03a-parameter-estimation.qmd

title	subtitle	author	pdf-engine	format
Nonlinear Modeling: Parameter Estimation	Introduction to Statistical Modelling	Prof. Joris Vankerschaver	lualatex	beamer theme colortheme fonttheme header-includes Pittsburgh default default \setbeamertemplate{frametitle}[default][left] \setbeamertemplate{footline}[frame number] \usepackage{emoji} \usepackage{luatexko}

```{r, include=FALSE} library(tidyverse) library(gridExtra) library(latex2exp) theme_set(theme_bw() + theme(text = element_text(size = 14))) ``` ## Outline \tableofcontents ## Learning outcomes You should be able to - Determine the parameters of a nonlinear model via minimization (using R) - Understand the principles behind various minimization algorithms, as well as their advantages and disadvantages - Be able to assess the fit of a model # Example: building a stock-recruitment model ## M. merluccius: stock-recruitment model :::: {.columns} ::: {.column width="50%"} \vspace*{0.5cm} European hake (*M. merluccius*) - Deep water fish - Important for European fisheries - Similar to 명태 in Korea ::: ::: {.column width="50%"}  ::: ::: ::: {.callout-note} ## Stock-recruitment model Model of **number of adult fish** (recruitment) as a function of **spawning biomass** (fish that can reproduce). ::: ## M.merluccius: Dataset 15 observations, 3 features: - `spawn.biomass`: spawning (stock) biomass - `num.fish`: number of fish (recruitment) - `year`: not used ```{r} #| out-width: 3in #| out-height: 2in #| fig-width: 4.5 #| fig-height: 3 #| fig-align: center load("datasets/03-parameter-estimation/M.merluccius.rda") M.merluccius |> ggplot(aes(spawn.biomass, num.fish)) + geom_point() ``` ## M. merluccius: Beverton-Holt model :::: {.columns} ::: {.column width="50%"} \vspace*{0.5cm} Beverton-Holt model (1956): $$ f(S; \alpha, k) = \frac{\alpha S}{1 + S/k} $$ ::: ::: {.column width="50%"} {fig-align=center width=75%} ::: :::: Parameters: - $\alpha$: initial growth rate (for $S = 0$) $$ \alpha = f'(0; \alpha, k) $$ - $k$: related to behavior for large $S$ $$ k \alpha = \lim_{S \to +\infty} f(S; \alpha, k) $$ ## Beverton-Holt: Effect of varying $\alpha$ and $k$ ```{r} #| out-width: 4.5in #| out-height: 2in #| fig-width: 7 #| fig-height: 3 #| fig-align: center beverton_holt <- function(S, theta) { alpha <- theta[[1]] k <- theta[[2]] y <- alpha * S / (1 + S / k) tibble(S = S, alpha = alpha, k = k, y = y) } alpha <- 2.0 ks <- c(0.5, 1.0, 2.0) alphas <- c(1.0, 2.0, 3.0) S <- seq(0, 10, length.out = 100) plot_data_ks <- map(ks, \(k) beverton_holt(S, c(alpha, k))) |> list_rbind() |> mutate(k = as.factor(k)) p <- ggplot(plot_data_ks, aes(x = S, y = y, color = k, group = k)) + geom_line() + ggtitle(paste0("Alpha = ", alpha, ", varying k")) k <- 1.0 plot_data_alphas <- map(alphas, \(alpha) beverton_holt(S, c(alpha, k))) |> list_rbind() |> mutate(alpha = as.factor(alpha)) q <- ggplot(plot_data_alphas, aes(x = S, y = y, color = alpha, group = alpha)) + geom_line() + ggtitle(paste0("Varying alpha (k = ", k, ")")) grid.arrange(p, q, ncol = 2) ``` ## Goals - **Parameter estimation**: Find values $\hat{\alpha}$ and $\hat{k}$ that best fit data. - **Uncertainty quantification**: Provide a measure of uncertainty for parameter values (confidence interval) - **Sensitivity analysis**: Understand how model changes if parameters are varied # Parameter estimation ## What is parameter estimation? Determining the **optimal values for the parameters** using the experimental data, assuming that the model is known. Example: For *M. merluccius*, we will see that $\hat{\alpha} = 5.75$, $\hat{k} = 33.16$. ```{r} #| out-width: 3in #| out-height: 2in #| fig-width: 4.5 #| fig-height: 3 #| fig-align: center bh_fit <- nls( num.fish ~ alpha * spawn.biomass / (1 + spawn.biomass / k), data = M.merluccius, start = list(alpha = 6, k = 20)) ggplot(M.merluccius, aes(spawn.biomass, num.fish)) + geom_point() + geom_function( fun = \(S) predict(bh_fit, newdata = data.frame(spawn.biomass = S)), xlim = c(0, 80)) ``` ## Specifying a model Assume that we are **given** a nonlinear model $$ y = f(x; \theta) + \epsilon $$ where $\epsilon \sim \mathcal{N}(0, \sigma^2)$ is normally distributed noise. - $x$: inputs, predictors, features (e.g. `spawn.biomass`) - $y$: outcome, depent variable (e.g. `num.fish`) - $\theta$: (vector of) parameters (e.g. $\theta = (\alpha, k)$) We will not talk about **building** a model (see one of your many other courses) ## The objective function Given a dataset $(x_1, y_1), \ldots, (x_N, y_N)$, we want to quantify how well the model fits the data. **Objective function**: measures difference (squared) between predictions $f(x_i; \theta)$ and actual values $y_i$: $$ J(\theta) = \sum_{i=1}^N (y_i - f(x_i; \theta))^2 $$ ## Minimizing the objective function **Goal:** Find the parameter value(s) $\hat{\theta}$ so that $J(\theta)$ is minimal: $$ \hat{\theta} = \text{argmin}_\theta\, J(\theta). $$ Problems: - Depending on $f(x; \theta)$ this can be very difficult - There may be multiple (local) minima - Almost always needs to be done numerically ## Example: linear regression In linear regression, $f(x; \theta) = \alpha + \beta x$, so that $$ J(\alpha, \beta) = \sum_{i = 1}^N (y_i - \alpha - \beta x_i)^2. $$ Minimizing $J(\alpha, \beta)$ can be done by setting the partial derivatives equal to zero and gives the usual formulas: $$ \hat{\beta} = R \frac{s_y}{s_x}, \quad \hat{\alpha} = \bar{y} - \hat{\beta} \bar{x}. $$ In general, **no closed-form formula exists** for the optimal parameters. ## Before parameter estimation: select parameters More parameters = more work and less certainty: - Solver may not converge - Wider uncertainty estimates for parameters and outputs - Correlations between parameters can make it impossible to find parameters Consider selecting subset of parameters to estimate: - Fix parameters at experimental values - Omit least sensitive parameters ## Before parameter estimation: select initial values Numerical optimization algorithm requires a good **starting guess** for the parameters. When choice is bad: - Algorithm will converge slowly (take many iterations) - Optimization will fail altogether How to find initial guess: - Determine from model properties (growth rate, asymptotes) - Use (known) experimental values - Use trial and error (select from grid of values) Doesn't need to be overly precise, a rough estimate is usually sufficient. ## Initial values for M. merluccius - Slope: $\alpha_0 = \frac{75}{15} = 6$ - Horizontal asymptote: $k_0 \alpha_0 = 120$, so $k_0 = 20$. ```{r} #| out-width: 3in #| out-height: 2in #| fig-width: 4.5 #| fig-height: 3 #| fig-align: center measure <- arrow(angle = 90, ends = "both", length = unit(0.1, "in")) M.merluccius |> ggplot(aes(spawn.biomass, num.fish)) + annotate("segment", x = 15, xend = 30, y = 30, yend = 30, color = "red", linewidth = 1, arrow = measure) + annotate("text", x = 22.5, y = 35, size = 5, color = "red", label = "15") + annotate("segment", x = 32, xend = 32, y = 30, yend = 105, color = "red", linewidth = 1, arrow = measure) + annotate("text", x = 34, y = 75, size = 5, color = "red", label = "75") + geom_hline(yintercept = 120, linewidth = 1, linetype = "dashed", color = "blue") + annotate("text", x = 25, y = 125, size = 5, color = "blue", label = "min.fish = 120") + geom_point() ``` Later, we will see that the initial guesses are close to the optimal parameters $\hat{\alpha} = 5.75$, $\hat{k} = 33.16$. ## Preparation: Determining boundaries for parameters Some parameters come with bounds, for example: - Kinetic rate: $k > 0$ - Probability: $0 \le p \le 1$ Two ways of accounting for parameter bounds: - Adding penalty terms to the objective function - Transforming the parameter so it becomes unconstrained ## Adding penalty terms Suppose we want $\alpha \le \theta \le \beta$. Add **penalty term** to objective function: $$ J_\text{constrained}(\theta) = J_\text{unconstrained}(\theta) + J_\text{penalty}(\theta) $$ where $J_\text{penalty}(\theta)$ is - Roughly zero between $\alpha$ and $\beta$ - Very large for $\theta < \alpha$ or $\theta > \beta$. {fig-align=center height=75%} ## Transformation parameters Transform constrained problem into equivalent **unconstrained** problem. Some examples: - If $\theta > 0$: write $\theta = \exp \varphi$ or $\theta = \varphi^2$ - If $-1 < \theta < 1$: write $\theta = \tanh \varphi$ In either case, $\varphi$ is unconstrained (can range from $-\infty$ to $+\infty$). Now substitute this transformation into the objective function, and optimize in terms of $\varphi$. ## Preparation: Dealing with non-identifiability In some cases, parameters cannot be determined uniquely. For example, exponential model with parameters $A, B, C$: $$ y = A \exp(Bx + C) = (A e^C) e^{Bx} $$ Only $B$ and the combination $Ae^C$ can be determined. - **Structural** identifiability: all parameters can be uniquely determined, given perfect data. - **Practical** identifiability: same, but from finite, noisy data. ## Preparation: Dealing with non-identifiability Minimization of objective function will **fail** if some parameters are not identifiable. Workarounds: - Add penalty term to $J$ to privilege certain parameter values - Rewrite $J$ so all parameters are identifiable Example: put $k = A e^C$ and write exponential model as $$ y = k \exp(Bx). $$ Both $k$ and $B$ are identifiable. # Minimizing the objective function ## General approach Recall that we are trying to find $\theta$ so that $$ J(\theta) = \sum_{i=1}^N (y_i - f(x_i; \theta))^2 $$ is minimized. - For **linear** model: direct, one-step solution - For **nonlinear** model: iterative algorithm. Typically: 1. Start with initial guess for $\hat{\theta}$ 2. Slightly change $\hat{\theta}$ and compute $J(\hat{\theta})$ 3. Repeat if $\hat{\theta}$ not good enough ## Very simple minimization algorithm: hill descender :::: {.columns} ::: {.column width="50%"} \footnotesize ```{r, echo=TRUE, eval=FALSE} # Initial guess theta <- 5.0 for (i in 1:100) { # Add random noise to theta theta_new <- theta + 0.5 * rnorm(1) # Accept if objective is lower if (J(theta_new) < J(theta)) { theta <- theta_new } } ``` ::: ::: {.column width="50%"} ```{r} #| out-width: 2in #| out-height: 2in #| fig-width: 3 #| fig-height: 3 #| fig-align: center # Run the algorithm again but now only plot output set.seed(1234) J <- function(theta) { (theta - 1)^2 } theta <- 5.0 successful_thetas <- c(theta) for (i in 1:100) { # Add some random noise to theta theta_new <- theta + 0.5 * rnorm(1) # Accept if objective is lower if (J(theta_new) < J(theta)) { theta <- theta_new successful_thetas <- c(successful_thetas, theta) } } trajectory <- tibble( theta = successful_thetas, J = J(successful_thetas), i = seq(1, length(theta))) ggplot(trajectory) + geom_function(fun = J, xlim = c(-4, 6)) + geom_point(aes(x = theta, y = J), color = "red") + geom_text(aes(x = theta, y = J, label = i), color = "red", check_overlap = TRUE, nudge_y = 2) + xlab(TeX("\\theta")) + ylab(TeX("J(\\theta)")) ``` ::: :::: ## Caveat: local and global minima - Linear problems: unique minium - Nonlinear problems: (typically) several local minima  Most minimization algorithms only guarantee **convergence to a local minimum**. # Minimization algorithms ## Gradient-based minimization algorithms Two main classes of minimization algorithms: 1. **Gradient-based methods** 2. Gradient-free methods Gradient-based methods: - Are typically faster - Require the objective function to be differentiable - Can fail to converge Examples: - Steepest descent - Newton - Gauss-Newton - Levenberg-Marquardt ## Method of steepest descent ::: columns ::: {.column width="50%"} You want to go down the mountain into the valley as efficiently as possible. \vspace*{0.5cm} The fog prevents you from seeing more than a few meters in every direction. \vspace*{0.5cm} How do you proceed? \vspace*{0.5cm} \emoji{light-bulb} Walk in the direction of **steepest descent** ::: ::: {.column width="50%"}  ::: ::: ## Direction of steepest descent :::: {.columns} ::: {.column width="60%"} \vspace*{0.5cm} Gradient: - Perpendicular to level sets of $J$ - Direction of steepest ascent ::: ::: {.column width="40%"} {fig-align=center width=50%} ::: :::: \vspace*{0.5cm} To **decrease** $J(\theta)$, take a small step in direction of negative gradient: \begin{eqnarray*} s_k & = & -\nabla J(\theta^k) \\ & = & -\left[ \begin{array}{c} \frac{\partial J(\theta)}{\partial \theta_1} |_{\theta^k} \\ \frac{\partial J(\theta)}{\partial \theta_2} |_{\theta^k} \\ \vdots \\ \frac{\partial J(\theta)}{\partial \theta_n} |_{\theta^k} \end{array}\right]. \end{eqnarray*} ## Method of steepest descent: Algorithm Algorithm: - Compute gradient $\nabla J(\theta^k)$ at current value $\theta^k$. - Follow negative gradient to update $\theta^k$: $$ \theta^{k+1} = \theta^k - \alpha_k \nabla J(\theta^k), $$ with $\alpha_k$ the step size. - Repeat until convergence Step size $\alpha_k$ can be - Fixed: $\alpha_k = \alpha$ for a small fixed $\alpha$ (e.g. $\alpha = 0.01$). - Adaptive: determine the best $\alpha_k$ at each step. ## Method of steepest descent: variable step size ```{r, echo=FALSE} source("scripts/03a-parameter-estimation//quadratic-function.R", local = knitr::knit_global()) ``` ## Method of steepest descent: disadvantages ```{r, echo=FALSE, fig.height=4.5} source("scripts/03a-parameter-estimation//01-rosenbrock.R", local = knitr::knit_global()) ``` - Convergence can be slow (e.g for minimum hidden inside narrow "valley") - Steepest descent path will zigzag towards minimum, making little progress at each iteration. ## Method of Newton: 1D case Find a minimum of $J(\theta)$ by solving $J'(\theta) = 0$. ::: columns ::: {.column width="60%"} - For a starting point $\theta_k$, look for a search direction $s_k$ such that $J'(\theta_k + s_k) \approx 0$. - Taylor: $J'(\theta_k + s_k)$ is approximately $$ J'(\theta_k + s_k) \approx J'(\theta_k) + s_k J''(\theta_k). $$ - Search direction: $$ s_k = -\frac{J'(\theta_k)}{J''(\theta_k)} $$ ::: ::: {.column width="30%"}  ::: ::: Uses information from **first** and **second** derivatives. ## Method of Newton: properties For a quadratic function $J(x) = Ax^2 + Bx + C$, Newton's method finds the minimum in **one step**. Geometric interpretation: - Approximate $J(x)$ around $x_k$ by best-fitting parabola. - Jump to bottom of parabola to find $x_{k+1}$. - Repeat! ```{r, echo=FALSE, fig.height=3} source("scripts/03a-parameter-estimation//newton-polynomial.R", local = knitr::knit_global()) ``` ## Method of Newton: higher dimensions Search direction uses gradient and **Hessian** $$ s_k = -\left[ H(\theta^k)\right]^{-1} \nabla J(\theta^k) $$ where $$ H(\theta^k) = \nabla^2 J(\theta^k) = \left[ \begin{array}{cccc} \frac{\partial^2 J(\theta)}{\partial \theta_1^2} |_{\theta^k} & \frac{\partial^2 J(\theta)}{\partial \theta_1 \partial \theta_2} |_{\theta^k} & \cdots & \frac{\partial^2 J(\theta)}{\partial \theta_1 \partial \theta_n} |_{\theta^k} \\ \frac{\partial^2 J(\theta)}{\partial \theta_2 \partial \theta_1} |_{\theta^k} & \frac{\partial^2 J(\theta)}{\partial \theta_2^2} |_{\theta^k} & \cdots & \frac{\partial^2 J(\theta)}{\partial \theta_2 \partial \theta_n} |_{\theta^k} \\ \vdots & \vdots & \ddots & \vdots \\ \frac{\partial^2 J(\theta)}{\partial \theta_n \partial \theta_1} |_{\theta^k} & \frac{\partial^2 J(\theta)}{\partial \theta_n \partial \theta_2} |_{\theta^k} & \cdots & \frac{\partial^2 J(\theta)}{\partial \theta_n^2} |_{\theta^k} \end{array}\right] $$ - In practice, not necessary to invert $H(\theta)$ - Still requires $\mathcal{O}(D^2)$ computation at each step (expensive) ## Method of Newton: advantages and disadvantages Advantages: - Less iterations needed - Choice direction more efficient: descent and curvature Disadvantages: - More sensitive to local extrema - First **and** second order differentials - Step size $\alpha=1$. If initial vector too far from minimum, method will often not converge to minimum. ## Method of Newton: convergence ```{r, echo=FALSE, fig.height=4.5} source("scripts/03a-parameter-estimation//rosenbrock-newton.R", local = knitr::knit_global()) ``` - Very fast convergence for Rosenbrock function (3 iterations) - In general: **quadratic convergence** ## Many advanced gradient-based methods exist - Broyden-Fletcher-Goldfarb-Shanno (BFGS): approximation of Hessian - Levenberg-Marquardt: very popular, combines - Steepest descent: robust but slow - Method of Newton: fast, but often not convergent - Powell/Brent: search along set of directions ::: {.callout-note} ## Optimization in R Use `optim(par, fn)`, where - `par`: initial guess - `fn`: the function to optimize - `method`: "Nelder-Mead" (default), "BFGS", "Brent", ... ::: ## Worked-out example: M. merluccius 1. Define the objective function: ```{r} beverton_holt <- function(S, theta) { return(theta[[1]]*S/(1 + S/theta[[2]])) } ``` ```{r, echo=TRUE} J <- function(theta, x, y) { resid <- y - beverton_holt(x, theta) return(sum(resid^2)) } ``` 2. Specify the initial parameters: ```{r, echo=TRUE} theta0 <- c(6, 20) ``` ## 3. Run the optimizer \footnotesize ```{r, echo=TRUE} fit <- optim(theta0, J, method = "BFGS", x = M.merluccius$spawn.biomass, y = M.merluccius$num.fish) fit ``` ## 4. Evaluate the fit ```{r} #| out-width: 3in #| out-height: 2in #| fig-width: 4.5 #| fig-height: 3 #| fig-align: center ggplot(M.merluccius, aes(spawn.biomass, num.fish)) + geom_point() + geom_function( fun = \(S) beverton_holt(S, fit$par), xlim = c(0, 80)) ``` More sophisticated ways to look at the fit will come later. ## Gradient-free minimization algorithms Two main classes of minimization algorithms: 1. Gradient-based methods 2. **Gradient-free methods** Gradient-free methods: - Are typically slower - Can work even if the objective function is not differentiable - Are more robust Examples: - Direction set (Powell, Brent) - Simplex - Global minimisation ## Simplex algorithm (Nelder-Mead 1965) Basic idea: Capture optimal value inside simplex (triangle, pyramid, ...) - Start with random simplex. - Adjust worst corner of simplex by using different "actions". - Repeat until convergence. {fig-align=center} ## Simplex algorithm  ## Simplex algorithm: advantages and disadvantages - Does not require gradient, Hessian, ... information - Robust: often finds a minimum where other optimizers cannot. - Can find a rough approximation of a minimum in just a few updates... - ... but may take a long time to converge completely. ## Example: M. mercullius ```{r, echo=TRUE} fit <- optim(theta0, J, method = "Nelder-Mead", x = M.merluccius$spawn.biomass, y = M.merluccius$num.fish) fit$par fit$count ``` Compared to BFGS: - Almost same parameter values - More function evaluations, no gradient evaluations ## Global minimization - Disadvantage local techniques: local minima can never be completely excluded - Global techniques insensitive to this problem - Disadvantage: needs a lot of evaluations of $J$ - Types: - Gridding - Random methods ## Global minimisation: Gridding - Evaluate $J$ for a grid of parameter values $\theta$ - Select minimum among grid values ```{r, echo=FALSE, fig.height=6} source("scripts/03a-parameter-estimation//gridding.R", local = knitr::knit_global()) ``` ## Global minimisation: Gridding The finer the grid: - the more likely to find the optimum, - BUT the more calculations needed Iterative: - Start with a coarse-grained grid - Refine parameter domain and repeat Brute force, inefficient ## Global minimisation: Random methods Evaluate $J$ for random parameter sets - Choose PDF for each parameter - Random sampling; Latin hypercube sampling Retain - Optimal set (with $J_{min}$) - Some sets below certain critical value ($J_{crit}$) Examples: - Genetic algorithms - Shuffled complex evolution - Ant colony optimization - Particle swarm optimization - Simulated annealing - ... # Assessing the quality of a fit ## Residuals Model: $$ y = f(x; \theta) + \epsilon $$ where $\epsilon$ is normally distributed. If the model is well-fit, the residuals $e_i = y_i - f(x_i; \theta)$ should be - Independent - Normally distributed with mean 0 and constant variance. Can be checked with QQ-plot of residuals ## Example: M. mercullius ```{r} #| out-width: 4.5in #| out-height: 2in #| fig-width: 7 #| fig-height: 3 #| fig-align: center resids <- with(M.merluccius, { num.fish - beverton_holt(spawn.biomass, fit$par) }) easy_qqplot <- function(data) { ggplot(tibble(sample = data), aes(sample = sample)) + stat_qq_line(color = "gray") + stat_qq() + xlab(NULL) + ylab(NULL) } p <- ggplot(tibble(x = seq_along(resids), y = resids), aes(x, y)) + geom_point() + xlab(NULL) + ylab("Residual") q <- easy_qqplot(resids) grid.arrange(p, q, ncol = 2) ``` No pattern in residuals + normality: model appears well-fit. # Correlations in time series (Optional) ## Residuals: correlation and independence - We often assume that residuals are independent. But this is not always the case, especially in **time series**. - Correlations in residuals are often a sign that something is missing from model fit. How can we detect patterns, correlations, ... in residuals? \vspace*{1cm} ```{r, echo=FALSE} #| out-width: 4.5in #| out-height: 2in #| fig-width: 7 #| fig-height: 3 #| fig-align: center set.seed(1234) n <- 50 x <- seq(1, n) resids_hetero <- sin(2*pi*x/n) + 1.1 * rnorm(n) resids_homo <- rnorm(n) data_plot <- function(id, col, title) { df <- data.frame(id=id, col=col) df %>% ggplot(aes(id, col)) + geom_point() + xlab("Time") + ylab("") + ggtitle(title) } p1 <- data_plot(x, resids_homo, "Random residuals") p2 <- data_plot(x, resids_hetero, "Correlated residuals") grid.arrange(p1, p2, ncol = 2) ``` ## Autocorrelation: how are residuals related? **Autocorrelation** with lag $\tau$ answers the following questions: - To what extent does a residual depend on a previous residual? - Is there correlation between residuals in time? $$ r_\varepsilon(\tau) = \frac{1}{r_\varepsilon(0)}\sum_{k=1}^{N-\tau} \frac{\varepsilon(t_k) \cdot \varepsilon(t_k+\tau)}{N-\tau} $$ where $r_\varepsilon(0)=\sum_{k=1}^{N} \frac{\varepsilon^2(t_k)}{N}$ ## Detecting significant autocorrelations If data is uncorrelated, then autocorrelation is normally distributed: $$ r_\varepsilon(\tau) \sim \mathcal{N}\left(0, \frac{1}{N}\right). $$ Can be used to detect "abnormally high" correlations: - Only about 5% of values outside range $\pm 1.96/\sqrt{N}$. - If more, sign that data is correlated. ## Example: Energy consumption in Korea (2017-19) Autocorrelation uncovers repeating patterns in signal: - Highly correlated over 12-month basis - Anticorrelated over 6-month basis ```{r} #| out-width: 4.5in #| out-height: 2in #| fig-width: 7 #| fig-height: 3 #| fig-align: center months <- c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec") energy <- read.csv("scripts/03a-parameter-estimation/energy.csv") %>% fill(Year) %>% mutate(Date = make_date(Year, match(Month, months), 1)) autocorr_plot <- function(x, plot_thresholds = FALSE, conf_level = 0.95) { plotdata <- with(acf(x, plot = FALSE), data.frame(lag, acf)) p <- ggplot(plotdata, aes(x = lag, y = acf)) + geom_bar(stat = "identity", position = "identity") + xlab("Lag") + ylab("ACF") if (plot_thresholds) { threshold <- qnorm((1 - conf_level) / 2) / sqrt(length(x)) p <- p + geom_hline(yintercept=c(threshold, -threshold), linetype="dashed", color = "red", linewidth = 1) } p } p <- energy %>% ggplot(aes(Date, Consumption)) + geom_line() + geom_point() + theme_classic() + scale_x_date(NULL, breaks = scales::breaks_width("3 months"), labels = scales::label_date_short()) + scale_y_continuous("Energy consumption (1000s of TOE)", breaks = scales::breaks_extended(8), ) q <- autocorr_plot(energy$Consumption, plot_thresholds = TRUE) grid.arrange(p, q, ncol = 2) ``` Source: Korea Energy Economics Institute. ## How to deal with correlations in residuals? - **Make model bigger**: next slides - Subsample data to reduce strength of correlations: not recommended - Use modelling technique that does not need uncorrelated residuals (e.g. autoregressive models): outside scope of this course ## Example: Calcium flows (simulated data) Over the course of exercise, calcium ions flow in and out of the muscle cells. On biological grounds, model calcium concentration as exponentially damped sine: $$ C(t) = \exp(-A t) \sin(t) $$ Data and model fit: ```{r} #| out-width: 3in #| out-height: 2in #| fig-width: 4.5 #| fig-height: 3 #| fig-align: center set.seed(1234) t <- seq(0, 20, length.out = 50) y_large <- exp(-t/10)*sin(t) y_perturb <- 0.2 * cos(t) y_noise <- 0.1 * rnorm(length(t)) y_full <- y_large + y_perturb + y_noise fit <- nls(y ~ exp(-t/A)*sin(t), data = data.frame(t = t, y = y_full), start = list(A = 10)) A_fitted <- coef(fit)["A"] tibble(t = t, y_full = y_full, y_predict = predict(fit)) |> ggplot() + geom_point(aes(t, y_full)) + geom_line(aes(t, y_predict)) + xlab("Time") + ylab("Calcium conc.") ``` ## Residual plot Model fit is good, but not perfect. Clear **repeating pattern** in the residuals. ```{r} #| out-width: 3in #| out-height: 2in #| fig-width: 4.5 #| fig-height: 3 #| fig-align: center resids <- y_full - predict(fit) tibble(t = t, resids = resids) |> ggplot(aes(t, resids)) + geom_point() + geom_line(linetype = "dashed") + xlab("Time") + ylab("Residual") ``` ## Autocorrelation plot Lack of model fit, repeating pattern in the residuals can also be seen from the autocorrelation plot. ```{r} #| out-width: 3in #| out-height: 2in #| fig-width: 4.5 #| fig-height: 3 #| fig-align: center autocorr_plot(resids, plot_thresholds = TRUE) ``` - Red lines: thresholds $1.96 / \sqrt{50} = 0.227$. - 13 out of 17 autocorrelations (76%) exceed threshold ## Expanding the model Pattern in residuals is a clear sign that **something is missing** in our modelling approach. Given the periodic oscillations, propose $$ C(t) = \exp(-At)\sin(t) + B\cos(\omega t). $$ ```{r} #| out-height: 2in #| out-width: 4in #| fig-height: 3 #| fig-width: 6 #| fig-align: center fit_full <- nls(y ~ exp(-t/A)*sin(t) + B*cos(C*t), data = data.frame(t = t, y = y_full), start = list(A = 10, B = 1.0, C = 1.0)) A_fitted <- coef(fit)["A"] B_fitted <- coef(fit)["B"] C_fitted <- coef(fit)["C"] easy_predict <- function(model, t) { predict(model, newdata = data.frame(t = t)) } data <- tibble(t = t, y_full = y_full) t_dense <- seq(min(t), max(t), length.out = 500) curves <- tibble( t = t_dense, y_p = easy_predict(fit, t_dense), y_p_full = easy_predict(fit_full, t_dense)) ggplot() + geom_point(data = data, aes(t, y_full)) + geom_line(data = curves, aes(t, y_p, linetype = "Original"), color = "gray50") + geom_line(data = curves, aes(t, y_p_full, linetype = "Expanded")) + xlab("Time") + ylab("Calcium conc.") + scale_linetype_manual( values = c("Expanded" = "solid", "Original" = "dashed"), name = "Model") ``` ## Residual and autocorrelation plot No residual pattern visible in residuals. The model is well fit. ```{r} #| out-width: 4.5in #| out-height: 2in #| fig-width: 7 #| fig-height: 3 #| fig-align: center resids_full <- y_full - predict(fit_full) p <- tibble(t = t, resids = resids_full) |> ggplot(aes(t, resids)) + geom_point() + geom_line(linetype = "dashed") + xlab("Time") + ylab("Residual") q <- autocorr_plot(resids_full, plot_thresholds = TRUE) grid.arrange(p, q, ncol = 2) ``` ## Residual QQ-plots ```{r} #| out-width: 4.5in #| out-height: 2in #| fig-width: 7 #| fig-height: 3 #| fig-align: center p <- easy_qqplot(resids) + ggtitle("Original model") q <- easy_qqplot(resids_full) + ggtitle("Expanded model") grid.arrange(p, q, ncol = 2) ```