Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
211 lines (196 sloc) 5.92 KB
library(tibble)
library(dplyr)
## Implemented SI models
model_details <- tibble(
model = c("SI_ode", "SI_demographics_ode"),
model_family = "SI",
time = "continuous",
type = "deterministic",
recovered = "no",
exposed = "no",
treated = "no",
susceptible = "no",
risk_stratified = "no",
non_exponential = "no",
simple_demographics = c("no", "yes"),
vaccination = "yes",
disease_example = "none",
language = "R",
parameters = list(c("beta"), c("beta", "mu"))
)
## Add implemented SIR models
model_details <- model_details %>%
bind_rows(
tibble(
model = c("SIR_ode", "SIR_demographics_ode", "SIR_vaccination_ode", "SIR_vaccination_demographics_ode"),
model_family = "SIR",
time = "continuous",
type = "deterministic",
recovered = "no",
exposed = "no",
treated = "no",
susceptible = "no",
risk_stratified = "no",
non_exponential = "no",
simple_demographics = c("no", "yes", "no", "yes"),
vaccination = c("no", "no", "yes", "yes"),
disease_example = "none",
language = "R",
parameters = list(c("beta", "tau"), c("beta", "tau", "mu"),
c("beta", "tau", "lambda"), c("beta", "tau", "lambda", "alpha", "mu"))
)
)
## Add implemented SIS models
model_details <- model_details %>%
bind_rows(
tibble(
model = c("SIS_ode", "SIS_demographics_ode"),
model_family = "SIS",
time = "continuous",
type = "deterministic",
recovered = "no",
exposed = "no",
treated = "no",
susceptible = "yes",
risk_stratified = "no",
non_exponential = "no",
simple_demographics = c("no", "yes"),
vaccination = c("no", "no"),
disease_example = "none",
language = "R",
parameters = list(c("beta", "chi"), c("beta", "chi", "mu"))
)
)
## Add implemented SEI models
model_details <- model_details %>%
bind_rows(
tibble(
model = c("SEI_ode", "SEI_demographics_ode"),
model_family = "SEI",
time = "continuous",
type = "deterministic",
recovered = "no",
exposed = "yes",
treated = "no",
susceptible = "no",
risk_stratified = "no",
non_exponential = "no",
simple_demographics = c("no", "yes"),
vaccination = "no",
disease_example = "none",
language = "R",
parameters = list(c("beta", "gamma"), c("beta", "gamme", "mu"))
)
)
## Add implemented SEIR models
model_details <- model_details %>%
bind_rows(
tibble(
model = c("SEIR_ode", "SEIR_demographics_ode"),
model_family = "SEIR",
time = "continuous",
type = "deterministic",
recovered = "yes",
exposed = "yes",
treated = "no",
susceptible = "no",
risk_stratified = "no",
non_exponential = "no",
simple_demographics = c("no", "yes"),
vaccination = "no",
disease_example = "none",
language = "R",
parameters = list(c("beta", "gamma", "tau"), c("beta", "gamme", "tau", "mu"))
)
)
## Add implemented SEIS models
model_details <- model_details %>%
bind_rows(
tibble(
model = c("SEIS_ode", "SEIS_demographics_ode"),
model_family = "SEIS",
time = "continuous",
type = "deterministic",
recovered = "no",
exposed = "yes",
treated = "no",
susceptible = "yes",
risk_stratified = "no",
non_exponential = "no",
simple_demographics = c("no", "yes"),
vaccination = "no",
disease_example = "none",
language = "R",
parameters = list(c("beta", "gamma", "chi"), c("beta", "gamme", "chi", "mu"))
)
)
## Add implemented SEIRS models
model_details <- model_details %>%
bind_rows(
tibble(
model = c("SEIRS_ode", "SEIRS_demographics_ode"),
model_family = "SEIRS",
time = "continuous",
type = "deterministic",
recovered = "yes",
exposed = "yes",
treated = "no",
susceptible = "yes",
risk_stratified = "no",
non_exponential = "no",
simple_demographics = c("no", "yes"),
vaccination = "no",
disease_example = "none",
language = "R",
parameters = list(c("beta", "gamma", "tau", "chi"), c("beta", "gamma", "tau", "chi", "mu"))
)
)
## Add implemented SHLIR models
model_details <- model_details %>%
bind_rows(
tibble(
model = c("SHLIR_ode", "SHLIR_demographics_ode"),
model_family = "SHLIR",
time = "continuous",
type = "deterministic",
recovered = "yes",
exposed = "yes",
treated = "no",
susceptible = "no",
risk_stratified = "no",
non_exponential = "yes",
simple_demographics = c("no", "yes"),
vaccination = "no",
disease_example = "none",
language = "R",
parameters = list(c("beta", "gamma_H", "nu", "gamma_L", "tau"),
c("beta", "gamma_H", "nu", "gamma_L", "tau", "mu"))
)
)
## Add implemented SHLITR models
model_details <- model_details %>%
bind_rows(
tibble(
model = c("SHLITR_ode", "SHLIR_demographics_ode", "SHLITR_risk_ode", "SHLITR_risk_demographics_ode"),
model_family = "SHLITR",
time = "continuous",
type = "deterministic",
recovered = "yes",
exposed = "yes",
treated = "yes",
susceptible = "no",
risk_stratified = c("no", "no", "yes", "yes"),
non_exponential = "no",
simple_demographics = c("no", "yes", "no", "yes"),
vaccination = "no",
disease_example = "tuberculosis",
language = "R",
parameters = list(c("beta", "gamma_H", "nu", "gamma_L", "epsilon", "tau"),
c("beta", "gamma_H", "nu", "gamma_L", "epsilon", "tau", "mu"),
c("beta", "beta_H", "M", "gamma_H", "nu", "gamma_L", "epsilon", "tau"),
c("beta", "beta_H", "M", "gamma_H", "nu", "gamma_L", "epsilon", "tau", "p", "mu"))
)
)
## Add to package
usethis::use_data(model_details, overwrite = TRUE)
saveRDS(model_details, "model_details.rds")
You can’t perform that action at this time.