library(fabletools)
#> Registered S3 method overwritten by 'tsibble':
#> method from
#> as_tibble.grouped_df dplyrWriting a time series model using fabletools provides your model with many additional features without extra effort. Features that aren’t model specific are handled by fabletools, allowing you to spend more time writing methods for your model. Some functionality handled by fabletools includes:
The fabletools package promotes consistent interfaces and output structures that allow various time series models to work well together. This vignette will guide you through creating a fabletools model, and provide a glimpse into the steps used to convert user data to modelling inputs, and modelling outputs to user data.
As an example, we’ll create a fabletools model that uses seasonal
averages: SMEAN(). It can be thought of as a seasonal
version of fable::MEAN(), which instead of averaging the
entire series, it averages values from each season.
Much like cross-sectional models (such as lm()), tidy
time-series models use a formula based interface. Of course not all
arguments need to be specified from within the formula (much like
na.action in lm()). The model formula is a
familiar and user friendly interface for specifying key model concepts
(like pdq() in ARIMA()), and data-varying
inputs (such as holidays and exogenous regressors). Model specific
formula functions (like pdq()) are known as specials (much
like specials from
stats::terms.formula()).
Before writing code, it is a good idea to think about what interface
best suits your model. This is often model specific, however you may
find it useful to look at existing interfaces to see how yours could be
written consistently. A good example of this is with seasonality:
fourier terms are specified with the fourier(period, K)
special, and seasonal dummy variables use
season(period).
A potential interface for the SMEAN() model could
be:
At minimum, a model consists of a model function (something that returns a model definition), a set of specials, and a training function.
Model functions typically consist of two function calls. A model
class (defining the training method, the specials, and data checks) with
new_model_class(), and new_model_definition to
return the model definition:
#' Seasonal mean models
#'
#' Add the rest of your documentation here.
#' Typically this includes a "Specials" section
#'
#' @export
SMEAN <- function(formula, ...) {
# Create a model class which combines the training method, specials, and data checks
model_smean <- new_model_class("smean",
# The training method (more on this later)
train = train_smean,
# The formula specials (the next section)
specials = specials_smean,
# Any checks of the unprocessed data, like gaps, ordered, regular, etc.
check = function(.data) {
if (!tsibble::is_regular(.data)) stop("Data must be regular")
}
)
# Return a model definition which stores the user's model specification
new_model_definition(model_smean, {{formula}}, ...)
}Anything passed to ... of
new_model_definition() will be passed onward to the model
training function. Note that the formula needs to be embraced with
{{formula}} in order to allow for non-formula inputs like
SMEAN(y).
The specials for a model are created using
new_specials(). The functions specified here will be used
to compute specials each time the model is provided with new data (model
training, forecasting, refitting, etc.). The results of these functions
will be passed to the subsequent method via the specials
argument (more on this later).
To enable automatic model specification (with SMEAN(y)),
the .required_specials argument will ensure that the
special is called at least once. By setting season() as a
required special, SMEAN(y) will be parsed as
SMEAN(y ~ season()). As no arguments will be provided for
omitted required specials, make sure they have good defaults. The
fabletools::get_frequencies() function is a useful helper
for handling seasonal periods, as automatically chooses appropriate
seasonalities when period = NULL, and is able to handle
inputs like period = "week".
Anything not handled by defined specials will be treated as exogenous
regressors and passed to the xreg() special. That is to say
SMEAN(y ~ season("year") + x) will be parsed as
SMEAN(y ~ season("year") + xreg(x)). The
xreg() special should be defined by all models, even if
your model doesn’t support it.
specials_smean <- new_specials(
season = function(period = NULL) {
# Your input handling code here.
get_frequencies(period, self$data, .auto = "smallest")
},
xreg = function(...) {
# This model doesn't support exogenous regressors, time to error.
stop("Exogenous regressors aren't supported by `SMEAN()`")
},
# This model requires `season()`
# Adding this allows `SMEAN(y)` to automatically include the `season()` special
.required_specials = "season"
)The specials are the only thing needed for the formula to work, as the fabletools handles the transformations and response variables specified in the formula’s left side.
This function is used to apply the model definition created by the
model function (SMEAN()) to users data when they use
model(data, SMEAN()).
The .data argument is a single series tsibble (no keys),
representing the parsed left side of the formula. The index of
.data is the time of the measurement, and the measured
variables are the transformed response variable(s).
The specials argument is a list of results from parsing
the specials used in the right side of the formula. The result from the
season() special in SMEAN(y ~ season("year"))
would be accessible from specials$season[[1]]. As specials
can be used more than once, the nth usage of special xyz()
can be accessed with specials$xyz[[n]].
As mentioned earlier, ... will contain additional
parameters passed ... of
new_model_definition().
The function should return an S3 object that contains everything you need for your future methods (such as forecasting, getting fitted values, refitting, etc.).
train_smean <- function(.data, specials, ...){
# Extract a vector of response data
mv <- tsibble::measured_vars(.data)
if(length(mv) > 1) stop("SMEAN() is a univariate model.")
y <- .data[[mv]]
# Pull out inputs from the specials
if(length(specials$season) > 1) stop("The `season()` special of `SMEAN()` should only be used once.")
m <- specials$season[[1]]
# Compute the seasonal averages
season_id <- seq(0, length(y) - 1) %% m
season_y <- split(y, season_id)
season_avg <- vapply(season_y, FUN = mean, FUN.VALUE = numeric(1L),
USE.NAMES = FALSE)
# Compute fitted values and residuals
fit <- season_avg[season_id+1]
e <- y - fit
# Create S3 model object
# It should be small, but contain everything needed for methods below
structure(
list(
coef = season_avg,
n = length(y),
y_name = mv,
fitted = fit,
residuals = e,
sigma2 = var(e, na.rm = TRUE)
),
class = "model_smean"
)
}Great, that’s the bare minimum for a model complete with interface and training method. Let’s try it out.
fit <- tsibbledata::aus_production %>%
model(SMEAN(Beer))
fit
#> # A mable: 1 x 1
#> `SMEAN(Beer)`
#> <model>
#> 1 <modl_smn>It doesn’t look like much, but it has used the above specials and training method to compute the seasonal average and store it in the object. However we can’t see any details about the model yet. To make the model useful, we’ll need to define some methods.
| Method | Value | Description |
|---|---|---|
model_sum() |
character(1L) |
A short summary of the model to display in the mable |
report() |
console output | A detailed summary of the model, similar to
summary() |
equation() |
character(1L) | The mathematical equation for the fitted model |
forecast() |
distribution | Produce forecasts from the model |
stream() |
updated model | Extend the fit of the model with additional data |
generate() |
tsibble | Generate potential reponse values at certain times from the model |
interpolate() |
tsibble | Interpolate missing values using the model |
refit() |
refitted model | Apply the model to a new dataset |
tidy() |
tibble of coefficients | Extract coefficients from the model |
glance() |
tibble of statistics | Extract summary statistics from the model |
augment() |
tibble of data | Augment a dataset with information from the model |
components() |
dable of components | Extract decomposed elements from the model |
fitted() |
numeric | Extract fitted values from the model |
residuals() |
numeric | Extract residuals from the model |
#' @importFrom fabletools model_sum
#' @export
model_sum.model_smean <- function(x){
sprintf("SMEAN[%i]", length(x$coef))
}
fit
#> # A mable: 1 x 1
#> `SMEAN(Beer)`
#> <model>
#> 1 <SMEAN[4]>#' @importFrom fabletools report
#' @export
report.model_smean <- function(x){
m <- length(x$coef)
cat("\n")
cat(paste("Seasonal period:", m))
cat("\n\n")
cat("Seasonal averages:\n")
print.default(
setNames(x$coef, paste0("s", seq_len(m))),
print.gap = 2
)
cat(paste("\nsigma^2:", round(x$sigma2, 4), "\n"))
}
report(fit)
#> Series: Beer
#> Model: SMEAN[4]
#>
#> Seasonal period: 4
#>
#> Seasonal averages:
#> s1 s2 s3 s4
#> 416.8182 372.6182 387.3704 485.4444
#>
#> sigma^2: 5494.6686#' @importFrom fabletools tidy
#' @export
tidy.model_smean <- function(x){
tibble::tibble(
term = paste0("season_", seq_along(x$coef)),
estimate = x$coef
)
}
tidy(fit)
#> # A tibble: 4 × 3
#> .model term estimate
#> <chr> <chr> <dbl>
#> 1 SMEAN(Beer) season_1 417.
#> 2 SMEAN(Beer) season_2 373.
#> 3 SMEAN(Beer) season_3 387.
#> 4 SMEAN(Beer) season_4 485.#' @importFrom fabletools glance
#' @export
glance.model_smean <- function(x){
tibble::tibble(
sigma2 = x$sigma2
)
}
glance(fit)
#> # A tibble: 1 × 2
#> .model sigma2
#> <chr> <dbl>
#> 1 SMEAN(Beer) 5495.#' @importFrom fabletools forecast
#' @export
forecast.model_smean <- function(object, new_data, ...){
# Extract required parameters
h <- NROW(new_data)
n <- object$n
m <- length(object$coef)
coef <- object$coef
# Compute forecast variance
season_id <- seq(0, n - 1) %% m
season_e <- split(object$residuals, season_id)
season_sd <- vapply(season_e, FUN = sd, FUN.VALUE = numeric(1L),
USE.NAMES = FALSE, na.rm = TRUE)
# Create forecast distributions
fc_id <- (seq(0, h-1) + n %% m) %% m + 1
mu <- coef[fc_id]
sigma <- season_sd[fc_id]
distributional::dist_normal(mu, sigma)
}
forecast(fit)
#> # A fable: 8 x 4 [1Q]
#> # Key: .model [1]
#> .model Quarter
#> <chr> <qtr>
#> 1 SMEAN(Beer) 2010 Q3
#> 2 SMEAN(Beer) 2010 Q4
#> 3 SMEAN(Beer) 2011 Q1
#> 4 SMEAN(Beer) 2011 Q2
#> 5 SMEAN(Beer) 2011 Q3
#> 6 SMEAN(Beer) 2011 Q4
#> 7 SMEAN(Beer) 2012 Q1
#> 8 SMEAN(Beer) 2012 Q2
#> # ℹ 2 more variables: Beer <dist>, .mean <dbl>#' @importFrom fabletools stream
#' @export
stream.model_smean <- function(object, new_data, specials, ...){
# Extract a vector of response data
mv <- tsibble::measured_vars(new_data)
y <- new_data[[mv]]
# Compute the new seasonal averages
m <- length(object$coef)
season_id <- (seq(0, length(y) - 1) + object$n %% m) %% m
season_y <- split(y, season_id)
season_avg <- vapply(season_y, FUN = mean, FUN.VALUE = numeric(1L),
USE.NAMES = FALSE)
weight_new <- vapply(season_y, FUN = length, FUN.VALUE = integer(1L),
USE.NAMES = FALSE)
# Update coefficients to include new estimates
weight_orig <- rep(object$n %/% m, m) + c(rep(1, object$n %% m), rep(0, m - object$n %% m))
new_coef <- (object$coef * weight_orig + season_avg * weight_new) / (weight_orig + weight_new)
coef_change <- new_coef - object$coef
# Update model
new_fits <- new_coef[season_id+1]
new_e <- y - new_fits
object$coef <- new_coef
object$fitted <- c(object$fitted + rep_len(coef_change, object$n), new_fits)
object$residuals <- c(object$residuals - rep_len(coef_change, object$n), new_e)
object$n <- object$n + length(y)
object$sigma2 <- var(object$residuals, na.rm = TRUE)
# Return updated model object
object
}
us_acc_deaths <- as_tsibble(USAccDeaths)
fit_stream <- us_acc_deaths %>%
dplyr::slice(1:60) %>%
model(SMEAN(value))
report(fit_stream)
#> Series: value
#> Model: SMEAN[12]
#>
#> Seasonal period: 12
#>
#> Seasonal averages:
#> s1 s2 s3 s4 s5 s6 s7 s8
#> 8085.6 7362.2 8116.6 8292.0 9126.2 9627.6 10446.6 9733.6
#> s9 s10 s11 s12
#> 8618.4 8974.2 8434.0 8616.8
#>
#> sigma^2: 251827.8712
# Update the model with new data
us_acc_deaths_new <- us_acc_deaths %>% dplyr::slice(61:72)
fit_stream <- fit_stream %>%
stream(us_acc_deaths_new)
report(fit_stream)
#> Series: value
#> Model: SMEAN[12]
#>
#> Seasonal period: 12
#>
#> Seasonal averages:
#> s1 s2 s3 s4 s5 s6 s7
#> 8044.000 7283.833 8062.333 8275.333 9124.333 9595.333 10452.833
#> s8 s9 s10 s11 s12
#> 9749.167 8700.333 8990.167 8467.167 8720.667
#>
#> sigma^2: 222480.9038
# Check that it matches a model of the full data
us_acc_deaths %>%
model(SMEAN(value)) %>%
report()
#> Series: value
#> Model: SMEAN[12]
#>
#> Seasonal period: 12
#>
#> Seasonal averages:
#> s1 s2 s3 s4 s5 s6 s7
#> 8044.000 7283.833 8062.333 8275.333 9124.333 9595.333 10452.833
#> s8 s9 s10 s11 s12
#> 9749.167 8700.333 8990.167 8467.167 8720.667
#>
#> sigma^2: 222480.9038#' @importFrom fabletools fitted
#' @export
fitted.model_smean <- function(object, ...){
object$fitted
}
fitted(fit)
#> # A tsibble: 218 x 3 [1Q]
#> # Key: .model [1]
#> .model Quarter .fitted
#> <chr> <qtr> <dbl>
#> 1 SMEAN(Beer) 1956 Q1 417.
#> 2 SMEAN(Beer) 1956 Q2 373.
#> 3 SMEAN(Beer) 1956 Q3 387.
#> 4 SMEAN(Beer) 1956 Q4 485.
#> 5 SMEAN(Beer) 1957 Q1 417.
#> 6 SMEAN(Beer) 1957 Q2 373.
#> 7 SMEAN(Beer) 1957 Q3 387.
#> 8 SMEAN(Beer) 1957 Q4 485.
#> 9 SMEAN(Beer) 1958 Q1 417.
#> 10 SMEAN(Beer) 1958 Q2 373.
#> # ℹ 208 more rows#' @importFrom fabletools residuals
#' @export
residuals.model_smean <- function(object, ...){
object$residuals
}
residuals(fit)
#> # A tsibble: 218 x 3 [1Q]
#> # Key: .model [1]
#> .model Quarter .resid
#> <chr> <qtr> <dbl>
#> 1 SMEAN(Beer) 1956 Q1 -133.
#> 2 SMEAN(Beer) 1956 Q2 -160.
#> 3 SMEAN(Beer) 1956 Q3 -160.
#> 4 SMEAN(Beer) 1956 Q4 -177.
#> 5 SMEAN(Beer) 1957 Q1 -155.
#> 6 SMEAN(Beer) 1957 Q2 -145.
#> 7 SMEAN(Beer) 1957 Q3 -151.
#> 8 SMEAN(Beer) 1957 Q4 -165.
#> 9 SMEAN(Beer) 1958 Q1 -145.
#> 10 SMEAN(Beer) 1958 Q2 -140.
#> # ℹ 208 more rows#' @importFrom fabletools components
#' @export
components.model_smean <- function(object, ...){
# Create a tsibble of the components
dcmp <- tibble::tibble(
!!object$y_name := fitted(object) + residuals(object),
season = fitted(object),
remainder = residuals(object)
)
# Describe how the components combine into other columns
aliases <- tibble::lst(!!object$y_name := quote(season + remainder))
# Define the behaviour of seasonal components
# This is used for automatic modelling of seasonal components in `decomposition_model()`
# It may also be used for plotting in the future.
seasonalities <- list(season = list(period = length(object$coef)))
# Return a dable
as_dable(
dcmp,
resp = !!sym(object$y_name), method = model_sum(object),
seasons = seasonalities, aliases = aliases
)
}
components(fit) # Need to store index somewhere. This workflow should improve.