Merge branch 'dev' into bug/benchmark

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,phi0,0.9368, White (2018); doi: 10.1038/s41467-018-05860-8; phi0 is equivalent to phi_D_max (0.9368)
+vivax,phi1,0.0139, White (2018); doi: 10.1038/s41467-018-05860-8; phi1 is equivalent to phi_D_min/phi_D_max (0.013/0.9368)
+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