#TODO refer to manuscript or somewhere else for explanation of each compartment symbol
#' Postprocess output from age-structured SEIR ODE model of vaccination
#' with 2 doses and delay to protection
#' @param dat output from seir model as a data frame
#' @return List of summary results
#' @keywords vacamole
#' @importFrom stringr str_detect
#' @export
postprocess_age_struct_model_output <- function(dat) {
S <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "S[:digit:]")])
Shold_1d <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "Shold_1d[:digit:]")])
Sv_1d <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "Sv_1d[:digit:]")])
Shold_2d <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "Shold_2d[:digit:]")])
Sv_2d <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "Sv_2d[:digit:]")])
# Shold_3d <- dat %>%
# select(names(dat)[str_detect(names(dat), pattern = "Shold_3d[:digit:]")])
# Sv_3d <- dat %>%
# select(names(dat)[str_detect(names(dat), pattern = "Sv_3d[:digit:]")])
E <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "E[:digit:]")])
Ev_1d <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "Ev_1d[:digit:]")])
Ev_2d <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "Ev_2d[:digit:]")])
# Ev_3d <- dat %>%
# select(names(dat)[str_detect(names(dat), pattern = "Ev_3d[:digit:]")])
I <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "I[:digit:]")])
Iv_1d <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "Iv_1d[:digit:]")])
Iv_2d <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "Iv_2d[:digit:]")])
# Iv_3d <- dat %>%
# select(names(dat)[str_detect(names(dat), pattern = "Iv_3d[:digit:]")])
H <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "H[:digit:]")])
Hv_1d <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "Hv_1d[:digit:]")])
Hv_2d <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "Hv_2d[:digit:]")])
# Hv_3d <- dat %>%
# select(names(dat)[str_detect(names(dat), pattern = "Hv_3d[:digit:]")])
H_IC <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "H_IC[:digit:]")])
H_ICv_1d <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "H_ICv_1d[:digit:]")])
H_ICv_2d <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "H_ICv_2d[:digit:]")])
# H_ICv_3d <- dat %>%
# select(names(dat)[str_detect(names(dat), pattern = "H_ICv_3d[:digit:]")])
IC <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "IC[:digit:]")])
ICv_1d <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "ICv_1d[:digit:]")])
ICv_2d <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "ICv_2d[:digit:]")])
# ICv_3d <- dat %>%
# select(names(dat)[str_detect(names(dat), pattern = "ICv_3d[:digit:]")])
D <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "D[:digit:]")])
R <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "R[:digit:]")])
Rv_1d <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "Rv_1d[:digit:]")])
Rv_2d <- dat %>%
select(names(dat)[str_detect(names(dat), pattern = "Rv_2d[:digit:]")])
# Rv_3d <- dat %>%
# select(names(dat)[str_detect(names(dat), pattern = "Rv_3d[:digit:]")])
rtn <- list(
S = S,
Shold_1d = Shold_1d,
Sv_1d = Sv_1d,
Shold_2d = Shold_2d,
Sv_2d = Sv_2d,
# Shold_3d = Shold_3d,
# Sv_3d = Sv_3d,
E = E,
Ev_1d = Ev_1d,
Ev_2d = Ev_2d,
# Ev_3d = Ev_3d,
I = I,
Iv_1d = Iv_1d,
Iv_2d = Iv_2d,
# Iv_3d = Iv_3d,
H = H,
Hv_1d = Hv_1d,
Hv_2d = Hv_2d,
# Hv_3d = Hv_3d,
H_IC = H_IC,
H_ICv_1d = H_ICv_1d,
H_ICv_2d = H_ICv_2d,
# H_ICv_3d = H_ICv_3d,
IC = IC[, -c(1:9)],
ICv_1d = ICv_1d[, -c(1:9)],
ICv_2d = ICv_2d[, -c(1:9)],
# ICv_3d = ICv_3d[, -c(1:9)],
D = D,
R = R,
Rv_1d = Rv_1d,
Rv_2d = Rv_2d
# Rv_3d = Rv_3d
)
return(rtn)
}
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