cv_estimate_rt: Leave-kth-out cross validation for choosing a optimal...

In rtestim: Estimate the Effective Reproductive Number with Trend Filtering

Leave-kth-out cross validation for choosing a optimal parameter lambda

Description

Leave-kth-out cross validation for choosing a optimal parameter lambda

Usage

cv_estimate_rt(
  observed_counts,
  korder = 3L,
  dist_gamma = c(2.5, 2.5),
  nfold = 3L,
  error_measure = c("deviance", "mse", "mae"),
  x = 1:n,
  lambda = NULL,
  maxiter = 1000000L,
  delay_distn = NULL,
  delay_distn_periodicity = NULL,
  regular_splits = FALSE,
  invert_splits = FALSE,
  ...
)

Arguments

observed_counts	vector of the observed daily infection counts
korder	Integer. Degree of the piecewise polynomial curve to be estimated. For example, korder = 0 corresponds to a piecewise constant curve.
dist_gamma	Vector of length 2. These are the shape and scale for the assumed serial interval distribution. Roughly, this distribution describes the probability of an infectious individual infecting someone else after some period of time after having become infectious. As in most literature, we assume that this interval follows a gamma distribution with some shape and scale.
nfold	Integer. This number of folds to conduct the leave-kth-out cross validation. For leave-kth-out cross validation, every kth observed_counts and their corresponding position (evenly or unevenly spaced) are placed into the same fold. The first and last observed_counts are not assigned to any folds. Smallest allowable value is nfold = 2.
error_measure	Metric used to calculate cross validation scores. Must be choose from mse, mae, and deviance. mse calculates the mean square error; mae calculates the mean absolute error; deviance calculates the deviance
x	a vector of positions at which the counts have been observed. In an ideal case, we would observe data at regular intervals (e.g. daily or weekly) but this may not always be the case. May be numeric or Date.
lambda	Vector. A user supplied sequence of tuning parameters which determines the balance between data fidelity and smoothness of the estimated Rt; larger lambda results in a smoother estimate. The default, NULL results in an automatic computation based on nlambda, the largest value of lambda that would result in a maximally smooth estimate, and lambda_min_ratio. Supplying a value of lambda overrides this behaviour. It is likely better to supply a decreasing sequence of lambda values than a single (small) value. If supplied, the user-defined lambda sequence is automatically sorted in decreasing order.
maxiter	Integer. Maximum number of iterations for the estimation algorithm.
delay_distn	in the case of a non-gamma delay distribution, a vector or matrix (or Matrix::Matrix()) of delay probabilities may be passed here. For a vector, these will be coerced to sum to 1, and padded with 0 in the right tail if necessary. If a time-varying delay matrix, it must be lower-triangular. Each row will be silently coerced to sum to 1. See also vignette("delay-distributions").
delay_distn_periodicity	Controls the relationship between the spacing of the computed delay distribution and the spacing of x. In the default case, x would be regular on the sequence 1:length(observed_cases), and this would be 1. But if x is a Date object or spaced irregularly, the relationship becomes more complicated. For example, weekly data when x is a date in the form YYYY-MM-DD requires specifying delay_distn_periodicity = "1 week". Or if observed_cases were reported on Monday, Wednesday, and Friday, then delay_distn_periodicity = "1 day" would be most appropriate.
regular_splits	Logical. If TRUE, the folds for k-fold cross-validation are chosen by placing every kth point into the same fold. The first and last points are not included in any fold and are always included in building the predictive model. As an example, with 15 data points and kfold = 4, the points are assigned to folds in the following way: 0 \; 1 \; 2 \; 3 \; 4 \; 1 \; 2 \; 3 \; 4 \; 1 \; 2 \; 3 \; 4 \; 1 \; 0 where 0 indicates no assignment. Therefore, the folds are not random and running cv_estimate_rt() twice will give the same result.
invert_splits	Logical. Typical K-fold CV would use K-1 folds for the training set while reserving 1 fold for evaluation (repeating the split K times). Setting this to true inverts this process, using a much smaller training set with a larger evaluation set. This tends to result in larger values of lambda that minimize CV.
...	additional parameters passed to estimate_rt() function

Value

An object with S3 class "cv_poisson_rt". Among the list components:

• full_fit An object with S3 class "poisson_rt", fitted with all observed_counts and lambda

• cv_scores leave-kth-out cross validation scores

• cv_se leave-kth-out cross validation standard error

• lambda.min lambda which achieved the optimal cross validation score

• lambda.1se lambda that gives the optimal cross validation score within one standard error.

• lambda the value of lambda used in the algorithm.

Examples

y <- c(1, rpois(100, dnorm(1:100, 50, 15) * 500 + 1))
cv <- cv_estimate_rt(y, korder = 3, nfold = 3, nsol = 30)
cv

rtestim documentation built on Aug. 8, 2025, 6:21 p.m.