#' @title Title
#'
#' @description Description
#'
#' @param x A number.
#' @param y A number.
#' @return return value here.
#' @details
#' Additional details here
#' @examples
#' example function call here
###########################################################
#' @export
viral_update_aim3_args_list_2 <- function(dat,timeIndex,ind)
{
#description:
#organizes variables into list for input into john's/aim3
#viral_update_modified_logisitic fxn; differs from
#"viral_update_modified_logistic_args_list_1" as list components are
#derived model quantities, not raw input parameters
list(Agent = ind,
time_0 = timeIndex-1,
time_final = timeIndex,
SPVL = dat$pop$SetPoint[ind],
Time_Inf = dat$pop$Time_Inf[ind],
Adherence1 = dat$pop$Adherence1[ind],
Adherence2 = dat$pop$Adherence2[ind],
Adherence3 = dat$pop$Adherence3[ind],
Adherence4 = dat$pop$Adherence4[ind],
Virus_DT = data.table::data.table(
V = dat$pop$V_vec[ind,],
I = dat$pop$I_vec[ind,],
M = dat$pop$M_vec[ind,],
L = dat$pop$L_vec[ind,]
),
K = dat$pop$K[ind],
CD4 = dat$pop$CD4[ind],
Drug1 = dat$pop$Drug1[ind],
Drug2 = dat$pop$Drug2[ind],
Drug3 = dat$pop$Drug3[ind],
Drug4 = dat$pop$Drug4[ind],
TherapyStarted = dat$pop$treated[ind],
SecondLineTherapyStarted = dat$pop$treated_2nd_line[ind],
ChronicPhaseBegins = dat$pop$ChronPhase[ind],
Immune_Response_Triggered = dat$pop$Imm_Trig[ind],
Aim3RoundingErrors = dat$pop$Aim3RoundingErrors[ind])
}
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