https://github.com/morgankain/RRV_HostVectorCompetence
Tip revision: be7e87c3c4c8af0420a8dd42cdcff5586fdbad90 authored by Morgan Kain on 25 May 2021, 16:23:11 UTC
Merge pull request #1 from morgankain/add-license-1
Merge pull request #1 from morgankain/add-license-1
Tip revision: be7e87c
14_data.R0_setup.R
#####
## Finally, make sure all the pieces are in the correct orientation for downstream calculations
#####
## Now have XXXX with and without _adj_to_com for physiological responses at the level of the individual host and
## a full community-wide response given the full community makeup
## Note: using only _all_samps for now for the full uncertainty
####
## h_to_m_trans_all_samps : host to mosquito transmission for the community of interest
####
## -- num_days x hosts x mosquitoes x samples
## -- 8 x 16 x 17 x 1000
# h_to_m_trans_all_samps_adj_to_com -- already complete
## -- 8 x 12 x 8 x 1000 FOR BRISBANE
## -- 8 x 12 x 7 x 1000 FOR CAIRNS
####
## m_to_h_trans_all_samps : mosquito to host transmission
####
## -- num_days x mosquitoes x samples
## -- 40 x 17 x 1000
# just last arrangement needed
m_to_h_trans_all_samps_adj_to_com <- m_to_h_trans_all_samps[ , match(mosq.ordered, dimnames(m_to_h_trans_all_samps)[[2]]), ]
## -- 40 x 8 x 1000 FOR BRISBANE
## -- 40 x 7 x 1000 FOR CAIRNS
####
## AUC for the mosquitoes
####
mosq_inf_AUC_all_samps_adj_to_com <- mosq_inf_AUC_all_samps[match(mosq.ordered, dimnames(mosq_inf_AUC_all_samps)[[1]]), ]
mosq_trans_AUC_all_samps_adj_to_com <- mosq_trans_AUC_all_samps[match(mosq.ordered, dimnames(mosq_inf_AUC_all_samps)[[1]]), ]
####
# mos_surv_for_R0_all_samps : mosquito survival
####
## -- num_days x mosquitoes x samples
## -- 40 x 17 x 1000
# just last arrangement needed
mosq_surv_for_R0_all_samps_adj_to_com <- mosq_surv_for_R0_all_samps[ , match(mosq.ordered, dimnames(mosq_surv_for_R0_all_samps)[[2]]), ]
## -- 40 x 8 x 1000 FOR BRISBANE
## -- 40 x 7 x 1000 FOR CAIRNS
####
# mosq_bite_pref_all_samps : mosquito biting preference given the host community
####
## -- mosquitoes x hosts x samples
## -- 10 x 12 x 1000
# just last arrangement needed
mosq_bite_pref_all_samps_adj_to_com <- mosq_bite_pref_all_samps[match(mosq.ordered, dimnames(mosq_bite_pref_all_samps)[[1]]),, ]
## -- 8 x 12 x 1000 FOR BRISBANE
## -- 7 x 12 x 1000 FOR CAIRNS
# host_prop_for_R0 : proportions of each host in the given community
## -- hosts x samples
## -- 12 x 1000 FOR BRISBANE
## -- 12 x 1000 FOR CAIRNS
# host_prop_for_R0_adj_to_com -- already complete
### Really only want full uncertainty so comment this stuff out for now
# m_to_h_trans_adj_to_com <- m_to_h_trans[ , match(mosq.ordered, dimnames(m_to_h_trans)[[2]])]
# mos_surv_for_R0_adj_to_com <- mos_surv_for_R0[ , match(mosq.ordered, dimnames(mos_surv_for_R0)[[2]])]
# mosq_bite_pref_adj_to_com <- mosq_bite_pref[match(mosq.ordered, dimnames(mosq_bite_pref)[[1]]), ]