diff --git a/touchstone/script.R b/touchstone/script.R index a494695bd..5e4095d78 100644 --- a/touchstone/script.R +++ b/touchstone/script.R @@ -9,8 +9,8 @@ touchstone::benchmark_run( expr_before_benchmark = { source("touchstone/setup.R") }, default = { epinow( reported_cases = reported_cases, - generation_time = fixed_generation_time, - delays = fixed_delays, + generation_time = generation_time_opts(fixed_generation_time), + delays = delay_opts(fixed_delays), rt = rt_opts(prior = list(mean = 2, sd = 0.2)), stan = stan_opts( cores = 2, samples = 500, chains = 2, @@ -25,7 +25,7 @@ touchstone::benchmark_run( expr_before_benchmark = { source("touchstone/setup.R") }, uncertain = { epinow( reported_cases = reported_cases, - generation_time = example_generation_time, + generation_time = generation_time_opts(example_generation_time), delays = delays, rt = rt_opts(prior = list(mean = 2, sd = 0.2)), stan = stan_opts( @@ -39,9 +39,9 @@ touchstone::benchmark_run( # benchmark readme example without delays touchstone::benchmark_run( expr_before_benchmark = { source("touchstone/setup.R") }, - no_delays = { epinow( + delay_opts(no_delays) = { epinow( reported_cases = reported_cases, - generation_time = fixed_generation_time, + generation_time = generation_time_opts(fixed_generation_time), rt = rt_opts(prior = list(mean = 2, sd = 0.2)), stan = stan_opts( cores = 2, samples = 500, chains = 2, @@ -56,8 +56,8 @@ touchstone::benchmark_run( expr_before_benchmark = { source("touchstone/setup.R") }, stationary = { epinow( reported_cases = reported_cases, - generation_time = fixed_generation_time, - delays = fixed_delays, + generation_time = generation_time_opts(fixed_generation_time), + delays = delay_opts(fixed_delays), rt = rt_opts(prior = list(mean = 2, sd = 0.2), gp_on = "R0"), stan = stan_opts( cores = 2, samples = 500, chains = 2, @@ -72,8 +72,8 @@ touchstone::benchmark_run( expr_before_benchmark = { source("touchstone/setup.R") }, random_walk = { epinow( reported_cases = reported_cases, - generation_time = fixed_generation_time, - delays = fixed_delays, + generation_time = generation_time_opts(fixed_generation_time), + delays = delay_opts(fixed_delays), rt = rt_opts(prior = list(mean = 2, sd = 0.2), rw = 7), gp = NULL, stan = stan_opts(