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Changed location of indices; bug fixes to xde_steady, xde_plot_PR, xd… #148

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Dec 18, 2023
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Changed location of indices; bug fixes to xde_steady, xde_plot_PR, xd… #148

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138 changes: 66 additions & 72 deletions R/adult-GeRM.R
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ MBionomics.GeRM <- function(t, y, pars) {
#' @return a [numeric] vector of length `nPatches`
#' @export
F_fqZ.GeRM <- function(t, y, pars) {
with(pars$MYZpar, f*q)*y[pars$MYZpar$Z_ix]
with(pars$MYZpar, f*q)*y[pars$ix$MYZ$Z_ix]
}

#' @title Number of eggs laid by adult mosquitoes
Expand All @@ -32,7 +32,7 @@ F_fqZ.GeRM <- function(t, y, pars) {
#' @export
F_eggs.GeRM <- function(t, y, pars) {
with(pars$MYZpar, {
G <- y[G_ix]
G <- y[pars$ix$MYZ$G_ix]
return(G*nu*eggsPerBatch)
})
}
Expand All @@ -42,16 +42,13 @@ F_eggs.GeRM <- function(t, y, pars) {
#' @inheritParams dMYZdt
#' @return a [numeric] vector
#' @export
dMYZdt.GeRM_ode <- function(t, y, pars, Lambda, kappa) {

nPatches <- pars$nPatches

dMYZdt.GeRM_ode <- function(t, y, pars, Lambda, kappa) {with(pars,{
with(pars$MYZpar,{

M <- y[M_ix]
G <- y[G_ix]
Y <- y[Y_ix]
Z <- y[Z_ix]
M <- y[ix$MYZ$M_ix]
G <- y[ix$MYZ$G_ix]
Y <- y[ix$MYZ$Y_ix]
Z <- y[ix$MYZ$Z_ix]

Omega <- make_Omega(g, sigma, calK, nPatches)
Upsilon <- expm(-Omega*eip)
Expand All @@ -63,7 +60,7 @@ dMYZdt.GeRM_ode <- function(t, y, pars, Lambda, kappa) {

return(c(dMdt, dGdt, dYdt, dZdt))
})
}
})}

#' @title Derivatives for adult mosquitoes
#' @description Implements [dMYZdt] for the GeRM DDE model.
Expand All @@ -72,35 +69,32 @@ dMYZdt.GeRM_ode <- function(t, y, pars, Lambda, kappa) {
#' @importFrom deSolve lagvalue
#' @importFrom deSolve lagderiv
#' @export
dMYZdt.GeRM_dde <- function(t, y, pars, Lambda, kappa) {
dMYZdt.GeRM_dde <- function(t, y, pars, Lambda, kappa) {with(pars,{

nPatches <- pars$nPatches
eip <- pars$MYZpar$eip

with(pars$MYZpar,{
with(MYZpar,{
if (t < eip) {
M_eip <- pars$MYZinits$M0
Y_eip <- pars$MYZinits$Y0
M_eip <- MYZinits$M0
Y_eip <- MYZinits$Y0
kappa_eip <- kappa
f_eip <- f
q_eip <- q
g_eip <- g
sigma_eip <- sigma
} else {
M_eip <- lagvalue(t = t - eip, nr = M_ix)
Y_eip <- lagvalue(t = t - eip, nr = Y_ix)
kappa_eip <- lagderiv(t = t-eip, nr = kappa_ix)
f_eip <- lagderiv(t = t-eip, nr = f_ix)
q_eip <- lagderiv(t = t-eip, nr = q_ix)
g_eip <- lagderiv(t = t-eip, nr = g_ix)
sigma_eip <- lagderiv(t = t-eip, nr = sigma_ix)
M_eip <- lagvalue(t = t - eip, nr = ix$MYZ$M_ix)
Y_eip <- lagvalue(t = t - eip, nr = ix$MYZ$Y_ix)
kappa_eip <- lagderiv(t = t-eip, nr = ix$MYZ$kappa_ix)
f_eip <- lagderiv(t = t-eip, nr = ix$MYZ$f_ix)
q_eip <- lagderiv(t = t-eip, nr = ix$MYZ$q_ix)
g_eip <- lagderiv(t = t-eip, nr = ix$MYZ$g_ix)
sigma_eip <- lagderiv(t = t-eip, nr = ix$MYZ$sigma_ix)
}

M <- y[M_ix]
G <- y[G_ix]
Y <- y[Y_ix]
Z <- y[Z_ix]
Upsilon <- matrix(data = y[Upsilon_ix], nrow = nPatches, ncol = nPatches)
M <- y[ix$MYZ$M_ix]
G <- y[ix$MYZ$G_ix]
Y <- y[ix$MYZ$Y_ix]
Z <- y[ix$MYZ$Z_ix]
Upsilon <- matrix(data = y[ix$MYZ$Upsilon_ix], nrow = nPatches, ncol = nPatches)

Omega <- make_Omega(g, sigma, calK, nPatches)
Omega_eip <- make_Omega(g_eip, sigma_eip, calK, nPatches)
Expand All @@ -113,7 +107,7 @@ dMYZdt.GeRM_dde <- function(t, y, pars, Lambda, kappa) {

return(c(dMdt, dGdt, dYdt, dZdt, dUdt, kappa, f, q, g, sigma))
})
}
})}

#' @title Setup the GeRM model for adult mosquitoes
#' @description Implements [setup_MYZ] for the GeRM model
Expand Down Expand Up @@ -253,17 +247,17 @@ make_MYZinits_GeRM = function(pars, MYZopts = list(),
#' @export
make_indices_MYZ.GeRM_ode <- function(pars) {

pars$MYZpar$M_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$MYZpar$M_ix, 1)
pars$ix$MYZ$M_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$ix$MYZ$M_ix, 1)

pars$MYZpar$G_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$MYZpar$G_ix, 1)
pars$ix$MYZ$G_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$ix$MYZ$G_ix, 1)

pars$MYZpar$Y_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$MYZpar$Y_ix, 1)
pars$ix$MYZ$Y_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$ix$MYZ$Y_ix, 1)

pars$MYZpar$Z_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$MYZpar$Z_ix, 1)
pars$ix$MYZ$Z_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$ix$MYZ$Z_ix, 1)

return(pars)
}
Expand All @@ -276,35 +270,35 @@ make_indices_MYZ.GeRM_ode <- function(pars) {
#' @export
make_indices_MYZ.GeRM_dde <- function(pars) {

pars$MYZpar$M_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$MYZpar$M_ix, 1)
pars$ix$MYZ$M_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$ix$MYZ$M_ix, 1)

pars$MYZpar$G_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$MYZpar$G_ix, 1)
pars$ix$MYZ$G_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$ix$MYZ$G_ix, 1)

pars$MYZpar$Y_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$MYZpar$Y_ix, 1)
pars$ix$MYZ$Y_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$ix$MYZ$Y_ix, 1)

pars$MYZpar$Z_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$MYZpar$Z_ix, 1)
pars$ix$MYZ$Z_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$ix$MYZ$Z_ix, 1)

pars$MYZpar$Upsilon_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches^2)
pars$max_ix <- tail(pars$MYZpar$Upsilon_ix, 1)
pars$ix$MYZ$Upsilon_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches^2)
pars$max_ix <- tail(pars$ix$MYZ$Upsilon_ix, 1)

pars$MYZpar$kappa_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$MYZpar$kappa_ix, 1)
pars$ix$MYZ$kappa_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$ix$MYZ$kappa_ix, 1)

pars$MYZpar$f_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$MYZpar$f_ix, 1)
pars$ix$MYZ$f_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$ix$MYZ$f_ix, 1)

pars$MYZpar$q_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$MYZpar$q_ix, 1)
pars$ix$MYZ$q_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$ix$MYZ$q_ix, 1)

pars$MYZpar$g_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$MYZpar$g_ix, 1)
pars$ix$MYZ$g_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$ix$MYZ$g_ix, 1)

pars$MYZpar$sigma_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$MYZpar$sigma_ix, 1)
pars$ix$MYZ$sigma_ix <- seq(from = pars$max_ix+1, length.out = pars$nPatches)
pars$max_ix <- tail(pars$ix$MYZ$sigma_ix, 1)

return(pars)
}
Expand All @@ -316,10 +310,10 @@ make_indices_MYZ.GeRM_dde <- function(pars) {
#' @export
parse_deout_MYZ.GeRM <- function(deout, pars) {
time = deout[,1]
M = deout[,pars$MYZpar$M_ix+1]
G = deout[,pars$MYZpar$G_ix+1]
Y = deout[,pars$MYZpar$Y_ix+1]
Z = deout[,pars$MYZpar$Z_ix+1]
M = deout[,pars$ix$MYZ$M_ix+1]
G = deout[,pars$ix$MYZ$G_ix+1]
Y = deout[,pars$ix$MYZ$Y_ix+1]
Z = deout[,pars$ix$MYZ$Z_ix+1]
y = Y/M
z = Z/M
gravid = G/M
Expand Down Expand Up @@ -395,10 +389,10 @@ make_inits_MYZ_GeRM_ode <- function(pars, M0, G0, Y0, Z0) {
#' @return none
#' @export
update_inits_MYZ.GeRM_ode <- function(pars, y0) {
M0 = y0[pars$MYZpar$M_ix]
G0 = y0[pars$MYZpar$G_ix]
Y0 = y0[pars$MYZpar$Y_ix]
Z0 = y0[pars$MYZpar$Z_ix]
M0 = y0[pars$ix$MYZ$M_ix]
G0 = y0[pars$ix$MYZ$G_ix]
Y0 = y0[pars$ix$MYZ$Y_ix]
Z0 = y0[pars$ix$MYZ$Z_ix]
pars = make_inits_MYZ_GeRM_ode(pars, M0, G0, Y0, Z0)
return(pars)
}
Expand All @@ -423,11 +417,11 @@ make_inits_MYZ_GeRM_dde <- function(pars, M0, G0, Y0, Z0, Upsilon0) {
#' @return none
#' @export
update_inits_MYZ.GeRM_dde <- function(pars, y0) {
M0 = y0[pars$MYZpar$M_ix]
G0 = y0[pars$MYZpar$G_ix]
Y0 = y0[pars$MYZpar$Y_ix]
Z0 = y0[pars$MYZpar$Z_ix]
Upsilon0 = y0[pars$MYZpar$Upsilon_ix]
M0 = y0[pars$ix$MYZ$M_ix]
G0 = y0[pars$ix$MYZ$G_ix]
Y0 = y0[pars$ix$MYZ$Y_ix]
Z0 = y0[pars$ix$MYZ$Z_ix]
Upsilon0 = y0[pars$ix$MYZ$Upsilon_ix]
pars = make_inits_MYZ_GeRM_dde(pars, M0, G0, Y0, Z0, Upsilon0)
return(pars)
}
Expand Down
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