diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index de73d2fb..4f18e3be 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -13,9 +13,9 @@ jobs: steps: - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 - - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-pandoc@v2 - name: Query dependencies run: | diff --git a/DESCRIPTION b/DESCRIPTION index 873446b5..b7aaa69a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -91,7 +91,7 @@ Suggests: ggplot2, covr, mgcv -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 Roxygen: list(markdown = TRUE) LinkingTo: Rcpp, diff --git a/NAMESPACE b/NAMESPACE index 0479fc4f..167c0f0e 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -13,6 +13,8 @@ export(get_parameters) export(parameterise_mosquito_equilibrium) export(parameterise_total_M) export(peak_season_offset) +export(r21_booster_profile) +export(r21_profile) export(rtss_booster_profile) export(rtss_profile) export(run_metapop_simulation) diff --git a/R/pev_parameters.R b/R/pev_parameters.R index a9509f96..bc0c4788 100644 --- a/R/pev_parameters.R +++ b/R/pev_parameters.R @@ -30,7 +30,7 @@ create_pev_profile <- function(vmax, alpha, beta, cs, rho, ds, dl) { #' @title RTS,S vaccine profile #' @description Parameters for a primary dose of RTS,S for use with the -#' set_mass_pev and set_pev_epi functions +#' set_mass_pev and set_pev_epi functions (White MT et al. 2015 Lancet ID) #' @export rtss_profile <- create_pev_profile( vmax = 0.93, @@ -38,13 +38,28 @@ rtss_profile <- create_pev_profile( beta = 99.4, cs = c(6.37008, 0.35), rho = c(2.37832, 1.00813), - ds = c(3.74502, 0.341185), # (White MT et al. 2015 Lancet ID) - dl = c(6.30365, 0.396515) # (White MT et al. 2015 Lancet ID) + ds = c(3.74502, 0.341185), + dl = c(6.30365, 0.396515) ) +#' @title R21 vaccine profile +#' @description Parameters for a primary dose of R21 for use with the +#' set_mass_pev and set_pev_epi functions (Schmit + Topazian et al. 2022 Lancet ID) +#' @export +r21_profile <- create_pev_profile( + vmax = 0.87, + alpha = 0.91, + beta = 471, + cs = c(9.3199677, 0.8387902), + rho = c(0.8071676, 0.6010363), + ds = c(3.7996007, 0.1618982), + dl = c(6.2820200, 0.4549185) +) + + #' @title RTS,S booster vaccine profile #' @description Parameters for a booster dose of RTS,S for use with the -#' set_mass_pev and set_pev_epi functions +#' set_mass_pev and set_pev_epi functions (White MT et al. 2015 Lancet ID) #' @export rtss_booster_profile <- create_pev_profile( vmax = 0.93, @@ -52,8 +67,22 @@ rtss_booster_profile <- create_pev_profile( beta = 99.4, cs = c(5.56277, 0.35), rho = c(1.03431, 1.02735), - ds = c(3.74502, 0.341185), # (White MT et al. 2015 Lancet ID) - dl = c(6.30365, 0.396515) # (White MT et al. 2015 Lancet ID) + ds = c(3.74502, 0.341185), + dl = c(6.30365, 0.396515) +) + +#' @title R21 booster vaccine profile +#' @description Parameters for a booster dose of R21 for use with the +#' set_mass_pev and set_pev_epi functions (Schmit + Topazian et al. 2022 Lancet ID) +#' @export +r21_booster_profile <- create_pev_profile( + vmax = 0.87, + alpha = 0.91, + beta = 471, + cs = c(9.2372858, 0.7188541), + rho = c(0.07140337, 0.54175154), + ds = c(3.7996007, 0.1618982), + dl = c(6.2820200, 0.4549185) ) #' @title Parameterise a pre-erythrocytic vaccine with an EPI strategy diff --git a/_pkgdown.yml b/_pkgdown.yml index 393e7f68..06822611 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -62,6 +62,8 @@ reference: contents: - set_species - set_carrying_capacity + - calculate_carrying_capacity + - get_init_carrying_capacity - arab_params - fun_params - gamb_params diff --git a/man/r21_booster_profile.Rd b/man/r21_booster_profile.Rd new file mode 100644 index 00000000..33be187c --- /dev/null +++ b/man/r21_booster_profile.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pev_parameters.R +\docType{data} +\name{r21_booster_profile} +\alias{r21_booster_profile} +\title{R21 booster vaccine profile} +\format{ +An object of class \code{list} of length 7. +} +\usage{ +r21_booster_profile +} +\description{ +Parameters for a booster dose of R21 for use with the +set_mass_pev and set_pev_epi functions (Schmit + Topazian et al. 2022 Lancet ID) +} +\keyword{datasets} diff --git a/man/r21_profile.Rd b/man/r21_profile.Rd new file mode 100644 index 00000000..836923ee --- /dev/null +++ b/man/r21_profile.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/pev_parameters.R +\docType{data} +\name{r21_profile} +\alias{r21_profile} +\title{R21 vaccine profile} +\format{ +An object of class \code{list} of length 7. +} +\usage{ +r21_profile +} +\description{ +Parameters for a primary dose of R21 for use with the +set_mass_pev and set_pev_epi functions (Schmit + Topazian et al. 2022 Lancet ID) +} +\keyword{datasets} diff --git a/man/rtss_booster_profile.Rd b/man/rtss_booster_profile.Rd index 14f5d40c..939986c9 100644 --- a/man/rtss_booster_profile.Rd +++ b/man/rtss_booster_profile.Rd @@ -12,6 +12,6 @@ rtss_booster_profile } \description{ Parameters for a booster dose of RTS,S for use with the -set_mass_pev and set_pev_epi functions +set_mass_pev and set_pev_epi functions (White MT et al. 2015 Lancet ID) } \keyword{datasets} diff --git a/man/rtss_profile.Rd b/man/rtss_profile.Rd index 2eef7b56..55d05e7b 100644 --- a/man/rtss_profile.Rd +++ b/man/rtss_profile.Rd @@ -12,6 +12,6 @@ rtss_profile } \description{ Parameters for a primary dose of RTS,S for use with the -set_mass_pev and set_pev_epi functions +set_mass_pev and set_pev_epi functions (White MT et al. 2015 Lancet ID) } \keyword{datasets}