ABM_code_DA.Rmd

---
title: "ABM_code_DA"
date: "Summer 2020"
output: html_document
---

## Experimental Branch; dopamine agent; will need integration into control_structure

Using this rnotebook to try ideas for the ADHD ABM;object oriented abm using reference classess (http://adv-r.had.co.nz/R5.html).

```{r}

# Dopamine agent; makes DA: 1) digests MPH tablet w/ aid of CESA1A & 2) transfering availed compounds to the bloodstream

DA <- setRefClass("dopamine",
                  #Fields indicate attributes this reference class will have
                  fields = list(Tyrosine_hydroxylase = "numeric",
                                DOPA_decarboxylase = "numeric"),
                  
                  #methods indicate what functions the reference class can perform
                  methods = list(
                    
                    #f(x) 
                    Biosynthesize = function(tyrosine){
                      L_DOPA <<- tyrosine*Tyrosine_hydroxylase # how do we know how tyrosine to start with? 
                      Dopamine <<- L_DOPA*DOPA_decarboxylase
                      return(list(L_DOPA,
                                  Dopamine))
                      }
                    )
                  )
```

```{r}


#liver starts off empty with no naturally occuring D_MPH or L_MPH, and some specified level of CES1A1 ??
da_0 <- DA$new(Tyrosine_hydroxylase=0.8,
               DOPA_decarboxylase = 0.6)
#provide gut with a tablet to 'digest'; tablet D_MPH and L_MPH need to be specified 
da_0$Biosynthesize(100) 

```

```{r}
library(tidyverse)
enzyme_df <- read_csv("Copy of CES1_ADHDME_kids_LIVER_score.csv")

#Standardize CES1A1 PRS
enzyme_df$PRS_1.0 <- (enzyme_df$PRS_1.0 - min(enzyme_df$PRS_1.0)) / (max(enzyme_df$PRS_1.0) - min(enzyme_df$PRS_1.0))
enzyme_df$ID <- as.numeric(str_sub(enzyme_df$ID1, start = -4))

local_enzyme <- enzyme_df%>% filter(ID == 003) ## SAMPLE ID PROVIDED TO AGENT 
ind_Tyrosine_hydroxylase <- local_enzyme$PRS_1.0
ind_DOPA_decaroxylas <- local_enzyme$PRS_1.0

#liver starts off empty with no naturally occuring D_MPH or L_MPH, and some specified level of CES1A1 ??
da_1 <- DA$new(Tyrosine_hydroxylase = ind_Tyrosine_hydroxylase,
               DOPA_decarboxylase = ind_DOPA_decaroxylas)
#provide gut with a tablet to 'digest'; tablet D_MPH and L_MPH need to be specified 
da_1$Biosynthesize(100) 
```