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Encode categorical encoding to binary encoding

Source: R/parseCode.R
encodeBinary.Rd

Converts a categorical parameter vector into a binary-encoded GA chromosome.

Usage

encodeBinary(categorical_string, search.space = "ivbase", custom_config)

Arguments

categorical_string

Numeric vector of categorical parameter values. Length must match the expected layout for the selected search.space.

search.space

Character string specifying which search space to use. Options are "ivbase", "oralbase", or "custom". Default is "ivbase".

custom_config

Optional named list defining a custom parameter structure. If provided, the parameter names are taken from the names of this list. If NULL, a default parameter structure is used based on the selected search space.

Value

Numeric vector of bits (0/1).

Details

This function converts a vector of categorical parameter values into a 0/1 bit string (a GA chromosome). The required input layout and the encoding rules depend on the selected search space.

Built-in search spaces: ivbase / oralbase

  • Expected input length:

    • ivbase: 10 categorical values

    • oralbase: 11 categorical values

  • Structure: the first value is no.cmpt and the last value is rv. All middle values are copied as-is (they are expected to be 0/1 flags). Specifically, ivbase copies indices 2..9 and oralbase copies indices 2..10.

  • no.cmpt and rv use the legacy 3-level 2-bit encoding:

    • 1 -> 01

    • 2 -> 10

    • 3 -> 11

    The code 00 is not used in this mapping.

  • Output length:

    • ivbase: 12 bits (2 + 8 + 2)

    • oralbase: 13 bits (2 + 9 + 2)

Custom search space: custom

For search.space = "custom", the function reads categorical values in the order given by params. If custom_config$params is provided and non-empty, that vector defines the parameter names and order; otherwise, the default 24-parameter layout is used:


no.cmpt, abs.type, abs.delay, abs.bio,
eta.vmax, eta.km, eta.cl, eta.vc, eta.vp, eta.vp2, eta.q, eta.q2,
eta.ka, eta.tlag, eta.D2, eta.F1, eta.Fr, eta.mtt, eta.n, eta.bio,
mm, mcorr, rv, allometric_scaling

  • Parameters encoded with 2 bits: no.cmpt, abs.type, abs.delay, rv, and allometric_scaling.

  • All other parameters must be single-bit flags (0 or 1) and are appended directly to the chromosome.

2-bit encoding rules

  • no.cmpt (1..3): 1->01, 2->10, 3->11 (00 unused)

  • abs.type (1..4): 1->00, 2->01, 3->10, 4->11

  • abs.delay (0..2): 0->00, 1->01, 2->10 (11 unused)

  • rv (1..4): 1->00, 2->01, 3->10, 4->11

  • allometric_scaling (0..3): 0->00, 1->01, 2->10, 3->11

See also

.twoBitCode, decodeBinary

Author

Zhonghui Huang

Examples

# ivbase: 10 categorical -> 12 bits
cat_iv <- c(1, rep(0, 8), 3)
encodeBinary(cat_iv, "ivbase")
#>  [1] 0 1 0 0 0 0 0 0 0 0 1 1

# Custom: 24 categorical -> 29 bits
cat_custom <- c(
  1, 2, 0, 1,
  rep(0, 16),
  0, 1, 3, 1
)
encodeBinary(cat_custom, "custom")
#>  [1] 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1