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  Spike Train Analysis Toolkit Options for Entropy Methods



Options and parameters are passed to the toolkit functions by way of a specialized data structure. The members of this data structure are described below. Items that are deprecated are in pink. Deprecated items will no longer be used in version 2.0 of the toolkit.

Options

Default selection in blue.

Name Description Options Method(s)
possible_words Strategy for computing the number of possible words x Use the positive integer value x, or Inf entropy_bub
entropy_nsb
entropy_tpmc
entropy_ww
"recommended" Use the independently recommended value for each method
"unique" Use number of unique observed words—corresponds to *_possible_words_strategy=0
"total" Use total number of observed words (direct methods only)—corresponds conceptually to *_possible_words_strategy=1
"possible" Use maximum number of possible words based on observed letters (direct methods only)
"min_tot_pos" Use minimum of "total" or "possible_obs" (direct methods only)—corresponds to *_possible_words_strategy=2 for tpmc and ww
"min_lim_tot_pos" Use minimum of 105, "total", or "possible_obs" (direct methods only)—corresponds to *_possible_words_strategy=2 for bub
tpmc_possible_words_strategy Strategy for computing the number of possible words 0 Use number of unique observed words entropy_tpmc
1 Use total number of observed words
2 Use maximum number of possible words
bub_possible_words_strategy Strategy for computing the number of possible words 0 Use number of unique observed words entropy_bub
1 Use total number of observed words
2 Use maximum number of possible words
bub_compat BUB compatibility parameter 0 Compatible with paper entropy_bub
1 Compatible with posted code
ww_possible_words_strategy Strategy for computing the number of possible words 0 Use number of unique observed words entropy_ww
1 Use total number of observed words
2 Use maximum number of possible words

Parameters

Name Description Type Range Default Method(s)
bub_lambda_0 Lagrange multiplier parameter λ0 for BUB double ≥ 0 0 entropy_bub
bub_K K parameter for BUB int > 0 11 entropy_bub
ww_beta β parameter for Dirichlet prior double ≥ 0 1 entropy_ww
boot_random_seed Seed for random number generation int 1 variance_boot
boot_num_samples Number of bootstrap samples int > 0 100 variance_boot
nsb_precision Relative precision for numerical integration double > 0 10-6 entropy_nsb



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