## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setupMorse, eval=FALSE--------------------------------------------------- # install.packages(morse) # install the package # library(morse) # load the package ## ----testJAGS, eval=FALSE----------------------------------------------------- # install.packages("runjags") # library("runjags") # testjags() ## ----pathJAGS, eval=FALSE----------------------------------------------------- # testjags(jags=runjags.getOption('jagspath')) # replace jagspath by the PATH to JAGS # # FOR INSTANCE, on the current machine I do: # testjags(jags=runjags.getOption('C:/Program Files/JAGS/JAGS-4.3.0/x64/bin/jags-terminal.exe')) ## ----fitSurv, eval=FALSE------------------------------------------------------ # library(morse) # data("propiconazole") # survData_PRZ = survData(propiconazole) # fit_cstSD = survFit(survData_PRZ, model_type = "SD") ## ----plotSurv, eval=FALSE----------------------------------------------------- # library(morse) # data("propiconazole") # survData_PRZ = survData(propiconazole) # fit_cstSD = survFit(survData_PRZ, model_type = "SD") # plot(fit_cstSD) ## ----LCxSurv, eval=FALSE------------------------------------------------------ # library(morse) # data("propiconazole") # survData_PRZ = survData(propiconazole) # fit_cstSD = survFit(survData_PRZ, model_type = "SD") # LCx(fit_cstSD, X = 50) ## ----plotLCxSurv, eval=FALSE-------------------------------------------------- # library(morse) # data("propiconazole") # survData_PRZ = survData(propiconazole) # fit_cstSD = survFit(survData_PRZ, model_type = "SD") # LCX_cstSD = LCx(fit_cstSD, X = 50) # plot(LCX_cstSD) ## ----MFx, eval=FALSE---------------------------------------------------------- # library(morse) # data("propiconazole") # survData_PRZ = survData(propiconazole) # fit_cstSD = survFit(survData_PRZ, model_type = "SD") # data_4MFx <- data.frame(time = 1:10, # conc = c(0,0.5,8,3,0,0,0.5,8,3.5,0)) # MFx_PRZ_cstSD <- MFx(object = fit_cstSD, data_predict = data_4MFx, ode = TRUE) ## ----plotMFx, eval=FALSE------------------------------------------------------ # library(morse) # data("propiconazole") # survData_PRZ = survData(propiconazole) # fit_cstSD = survFit(survData_PRZ, model_type = "SD") # data_4MFx <- data.frame(time = 1:10, # conc = c(0,0.5,8,3,0,0,0.5,8,3.5,0)) # MFx_PRZ_cstSD <- MFx(object = fit_cstSD, data_predict = data_4MFx, ode = TRUE) # plot(MFx_PRZ_cstSD) ## ----predictSurv, eval=FALSE-------------------------------------------------- # library(morse) # data("propiconazole") # survData_PRZ = survData(propiconazole) # fit_cstSD = survFit(survData_PRZ, model_type = "SD") # data_example <- data.frame( # time = c(1,1.9,2,15,15.1,20), # conc = c(0,0,20,20,0,0), # replicate = rep("example", 6) # ) # predict_example_NULL = predict_ode( # object = fit_cstSD, # data_predict = data_example, # mcmc_size = 10, # interpolate_length = NULL) ## ----plot1predictSurv, eval=FALSE--------------------------------------------- # plot(predict_example_NULL) ## ----plot2predictSurv, eval=FALSE--------------------------------------------- # predict_example_100 = predict_ode( # object = fit_cstSD, # data_predict = data_example, # mcmc_size = 10, # interpolate_length = 100) # plot(predict_example_100) ## ----plotpredictSurv_FOCUS, eval=FALSE---------------------------------------- # data("FOCUSprofile") # predict_FOCUS = predict_ode( # object = fit_cstSD, # data_predict = FOCUSprofile, # mcmc_size = 10, # interpolate_length = NULL) # plot(predict_FOCUS) ## ----predictNsurv, eval=FALSE------------------------------------------------- # library(morse) # data("propiconazole") # survData_PRZ = survData(propiconazole) # fit_cstSD = survFit(survData_PRZ, model_type = "SD") # data("propiconazole_pulse_exposure") # predict_Nsurv = predict_Nsurv_ode( # object = fit_cstSD, # data_predict = propiconazole_pulse_exposure # ) ## ----plotPredictNsurv, eval=FALSE--------------------------------------------- # library(morse) # data("propiconazole") # survData_PRZ = survData(propiconazole) # fit_cstSD = survFit(survData_PRZ, model_type = "SD") # data("propiconazole_pulse_exposure") # predict_Nsurv = predict_Nsurv_ode( # object = fit_cstSD, # data_predict = propiconazole_pulse_exposure # ) # plot(predict_Nsurv)