Merge pull request #333 from mrc-ide/r21_profiles

Add R21 PEV profiles

.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: |

DESCRIPTION

@@ -91,7 +91,7 @@ Suggests:
   ggplot2,
   covr,
   mgcv 
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 LinkingTo:
   Rcpp,

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)

R/pev_parameters.R

@@ -30,30 +30,59 @@ 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,
   alpha = 0.74,
   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,
   alpha = 0.74,
   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

_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