inst/examples/plotting.R

In dkaschek/dMod: Dynamic Modeling and Parameter Estimation in ODE Models

    
    ## Observation function
    fn <- eqnvec(
      sine = "1 + sin(6.28*omega*time)",
      cosine = "cos(6.28*omega*time)"
    )
    g <- Y(fn, parameters = "omega")
    
    ## Prediction function for time
    x <- Xt()
    
    ## Parameter transformations to split conditions
    p <- NULL
    for (i in 1:3) {
      p <- p + P(trafo = c(omega = paste0("omega_", i)), condition = paste0("frequency_", i))
    }
    
    ## Evaluate prediction
    times <- seq(0, 1, .01)
    pars <- structure(seq(1, 2, length.out = 3), names = attr(p, "parameters"))
    
    prediction <- (g*x*p)(times, pars)
    
    ## Plotting prediction
    # plot(prediction)
    plotPrediction(prediction)
    plotPrediction(prediction, scales = "fixed")
    plotPrediction(prediction, facet = "grid")
    plotPrediction(prediction, 
                   scales = "fixed",
                   transform = list(sine = "x^2", cosine = "x - 1"))
    
    ## Simulate data
    dataset <- wide2long(prediction)
    dataset <- dataset[seq(1, nrow(dataset), 5),]
    set.seed(1)
    dataset$value <- dataset$value + rnorm(nrow(dataset), 0, .1)
    dataset$sigma <- 0.1
    data <- as.datalist(dataset, split.by = "condition")
    
    ## Plotting data
    # plot(data)
    plot1 <- plotData(data)
     plot1
    ## Plotting data and prediction with subsetting
    # plot(prediction, data)
    plot2 <- plotCombined(prediction, data)
     plot2
    plot3 <- plotCombined(prediction, data, 
                 time <= 0.5 & condition == "frequency_1")
     plot3
    plot4 <- plotCombined(prediction, data, 
                 time <= 0.5 & condition != "frequency_1", 
                 facet = "grid")
     plot4
    plot5 <- plotCombined(prediction, data, aesthetics = list(linetype = "condition"))
     plot5