#' @export
baseline_alt_v0<- 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{# 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)
}
#
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