Sample Entropy Calculation

globals [ m                 ;; length of substrings that can be derived from the input-string
          substrings        ;; list of the substrings derived from the input-string
          substr-copy       ;; a copy of the previous list
          similar           ;; couple of similar substrings in the previous list
          sampen            ;; the sample entropy of the input-string
          index             ;; an index/pointer
         ]


;; --------- CALCULATING SAMPLE ENTROPY FOR THE INPUT-STRING SEQUENCE --------------------------------
;; ---------------------------------------------------------------------------------------------------

to compute-sample-entropy
  ca
  ifelse input-string = "" [output-print "No string to operate on"
    stop] [start-message]
  set input-string word input-string "_"
  ;; Creating patterns with m = 2
  set m 2
  set similar 0
  set substrings []
  built-substrings
  let substrings2 substrings
  output-print word "Set of patterns with m = 2       --> " substrings2
  ;; evaluate each pair of patterns
  ;; to determine if they are similar within a tolerance of 𝑟 = 0.
  set substr-copy substrings2
  calculate-distancies
  let S2 similar
  output-print word "Similar patterns of length = 2   -->  " S2
  output-print ""
    if S2 = 0 [stop-message stop]
  ;; Creating patterns with m = 3
  set m m + 1
  set index 0
  set similar 0
  set substrings []
  built-substrings
  set input-string but-last input-string
  let substrings3 substrings
  output-print word "Set of patterns with m + 1 = 3   --> " substrings3
  set substr-copy substrings3
  calculate-distancies
  let S3 similar
  output-print word "Similar patterns of length = 3   -->  " S3
  output-print ""
  if S3 = 0 [stop-message stop]
  ;; sample entropy computation
  set sampen precision (- ln (S3 / S2)) 5
  output-type word "***     SAMPLE ENTROPY = - ln " S3
  output-type word " / " S2
  output-type word " = " sampen
  output-print "     ***"
end 

to built-substrings
  set substrings lput (substring input-string index (index + m)) substrings
  set index index + 1
  if index < (length input-string - m) [built-substrings]
end 

to calculate-distancies
  set index 0
  let short.copy but-first substr-copy
  repeat length short.copy [
    if item 0 substr-copy = item index short.copy
      [set similar similar + 1]
       set index index + 1
       ]
  if length short.copy > 1 [
    set substr-copy but-first substr-copy
    calculate-distancies
  ]
  set index 0
end 

to start-message
  output-print ""
  output-print "Let's compute the sample entropy for the given sequence (with r=0 and m=2)."
  output-print ""
end 

to stop-message
  output-print "It is not possible to compute the sample entropy for this string"
  output-type "because the similar patterns of length " output-type m output-type " is null."
  if m = 2 [set input-string but-last input-string]
end 


;; Public Domain: to the extent possible under law, the author has waived
;; all copyright and related or neighboring rights to this model.