DEB_INF_GUTS_IBM_1.1.nlogo

; script-file DEB-INF-IBM
; Authors: Dave Civitello (dcivite@emory.edu), adapted from Ben Martin's DEB-IBM

; implementation of the DEB-infection equations of Civitello et al. XXXX in an IBM
; check ... for the user-manual and the ODD
; published in "...", ... 20XX
; ==========================================================================================================================================
; ========================== DEFINITION OF PARAMETERS AND STATE VARIABLES ==================================================================
; ==========================================================================================================================================
breed [snails snail]
breed [eggs egg]
;breed [embryo embryos]
;breed [juvenile juveniles]
;breed [adult adults]


; global parameters: are accessible for patches and turtles
globals[
  ;e0    ; t L^2, initial reserves of the embryos at the start of the simulation
  L_0      ; cm, initial structural volume
  resources ; type of food dynamics in the environment: cyclical or event-based
  resource_type ; type of food source: detritus or algae
  step      ; desired time step of simulations (days)
]
; ------------------------------------------------------------------------------------------------------------------------------------------
; parameters for the environment: here only prey density

patches-own[
  F        ; # / L, periphyton (food) density
  M        ; # total miracidia
  Z        ; # /L cercarial density
  G        ; # total eggs
  dF       ; change in food density per patch
  r        ; rate of food growth
]
; ------------------------------------------------------------------------------------------------------------------------------------------

; definition of parameters for the individuals:
; the notation follows the DEBtool-notation as far as possible
; deviation: rates are indicated with "_rate" rather than a dot
; each individual(turtle) in the model has the following parameters

snails-own[
  ; - - - - - - - - - - - - - - - STATE VARIABLES - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
      ; --- Host state variables ---
  L           ; cm, structural length
  ee         ; scaled reserve density of hosts
  D           ; host development
  RH         ; energy in reproduction buffer
  DAM         ; starvation-related damage
  HAZ         ; starvation-related hazard rate
  LG          ; cm, physical shell length
      ; --- Parasite state variables ---
  P           ; parasite biomass
  RPP         ; energy in parasite reproduction
  K           ; half saturation coefficient for food intake
  L-min       ; minimum shell length (host)
  L-max       ; maximum shell length (host)
]

eggs-own[
  ; - - - - - - - - - - - - - - - STATE VARIABLES - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  age         ; age of egg, hatches at 7 d
  ; - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  ; - - - - - - - - - - - - - - -  DEB PARAMETERS (with dimension and name) - - - - - - - - - - - - - - - - - - - - - - - - - - - -
]
; ==========================================================================================================================================
; ========================== SETUP PROCEDURE: SETTING INITIAL CONDITIONS ===================================================================
; ==========================================================================================================================================

to setup
  clear-all
  set step 1

  create-snails 60                   ; turtles are created in the beginning
  ask  snails  [
    set L-min 4 ; 4 mm length
    set L-max 16 ; 16 mm length
    set L L-min + random-float(L-max - L-min) ; random draw between min and max length ; random-float 2 + 4
    set ee 0.9
    set D 0
    set RH 0
    set P 0
    set RPP 0
    set DAM 0
    set HAZ 0
    set LG L
    set K 1
    ;individual-variability  ; first their individual variability in the parameter is set
  ;calc-embryo-reserve-investment     ; then the initial energy is calculated for each
  ]

;  create-juvenile count snails with [RH  = 0]
;  create-adult count snails with [RH > 0]

  ask patches [
    set F 1
    set M 0
    set Z 0
    set G 0]; set initial value of prey to their carrying capacity
  reset-ticks
end

; ==========================================================================================================================================
; ========================== SUBMODELS =====================================================================================================
; ==========================================================================================================================================

to am-I-dead
  if ee <= 0 [die]
  if random-float 1 <= (1 - exp (HAZ * -1)) [die] ; kill hosts when hazard rate becomes too high
end

; ------------------------------------------------------------------------------------------------------------------------------------------
; ----------------- DYNAMICS -------------------------------------------------------------------------------------------------------
; ------------------------------------------------------------------------------------------------------------------------------------------

to go
  ask snails [
    am-I-dead
  update-resources
  ]
  do-plots
  tick
end

; ------------------------------------------------------------------------------------------------------------------------------------------
; ----------------- UPDATE-RESOURCES -------------------------------------------------------------------------------------------------------
; ------------------------------------------------------------------------------------------------------------------------------------------
; ######### R #########
; calculate changes in food based on either cyclical or event-based dynamics

to update-resources
  if resources = "cyclical"
  [
    ; set dF K * F / (F + (K - F) * exp(- r * step)) - sum(F) ; change in food in environment (Env_F in DEB_IBM.R)
;    set dF F
    ]

  if resources = "event-based"
  [
;  set dF F
  ]

  if resource_type = "detritus"
  [
   ; set dF F
  ]
  ;set F F + dF ; change in food density
end

; ------------------------------------------------------------------------------------------------------------------------------------------
; ----------------- PLOT -------------------------------------------------------------------------------------------------------------------
; ------------------------------------------------------------------------------------------------------------------------------------------

to do-plots
 set-current-plot "stage class density"
; set-current-plot-pen "embryo"
; set-plot-pen-interval 1 / timestep
;    ifelse any? eggs  [plot count eggs / volume]
;    [plot 0]

  set-current-plot-pen "juvenile"
  set-plot-pen-interval 1
  ifelse any? snails with [RH  = 0] [plot count snails with [RH = 0]]
;  ifelse any? juvenile [plot count juvenile]
  [plot 0]

  set-current-plot-pen "adult"
  set-plot-pen-interval 1
  ifelse any? snails with [RH  > 0] [plot count snails with [RH  > 0]]
  ;  ifelse any? adult [plot count adult]
  [plot 0]

  set-current-plot-pen "infected"
  set-plot-pen-interval 1
  ifelse any? snails with [RPP  > 0] [plot count snails with [RPP  > 0]]
  ;  ifelse any? infected [plot count infected]
  [plot 0]




  set-current-plot "Environment"
  set-current-plot-pen "food density"
  set-plot-pen-interval 1
  plot mean [F] of patches
  set-current-plot-pen "miracidia"
  set-plot-pen-interval 1
  plot mean [M] of patches
    set-current-plot-pen "cercariae"
  set-plot-pen-interval 1
  ;ifelse (any? snails with [d_CERCS > 0]) [plot  mean [d_CERCS] of snails with [d_CERCS > 0]] [plot 0] ; [Z] of patches
  plot mean [Z] of patches
;
;  set-current-plot "population density"
;  set-plot-pen-interval 1 / timestep
; plot count snails with [D > 0]


;  set-current-plot "shrinkage distribution"
 ; histogram [L / LG] of snails
;
;    set-current-plot "juv e distribution"
;  histogram [e_H] of snails with [D  < D_R]
;
;    set-current-plot "adult e distribution"
;  histogram [e_H] of snails with [D  > D_R]
;
;    set-current-plot "parasite distribution"
;  histogram [d_CERCS * timestep] of snails with [d_CERCS > 0]

;  set-current-plot "parasite biomass"
;  set-plot-pen-interval 1
;  ifelse any? snails with [P  > 0] [plot count snails with [P  > 0]]
;  [plot 0]

end
@#$#@#$#@
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stage class density
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MONITOR
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MONITOR
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Food
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PENS
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@#$#@#$#@
# Model Overview

## For the full model description, instructions, and troubleshooting, go to https://github.com/darwinanddavis/SchistoIBM.

# Updates

### 15-1-19  
> added L-min and L-max shell length to randomise initial length of hosts 
> added detritus and algae options as resource type 

### 27-11-18  
> added `dF` parameter to updates changes in `F` in Netlogo environment based on `resources` global parameter
> added step (global) and K (host) variables 

### 26-11-18
> added embryo, juvenile, and adult breeds as temporary globals  
> added juvenile, adult, and infected counters to interface  

### 10-11-18
> added `resources` global -- cyclic or event-based  
@#$#@#$#@
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@#$#@#$#@
NetLogo 6.0.4
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
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@#$#@#$#@
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@#$#@#$#@
0
@#$#@#$#@