inst/doc/vignette_bioOED_isothermal.R

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

## ------------------------------------------------------------------------
library(tidyverse)

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

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pars <- list(z = 4.2, D_R = 3.9, temp_ref = 55)

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design_space <- expand.grid(seq(0, 100, length = 20),
                            seq(52.5,60, length = 20)
                            ) %>%
  set_names("times", "temperature")

head(design_space)

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my_sensitivities <- isothermal_sensitivities("Bigelow", design_space, pars)

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head(my_sensitivities$sensitivities)

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

## ---- fig.width=8--------------------------------------------------------
plot(my_sensitivities, limit = 7)

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n_points <- 5

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# opts <- list(maxeval=500,local_finish="DHC")
# 
# OED <- isothermal_OED("Bigelow", pars, n_points, criterion = "D",
#                       min_time = 0, max_time = 100,
#                       min_temp = 52.5, max_temp = 60,
#                       opts = opts)

## ------------------------------------------------------------------------
# OED$optim_design

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

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limit <- 7

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# OED_limit <- isothermal_OED_limit("Bigelow", pars, n_points, criterion = "D", limit,
#                                   min_time = 0, max_time = 100, min_temp = 95,
#                                   max_temp = 110, opts)

## ------------------------------------------------------------------------
# print(OED_limit$optim_design)

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