Animation showing effect of different priors

The hyper priors are the priors on the above parameters. They are named for the parameters to which they are attached, e.g. pr_m is the hyper prior for the m parameter.

pr_m: Normal distribution
pr_k: Gamma distribution with shape and rate (inverse scale) parameters
pr_v: Inverse gamma distribution with shape and scale parameters
pr_s2: Inverse gamma distribution with shape and scale parameters

- name: Eccentricity
  coltype: !Continuous
    hyper:
      pr_m:
        mu: 0.02465318142734303
        sigma: 0.1262297091840037
      pr_k:
        shape: 1.0
        rate: 1.0
      pr_v:
        shape: 7.0587581525186648
        scale: 7.0587581525186648
      pr_s2:
        shape: 7.0587581525186648
        scale: 0.015933939480678149
    prior:
      m: 0.0
      k: 1.0
      s2: 7.0
      v: 1.0
    # To not define the prior add a `~`
    # prior: ~
  notes: ~
  missing_not_at_random: false

Categorical

In addition to prior and hyper, Categorical has additional special fields:

k: the number of values the variable can assume
value_map: An optional map of integers in [0, ..., k-1] mapping the integer code (how the value is represented internally) to the string value. If value_map is not defined, it is usually assume that classes take on only integer values in [0, ..., k-1].

The hyper is an inverse gamma prior on the prior parameter alpha

- name: Class_of_Orbit
  coltype: !Categorical
    k: 4
    hyper:
      pr_alpha:
        shape: 1.0
        scale: 1.0
    value_map: !string
      0: Elliptical
      1: GEO
      2: LEO
      3: MEO
    prior:
      alpha: 0.5
      k: 4
    # To not define the prior add a `~`
    # prior: ~
  notes: ~
  missing_not_at_random: false

Editing the codebook

You should use the default codebook generated by the Lace CLI as a starting point for custom edits. Generally the only edits you will make are

Adding notes/comments
changing the state_alpha_prior and view_alpha_prior (though you should only do this if you know what you're doing)
converting a Count column to a Categorical column. Usually there will be no need to change between other column types.

Lace Documentation