Skip to contents

Decode binary encoding to categorical encoding

Source: R/parseCode.R
decodeBinary.Rd

Converts a binary-encoded GA chromosome (0/1 vector) into a categorical parameter vector.

Usage

decodeBinary(binary_string, search.space = "ivbase", custom_config)

Arguments

binary_string

Numeric vector of bits (0/1). 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 categorical parameter values.

Details

Supported search spaces:

  • "ivbase": binary string has 12 bits and decodes to 10 values.

  • "oralbase": binary string has 13 bits and decodes to 11 values.

  • "custom": binary string has 29 bits and decodes to 24 values.

Legacy layout ("ivbase" and "oralbase"):

  • The first two bits encode the number of compartments (no.cmpt) as 00 or 01 for 1, 10 for 2, and 11 for 3.

  • The middle parameters are copied directly and preserve values such as 0, 1, and -1.

  • The last two bits encode the residual error model (rv) as 00 or 01 for 1, 10 for 2, and 11 for 3.

Custom layout ("custom"):

  • Multi-level parameters are stored as 2-bit fields (for example, no.cmpt, absorption type, absorption delay, residual error model, and allometric scaling).

  • Binary flags are stored as single bits, including absolute bioavailability (abs.bio), the Michaelis-Menten indicator (mm), and the correlation indicator (mcorr).

  • Inter-individual variability indicators (eta.*) are stored as 16 single-bit flags in a fixed order.

For "custom", the categorical output order is:


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

See also

.twoBitCode, encodeBinary

Author

Zhonghui Huang

Examples

binary_iv <- c(0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1)
decodeBinary(binary_iv, "ivbase")
#>  [1] 1 0 1 0 0 0 0 0 0 3

binary_oral <- c(0, 1, rep(0, 9), 1, 1)
decodeBinary(binary_oral, "oralbase")
#>  [1] 1 0 0 0 0 0 0 0 0 0 3

binary_custom <- c(
  0, 0, 0, 1, 1, 1, 1, rep(0, 16), 0, 1, 1, 0, 0, 1
)
decodeBinary(binary_custom, "custom")
#>  [1] 1 2 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1