diff --git a/NAMESPACE b/NAMESPACE index 3bff906cdb5f8aaf918c89a6334e2b4e09670ee5..86c404926f1e12c15eb99af0694b69cf34fef61f 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -7,7 +7,6 @@ export(cum_discr_si) export(departures.FUN) export(get_prev.FUN) export(get_times) -export(icm.seiqhrf) export(infection.FUN) export(init_status.icm) export(initialize.FUN) @@ -15,6 +14,7 @@ export(plot_models) export(plot_times) export(recovery.FUN) export(saveout.seiqhrf.icm) +export(seiqhrf) export(simulate_seiqhrf) export(summary_seiqhrf) export(vary_param) diff --git a/R/crosscheck.seiqhrf.R b/R/crosscheck.R similarity index 100% rename from R/crosscheck.seiqhrf.R rename to R/crosscheck.R diff --git a/R/icm_seiqhrf.R b/R/seiqhrf.R similarity index 99% rename from R/icm_seiqhrf.R rename to R/seiqhrf.R index 3ffbe83dcb24391b52c90414f166cad2332cbb58..e5b67988b90eba2c1bb3eb63139f8bcd8b4b3233 100644 --- a/R/icm_seiqhrf.R +++ b/R/seiqhrf.R @@ -69,7 +69,7 @@ merge.seiqhrf.icm <- function(x, y, ...) { #' @importFrom EpiModel verbose.icm #' @importFrom future availableCores #' @export -icm.seiqhrf <- function(param, init, control, seed = NULL) { +seiqhrf <- function(param, init, control, seed = NULL) { crosscheck.seiqhrf.icm(param, init, control) diff --git a/R/simulation.R b/R/simulation.R index f079ac5ef51f19c2a897becdb2f54201aef284fd..d8cb204a4a8aecc67a3909b2b74972ef8d50ce0a 100644 --- a/R/simulation.R +++ b/R/simulation.R @@ -345,7 +345,7 @@ simulate_seiqhrf <- function(type = "SEIQHRF", dh.rate = dh.rate, dr.rate = dr.rate) - sim <- icm.seiqhrf(param, init, control) + sim <- seiqhrf(param, init, control) sim_df <- as.data.frame(sim, out=out) return(list(sim=sim, df=sim_df)) diff --git a/man/crosscheck.seiqhrf.icm.Rd b/man/crosscheck.seiqhrf.icm.Rd index 8490774300b5b0f2c9f805bb190cf1ddbdf9dba4..90a5149bcfa27aec4629dcd1e5690b8f03d5ec30 100644 --- a/man/crosscheck.seiqhrf.icm.Rd +++ b/man/crosscheck.seiqhrf.icm.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/crosscheck.seiqhrf.R +% Please edit documentation in R/crosscheck.R \name{crosscheck.seiqhrf.icm} \alias{crosscheck.seiqhrf.icm} \title{Cross Checking of Inputs for Stochastic Individual Contact Models} diff --git a/man/icm.seiqhrf.Rd b/man/seiqhrf.Rd similarity index 82% rename from man/icm.seiqhrf.Rd rename to man/seiqhrf.Rd index 0569a61fa9aea44b28683780f1b7ac07d8180781..dd902c411a01b2d3f974695cedac42164c89cde9 100644 --- a/man/icm.seiqhrf.Rd +++ b/man/seiqhrf.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/icm_seiqhrf.R -\name{icm.seiqhrf} -\alias{icm.seiqhrf} +\name{seiqhrf} +\alias{seiqhrf} \title{SEIQHRF function} \usage{ -icm.seiqhrf(param, init, control, seed = NULL) +seiqhrf(param, init, control, seed = NULL) } \arguments{ \item{param}{ICM parameters.} diff --git a/tests/testthat/test-icm-seiqhrf.R b/tests/testthat/test-icm-seiqhrf.R index e9edfd62bff8a5c6a2901b2fa83da7d80acf7fca..6a69133bb0debd5b0d741db36f54aca001c1d86e 100644 --- a/tests/testthat/test-icm-seiqhrf.R +++ b/tests/testthat/test-icm-seiqhrf.R @@ -19,8 +19,8 @@ test_that("Identical output as Churches' original function: icm_seiqhrf", { comp <- rep(NA, No_seeds) i <- 1 for(seed in seed_list){ - sim1 <- icm.seiqhrf(param, init, control1, seed) - sim2 <- icm.seiqhrf(param, init, control2, seed) + sim1 <- seiqhrf(param, init, control1, seed) + sim2 <- seiqhrf(param, init, control2, seed) comp[i] <- identical(sim1, sim2) i <- i + 1 }