inst/doc/vignette_bioOED.R

In bioOED: Sensitivity Analysis and Optimum Experiment Design for Microbial Inactivation

## ------------------------------------------------------------------------
library(bioOED)

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inactivation_model <- "Bigelow"

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temp_profile <- data.frame(time = c(0, 60),
                           temperature = c(30, 60))

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parms_fix <- c(temp_ref = 57.5, N0 = 1e6)
parms <- c(D_R = 3.9,
           z = 4.2
           )

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sensitivity <- sensitivity_inactivation(inactivation_model,
                                        parms, temp_profile,
                                        parms_fix)

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head(sensitivity)

## ---- fig.width=8, fig.height=6------------------------------------------
plot(sensitivity)

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parms_fix <- c(temp_ref = 57.5)
parms <- c(delta_ref = 3.9, z = 4.2, p = 1, N0 = 1e6)
temp_profile <- data.frame(time = c(0, 60), temperature = c(30, 60))
pars_correlation <- calculate_pars_correlation("Mafart", parms,
                                               temp_profile, parms_fix)

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print(pars_correlation)

## ---- fig.width=8--------------------------------------------------------
plot(pars_correlation)

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temp_ref0 <- 57
lower <- 50
upper <- 70

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inactivation_model <- "Mafart"

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temp_profile <- data.frame(time = c(0, 60),
                           temperature = c(30, 60))

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parms <- c(delta_ref = 3.9, z = 4.2, p = 1, N0 = 1e6)
parms_fix <- c()

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optim_refTemp <- optimize_refTemp(temp_ref0, lower, upper,
                                  inactivation_model, parms, temp_profile,
                                  parms_fix)

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print(optim_refTemp$par)

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print(optim_refTemp$convergence)

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inactivation_model <- "Mafart"

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parms_fix <- c(temp_ref = 57.5)
parms <- c(delta_ref = 3.9,
           z = 4.2,
           p = 1,
           N0 = 1e6
           )

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temp_profile <- data.frame(time = c(0, 60), temperature = c(30, 60))

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n_points <- 5

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# opts_global <- list(maxeval=1000,  local_solver=0,
#                     local_finish="DHC", local_iterprint=1)
# 
# global_OED <- inactivation_OED(inactivation_model, parms, temp_profile,
#                                parms_fix, n_points, criteria = "D",
#                                opts_global = opts_global)


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# print(global_OED$optim_times)

## ---- fig.width=8--------------------------------------------------------
# plot(global_OED)

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# time_min <- 8

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# global_OED_penalty <- inactivation_OED_penalty(inactivation_model, parms,
#                                                temp_profile, parms_fix,
#                                                n_points, time_min,
#                                                criteria = "D", 
#                                                opts_global = opts_global)

## ------------------------------------------------------------------------
# print(global_OED_penalty$optim_times)

## ---- fig.width=8--------------------------------------------------------
# plot(global_OED_penalty)