【R】biogrowth

1. はじめに

biogrowthは、微生物の成長モデルを扱うパッケージです。

2. インストール

CRANからインストールできます。

install.packages("biogrowth")

3. つかってみる

library(biogrowth)
library(tidyverse)

my_model <- "modGompertz"
my_pars <- list(logN0 = 2, C = 6, mu = .2, lambda = 25)
my_time <- seq(0, 100, length = 1000)

static_prediction <- predict_isothermal_growth(my_model, my_time, my_pars)

plot(static_prediction) 

my_conditions <- tibble(time = c(0, 5, 40),
                        temperature = c(20, 30, 35),
                        pH = c(7, 6.5, 5)
)
my_primary <- list(mu_opt = 2,
                   Nmax = 1e8,
                   N0 = 1e0,
                   Q0 = 1e-3)

sec_temperature <- list(model = "Zwietering",
                        xmin = 25,
                        xopt = 35,
                        n = 1)

sec_pH = list(model = "CPM",
              xmin = 5.5,
              xopt = 6.5,
              xmax = 7.5,
              n = 2)

my_secondary <- list(
  temperature = sec_temperature,
  pH = sec_pH
)

my_times <- seq(0, 50, length = 1000)

dynamic_prediction <- predict_dynamic_growth(my_times,
                                             my_conditions, my_primary,
                                             my_secondary)

plot(dynamic_prediction, 
     add_factor = "temperature",
     line_col = "blue")

4. さいごに

微生物のことは分かりませんが、便利そうなパッケージです。