Added parameters csv file that contains falciparum and vivax specific…

… parameter sets. These parameter values are associated with the set that fixes b = 0.25 and sigma_squared = 1.67, as recommended by Michael White.

These parameters are selected in the get_parameters() function by specifying parasite == "falciparum" or "vivax". The functions then selects the parasite-specific values and combines then withe the non-parasite specific values.

In order to allow the vivax code to run without full functionality, we have included additional falciparum parameters in the vivax parameter set. These will be removed in the following stages.

Pv parameter draws have been added, with code to read them into the package.

Added tests to check parameters are behaving as expected.

A new vignette has been started to reflect the P. vivax additions that have been made.

R/data.R

@@ -1,9 +1,29 @@
-#' Parameter draws
+#' Parasite parameters
 #'
-#' 1000 draws from the joint posterior fit from
+#' Parasite-specific parameters for P. falciparum and vivax for use in malariasimulation
+#'
+#' @format ## `parasite_parameters`
+#' A 
+#'
+#' @source <https://www.nature.com/articles/ncomms4136>, <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097992/>
+"parasite_parameters"
+
+#' Parameter draws (P. falciparum)
 #'
-#' @format ## `parameter_draws`
+#' A list of 1000 draws from the joint posterior fit from
+#'
+#' @format ## `parameter_draws_pf`
 #' A list of lists of length 1000, each level contains a list of drawn parameters
 #'
 #' @source <https://www.nature.com/articles/ncomms4136>
-"parameter_draws"
+"parameter_draws_pf"
+
+#' Parameter draws (P. vivax)
+#'
+#' 1000 draws from the joint posterior fit from
+#'
+#' @format ## `parameter_draws_pv`
+#' A list of lists of length 1000, each level contains a list of drawn parameters
+#'
+#' @source <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097992/>
+"parameter_draws_pv"

data-raw/parameter_draws.R

@@ -1,15 +1,55 @@
-## code to prepare parameter draws
+## code to prepare parameter draws: pf
+pd_pf <- read.csv("data-raw/parameter_draws_pf.csv")
 
-pd <- read.csv("data-raw/parameter_draws.csv")
+# Split individual draws_pf into a list of named parameter lists
+draws_pf <- 1:max(pd_pf$draw)
+parameter_draws_pf <- list()
+for(draw in draws_pf){
+  pars <- as.list(pd_pf[pd_pf$draw == draw, "value"])
+  names(pars) <- pd_pf[pd_pf$draw == draw, "parameter"]
+  parameter_draws_pf[[draw]] <- pars
+}
+names(parameter_draws_pf) <- draws_pf
+
+usethis::use_data(parameter_draws_pf, overwrite = TRUE)
+
+## code to prepare parameter draws: pv
+## this dataset does not match the default parameters, but the code should still be functional.
+pd_pv <- read.csv("data-raw/parameter_draws_pv.csv", header = T) |> 
+  tibble::rownames_to_column(var = "draw") |> 
+  dplyr::mutate(phi0  = phi_D_max,
+                phi1 = phi_D_min/phi_D_max) |> 
+  dplyr::select(-c(loglike, phi_D_min, phi_D_max)) |> 
+  tidyr::pivot_longer(cols = !draw, names_to = "parameter", values_to = "value") |> 
+  dplyr::mutate(parameter = dplyr::case_when(
+    parameter == "u_par" ~ "ua",
+    parameter == "phi_LM_max" ~ "philm_max",
+    parameter == "phi_LM_min" ~ "philm_min",
+    parameter == "A_LM_50pc" ~ "alm50",
+    parameter == "K_LM" ~ "klm",
+    parameter == "u_clin" ~ "ud",
+    parameter == "phi0" ~ "phi0",
+    parameter == "phi1" ~ "phi1",
+    parameter == "A_D_50pc" ~ "ic0",
+    parameter == "K_D" ~ "kc",
+    parameter == "A_d_PCR_50pc" ~ "apcr50",
+    parameter == "K_d_PCR" ~ "kpcr",
+    parameter == "d_PCR_max" ~ "dpcr_max",
+    parameter == "d_LM" ~ "da",
+    parameter == "P_MI" ~ "pcm",
+    parameter == "d_MI" ~ "rm"
+  ),
+  draw = as.numeric(draw)) |> 
+  as.data.frame()
 
-# Split individual draws into a list of named parameter lists
-draws <- 1:max(pd$draw)
-parameter_draws <- list()
-for(draw in draws){
-  pars <- as.list(pd[pd$draw == draw, "value"])
-  names(pars) <- pd[pd$draw == draw, "parameter"]
-  parameter_draws[[draw]] <- pars
+# Split individual draws_pf into a list of named parameter lists
+draws_pv <- 1:max(pd_pv$draw)
+parameter_draws_pv <- list()
+for(draw in draws_pv){
+  pars <- as.list(pd_pv[pd_pv$draw == draw, "value"])
+  names(pars) <- pd_pv[pd_pv$draw == draw, "parameter"]
+  parameter_draws_pv[[draw]] <- pars
 }
-names(parameter_draws) <- draws
+names(parameter_draws_pv) <- draws_pv
 
-usethis::use_data(parameter_draws, overwrite = TRUE)
+usethis::use_data(parameter_draws_pv, overwrite = TRUE)

data-raw/parasite_parameters.R

@@ -0,0 +1,9 @@
+## code to prepare parasite parameters
+parasite_csv <- read.csv("data-raw/parasite_parameters.csv")
+parasite_parameters <- lapply(unique(parasite_csv$parasite), function(x){
+  parameters <- as.list(parasite_csv[parasite_csv$parasite==x,c("default")])
+  names(parameters) <- parasite_csv[parasite_csv$parasite==x,c("parameter")]
+  return(parameters)
+})
+names(parasite_parameters) <- unique(parasite_csv$parasite)
+usethis::use_data(parasite_parameters, overwrite = TRUE)

data-raw/parasite_parameters.csv

@@ -0,0 +1,119 @@
+parasite,parameter,default,reference
+falciparum,dd,5,
+falciparum,dt,5,
+falciparum,da,195,
+falciparum,du,110,
+falciparum,init_ib,0,
+falciparum,init_ica,0,
+falciparum,init_iva,0,
+falciparum,init_icm,0,
+falciparum,init_ivm,0,
+falciparum,init_id,0,
+falciparum,rb,3650,
+falciparum,rc,10950,
+falciparum,rva,10950,
+falciparum,rid,3650,
+falciparum,rm,67.6952,
+falciparum,rvm,76.8365,
+falciparum,ub,7.2,
+falciparum,uc,6.06,
+falciparum,uv,11.4321,
+falciparum,ud,9.44512,
+falciparum,pcm,0.774368,
+falciparum,pvm,0.195768,
+falciparum,b0,0.59,
+falciparum,b1,0.5,
+falciparum,ib0,43.9,
+falciparum,kb,2.16,
+falciparum,fd0,0.007055,
+falciparum,ad,7993.5,
+falciparum,gammad,4.8183,
+falciparum,d1,0.160527,
+falciparum,id0,1.577533,
+falciparum,kd,0.476614,
+falciparum,phi0,0.792,
+falciparum,phi1,0.00074,
+falciparum,ic0,18.02366,
+falciparum,kc,2.36949,
+falciparum,theta0,0.0749886,
+falciparum,theta1,0.0001191,
+falciparum,iv0,1.09629,
+falciparum,kv,2.00048,
+falciparum,fv0,0.141195,
+falciparum,av,2493.41,
+falciparum,gammav,2.91282,
+falciparum,cd,0.068,
+falciparum,gamma1,1.82425,
+falciparum,cu,0.0062,
+falciparum,ct,0.021896,
+falciparum,de,12,
+falciparum,delay_gam,12.5,
+falciparum,dem,10,
+vivax,dd,5, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,dt,1, Pukrittayakamee (2008); Am J Trop Med Hyg
+vivax,da,16.942, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,dpcr_max,53.69, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,dpcr_min,10, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,kpcr,4.021, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,apcr50,9.8, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,init_iaa,0,
+vivax,init_iam,0,
+vivax,init_ica,0,
+vivax,init_icm,0,
+vivax,ra,3650, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,rc,10950, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,rm,64.584, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,ua,44.09, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,uc,4.29, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,pcm,0.306, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,b,0.25, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,philm_min,0.0131, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,philm_max,0.9329, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,klm,3.202, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,alm50,17.30, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,phi0,4.2857, White (2018); doi: 10.1038/s41467-018-05860-8; phi0 is equivalent to phi_D_max (4.2857)
+vivax,phi1,0.2186, White (2018); doi: 10.1038/s41467-018-05860-8; phi1 is equivalent to phi_D_min/phi_D_max (0.9368/4.2857)
+vivax,ic0,23.788, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,kc,5.41, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,cd,0.8, Kiattibutr (2017); doi: 10.1016/j.ijpara.2016.10.006
+vivax,ca,0.1, Kiattibutr (2017); doi: 10.1016/j.ijpara.2016.10.006
+vivax,cu,0.035, Kiattibutr (2017); doi: 10.1016/j.ijpara.2016.10.006
+vivax,ct,0.4, Kiattibutr (2017); doi: 10.1016/j.ijpara.2016.10.006
+vivax,de,10, Herrera (2011); DOI: doi: 10.4269/ajtmh.2011.09-0498
+vivax,delay_gam,0, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,dem,8.4, Gething (2011); doi: 10.1186/1756-3305-4-92
+vivax,f,0.02439024, White (2018); doi: 10.1186/s12936-018-2318-1
+vivax,gammal,0.002610966, White (2018): doi: 10.1186/s12936-018-2318-1
+vivax,init_hyp,0,
+vivax,kmax,10, White (2018); doi: 10.1038/s41467-018-05860-8
+vivax,du,110,to_be_removed
+vivax,init_iva,0,to_be_removed
+vivax,init_ivm,0,to_be_removed
+vivax,init_ib,0,to_be_removed
+vivax,init_id,0,to_be_removed
+vivax,ub,7.2,to_be_removed
+vivax,uv,11.4321,to_be_removed
+vivax,ud,9.44512,to_be_removed
+vivax,pvm,0.195768,to_be_removed
+vivax,rvm,76.8365,to_be_removed
+vivax,rb,3650,to_be_removed
+vivax,rva,10950,to_be_removed
+vivax,rid,3650,to_be_removed
+vivax,b0,0.59,to_be_removed
+vivax,b1,0.5,to_be_removed
+vivax,ib0,43.9,to_be_removed
+vivax,kb,2.16,to_be_removed
+vivax,theta0,0.0749886,to_be_removed
+vivax,theta1,0.0001191,to_be_removed
+vivax,iv0,1.09629,to_be_removed
+vivax,kv,2.00048,to_be_removed
+vivax,fv0,0.141195,to_be_removed
+vivax,av,2493.41,to_be_removed
+vivax,gammav,2.91282,to_be_removed
+vivax,gamma1,1.82425,to_be_removed
+vivax,fd0,0.007055,to_be_removed
+vivax,ad,7993.5,to_be_removed
+vivax,gammad,4.8183,to_be_removed
+vivax,d1,0.160527,to_be_removed
+vivax,id0,1.577533,to_be_removed
+vivax,kd,0.476614,to_be_removed