R/control_alternative.R

In holaanna/contactsimulator: Contact model simulator

#' @export
baseline_alt<- function(farm_pos_cat,vis_int_per_cat,farm_inf,farm_inf_on,min_tim_cont,indx_rem,indx_con,mm_1,nn_1){


  if(farm_inf[mm_1,nn_1]==0 & (min_tim_cont-farm_pos_cat$tim_lst_pos[indx_con])>=360*2){ # Either A or B

    if((min_tim_cont-farm_pos_cat$tim_lst_pos[indx_con])>10000  ){   # Never recorded
      eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "A"))
      indx<- which(vis_int_per_cat$cat=="A")

    }
    else{
      eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "B"))
      indx<- which(vis_int_per_cat$cat=="B")

    }

    eval.parent(substitute(farm_pos_cat$vis_int[indx_con]<- vis_int_per_cat$vis_int[indx]))
    eval.parent(substitute(farm_pos_cat$vis[indx_con]<- min_tim_cont+ vis_int_per_cat$vis_int[indx]))


  }

  else if(farm_inf[mm_1,nn_1]>0 & (min_tim_cont-farm_pos_cat$tim_lst_pos[indx_con])>=360*2){
    kk<- (farm_inf[mm_1,nn_1]>1) + (farm_inf[mm_1,nn_1]>10) + 1
    # if(min_tim_cont==2552){
    #   show(c(kk,min_tim_cont))
    #   show(farm_pos_cat[indx_con,])
    #   #stop("reach")
    # }

    switch(kk,
           { # 1 infection
             eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "C"))
             indx<- which(vis_int_per_cat$cat=="C")
           },
           { # 1-10 infections
             eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "D"))
             indx<- which(vis_int_per_cat$cat=="D")
           },
           { # >10 infections
             eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "E"))
             indx<- which(vis_int_per_cat$cat=="E")
           }
    )

    eval.parent(substitute(farm_pos_cat$vis_int[indx_con]<- vis_int_per_cat$vis_int[indx]))
    eval.parent(substitute(farm_pos_cat$vis[indx_con]<- min_tim_cont+ vis_int_per_cat$vis_int[indx]))

    eval.parent(substitute(farm_pos_cat$tim_lst_pos[indx_con]<- min_tim_cont))

  }

  else{# Either C, D or E

    k<- (farm_inf_on[mm_1,nn_1]>0) + 1
    indx<- which(vis_int_per_cat$cat==farm_pos_cat$cat[indx_con])
    # show(k)
    switch(k,
           {  # No infection during the visit


               eval.parent(substitute(farm_pos_cat$vis[indx_con]<- min_tim_cont+ vis_int_per_cat$vis_int[indx]))


           },

           { # >=1 infection
             kk<- (farm_inf[mm_1,nn_1]>1) + (farm_inf[mm_1,nn_1]>10) + 1
             switch(kk,
                    { # 1 infection
                      eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "C"))
                    },
                    { # 1-10 infections
                      eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "D"))
                    },
                    { # >10 infections
                      eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "E"))
                    }
             )

             indx<- which(vis_int_per_cat$cat==farm_pos_cat$cat[indx_con])
             eval.parent(substitute(farm_pos_cat$vis_int[indx_con]<- vis_int_per_cat$vis_int[indx]))
             eval.parent(substitute(farm_pos_cat$vis[indx_con]<- min_tim_cont+ vis_int_per_cat$vis_int[indx]))

             eval.parent(substitute(farm_pos_cat$tim_lst_pos[indx_con]<- min_tim_cont))
             eval.parent(substitute(farm_pos_cat$nb_round[indx_con]<- 360*2/vis_int_per_cat$vis_int[indx] -1))


           }

    )

    eval.parent(substitute(farm_inf[mm_1,nn_1]<- 0))

  }


}









#
#   if((min_tim_cont-farm_pos_cat$tim_lst_pos[indx_con])<0 ){   # Never recorded
#     if(farm_inf[mm_1,nn_1]==0){
#       eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "A"))
#       indx<- which(vis_int_per_cat$cat=="A")
#       eval.parent(substitute(farm_pos_cat$vis_int[indx_con]<- vis_int_per_cat$vis_int[indx]))
#       eval.parent(substitute(farm_pos_cat$vis[indx_con]<- min_tim_cont+ vis_int_per_cat$vis_int[indx]))
#     }
#     else{
#       kk<- (farm_inf[mm_1,nn_1]>1) + (farm_inf[mm_1,nn_1]>10) + 1
#       switch(kk,
#              { # 1 infection
#                eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "C"))
#              },
#              { # 1-10 infections
#                eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "D"))
#              },
#              { # >10 infections
#                eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "E"))
#              }
#       )
#       indx<- which(vis_int_per_cat$cat==farm_pos_cat$cat[indx_con])
#       eval.parent(substitute(farm_pos_cat$vis_int[indx_con]<- vis_int_per_cat$vis_int[indx]))
#       eval.parent(substitute(farm_pos_cat$vis[indx_con]<- min_tim_cont+ vis_int_per_cat$vis_int[indx]))
#
#       eval.parent(substitute(farm_pos_cat$tim_lst_pos[indx_con]<- min_tim_cont))
#     }
#
#   }
#
#   if((min_tim_cont-farm_pos_cat$tim_lst_pos[indx_con])>=360*2){ # Lat posive more than two years
#     if(farm_inf[mm_1,nn_1]==0){
#       eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "B"))
#       indx<- which(vis_int_per_cat$cat=="B")
#       eval.parent(substitute(farm_pos_cat$vis_int[indx_con]<- vis_int_per_cat$vis_int[indx]))
#       eval.parent(substitute(farm_pos_cat$vis[indx_con]<- min_tim_cont+ vis_int_per_cat$vis_int[indx]))
#     }
#     else{
#       kk<- (farm_inf[mm_1,nn_1]>1) + (farm_inf[mm_1,nn_1]>10) + 1
#       switch(kk,
#              { # 1 infection
#                eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "C"))
#              },
#              { # 1-10 infections
#                eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "D"))
#              },
#              { # >10 infections
#                eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "E"))
#              }
#       )
#       indx<- which(vis_int_per_cat$cat==farm_pos_cat$cat[indx_con])
#       eval.parent(substitute(farm_pos_cat$vis_int[indx_con]<- vis_int_per_cat$vis_int[indx]))
#       eval.parent(substitute(farm_pos_cat$vis[indx_con]<- min_tim_cont+ vis_int_per_cat$vis_int[indx]))
#       eval.parent(substitute(farm_pos_cat$tim_lst_pos[indx_con]<- min_tim_cont))
#     }
#
#   }
#
#   if((min_tim_cont-farm_pos_cat$tim_lst_pos[indx_con])<=360 & (min_tim_cont-farm_pos_cat$tim_lst_pos[indx_con])>0){
#     k<- (farm_inf[mm_1,nn_1]>0) + 1
#     # show(k)
#     switch(k,
#            {  # No infection during the visit
#              # show(farm_pos_cat$vis[indx_con])
#                indx<- which(vis_int_per_cat$cat==farm_pos_cat$cat[indx_con])
#                eval.parent(substitute(farm_pos_cat$vis_int[indx_con]<- vis_int_per_cat$vis_int[indx]))
#                eval.parent(substitute(farm_pos_cat$vis[indx_con]<- min_tim_cont+ vis_int_per_cat$vis_int[indx]))
#
#            },
#
#            { # >=1 infection
#              kk<- (farm_inf[mm_1,nn_1]>1) + (farm_inf[mm_1,nn_1]>10) + 1
#              switch(kk,
#                     { # 1 infection
#                       eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "C"))
#                     },
#                     { # 1-10 infections
#                       eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "D"))
#                     },
#                     { # >10 infections
#                       eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "E"))
#                     }
#              )
#
#              indx<- which(vis_int_per_cat$cat==farm_pos_cat$cat[indx_con])
#              eval.parent(substitute(farm_pos_cat$vis_int[indx_con]<- vis_int_per_cat$vis_int[indx]))
#              eval.parent(substitute(farm_pos_cat$vis[indx_con]<- min_tim_cont+ vis_int_per_cat$vis_int[indx]))
#
#              eval.parent(substitute(farm_pos_cat$tim_lst_pos[indx_con]<- min_tim_cont))
#
#            }
#
#     )
#
#     eval.parent(substitute(farm_inf[mm_1,nn_1]<- 0))
#
#   }
#
#
#   if((min_tim_cont-farm_pos_cat$tim_lst_pos[indx_con])< 2*360 & (min_tim_cont-farm_pos_cat$tim_lst_pos[indx_con])>360){
#     k<- (farm_inf[mm_1,nn_1]>0) + 1
#     # show(k)
#     switch(k,
#            {  # No infection during the visit
#              # show(farm_pos_cat$vis[indx_con])
#              indx<- which(vis_int_per_cat$cat==farm_pos_cat$cat[indx_con])
#              eval.parent(substitute(farm_pos_cat$vis_int[indx_con]<- vis_int_per_cat$vis_int[indx]))
#              eval.parent(substitute(farm_pos_cat$vis[indx_con]<- min_tim_cont+ vis_int_per_cat$vis_int[indx]))
#
#
#            },
#
#            { # >=1 infection
#              kk<- (farm_inf[mm_1,nn_1]>1) + (farm_inf[mm_1,nn_1]>10) + 1
#              switch(kk,
#                     { # 1 infection
#                       eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "C"))
#                     },
#                     { # 1-10 infections
#                       eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "D"))
#                     },
#                     { # >10 infections
#                       eval.parent(substitute(farm_pos_cat$cat[indx_con]<- "E"))
#                     }
#              )
#
#              indx<- which(vis_int_per_cat$cat==farm_pos_cat$cat[indx_con])
#              eval.parent(substitute(farm_pos_cat$vis_int[indx_con]<- vis_int_per_cat$vis_int[indx]))
#              eval.parent(substitute(farm_pos_cat$vis[indx_con]<- min_tim_cont+ vis_int_per_cat$vis_int[indx]))
#
#              eval.parent(substitute(farm_pos_cat$tim_lst_pos[indx_con]<- min_tim_cont))
#
#            }
#
#     )
#
#     eval.parent(substitute(farm_inf[mm_1,nn_1]<- 0))
#
#   }
#
#   # show(farm_pos_cat$vst)
#
# }
#
#
#