Predict from a brokenstick model — predict.brokenstick • brokenstick

The predictions from a broken stick model coincide with the group-conditional means of the random effects. This function takes an object of class brokenstick and returns predictions in one of several formats. The user can calculate predictions for new persons, i.e., for persons who are not part of the fitted model, through the x and y arguments.

Usage

# S3 method for class 'brokenstick'
predict(
  object,
  newdata = NULL,
  ...,
  x = NULL,
  y = NULL,
  group = NULL,
  hide = c("right", "left", "boundary", "internal", "none"),
  shape = c("long", "wide", "vector"),
  include_data = TRUE,
  strip_data = TRUE,
  whatknots = "all"
)

Arguments

object: A brokenstick object.
newdata: Optional. A data frame in which to look for variables with which to predict. The training data are used if omitted and if object$light is FALSE.
...: Not used, but required for extensibility.
x: Optional. A numeric vector with values of the predictor. It could also be the special keyword x = "knots" replaces x by the positions of the knots.
y: Optional. A numeric vector with measurements.
group: A vector with group identifications
hide: Should output for knots be hidden in get, print, summary and plot functions? Can be "left", "right", "boundary", "internal" or "none". The default is "right".
shape: A string: "long" (default), "wide" or "vector" specifying the shape of the return value. Note that use of "wide" with many unique values in x creates an unwieldy, large and sparse matrix.
include_data: A logical indicating whether the observed data from object$data and newdata should be included into the return value. The default is TRUE. Use include_data = FALSE to keep only added data points (e.g. knots or observed data specified by x and y). Setting include_data = FALSE is useful in combination with shape = "wide" to avoid the warning Values from '.pred' are not uniquely identified. For convenience, in the special case x = "knots" the function overwrites include_data to FALSE to evade observed ages to show up in the wide matrix.
strip_data: Deprecated. Use include_data instead.
whatknots: Deprecated. Use hide instead.

Value

If shape == "long" a long data.frame of predictions. If x, y and group are not specified, the number of rows in the data frame is guaranteed to be the same as the number of rows in newdata.

If shape == "wide" a wide data.frame of predictions, one record per group. Note that this format could be inefficient if observations times vary between subjects.

If shape == "vector" a vector of predicted values, of all x-values and groups.

If the function finds no data, it throws a warnings and returns NULL.

Details

The function predict() calculates predictions for every row in newdata. If the user specifies no newdata argument, then the function sets newdata equal to the training data (object$data if object$light is FALSE). For a light object without a newdata argument, the function throws the warning "Argument 'newdata' is required for a light brokenstick object." and returns NULL.

It is possible to tailor the behaviour of predict() through the x, y and group arguments. What exactly happens depends on which of these arguments is specified:

If the user specifies x, but no y and group, the function returns - for every group in newdata - predictions at the specified x values. This method will use the data from newdata.
If the user specifies x and y but no group, the function forms a hypothetical new group with the x and y values. This method uses no information from newdata, and also works for a light brokenstick object.
If the user specifies group, but no x or y, the function searches for the relevant data in newdata and limits its predictions to those groups. This is useful if the user needs a prediction for only one or a few groups. This does not work for a light brokenstick object.
If the user specifies x and group, but no y, the function will create new values for x in each group, search for the relevant data in newdata and provide predictions at values of x in those groups.
If the user specifies x, y and group, the function assumes that these vectors contain additional data on top on what is already available in newdata. The lengths of x, y and group must match. For a light brokenstick object, case effectively becomes case 6. See below.
As case 5, but now without newdata available. All data are specified through x, y and group and form a data frame. Matching to newdata is attempted, but as long as group id's are different from the training sample effectively new cases will be made.

Examples

library("dplyr")
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union

# -- Data

train <- smocc_200[1:1198, ]
test <- smocc_200[1199:1940, ]
if (FALSE) { # \dontrun{
# -- Fit model

fit <- brokenstick(hgt_z ~ age | id, data = train, knots = 0:2, seed = 1)
fit_light <- brokenstick(hgt_z ~ age | id,
  data = train, knots = 0:2,
  light = TRUE, seed = 1
)

# -- Predict, standard cases

# Use train data, return column with predictions
pred <- predict(fit)
identical(nrow(train), nrow(pred))

# Predict without newdata, not possible for light object
predict(fit_light)

# Use test data
pred <- predict(fit, newdata = test)
identical(nrow(test), nrow(pred))

# Predict, same but using newdata with the light object
pred_light <- predict(fit_light, newdata = test)
identical(pred, pred_light)


# -- Predict, special cases


# -- Case 1: x, -y, -group

# Case 1: x as "knots", standard estimates, train sample (n = 124)
z <- predict(fit, x = "knots", shape = "wide")
head(z, 3)

# Case 1: x as values, linearly interpolated, train sample (n = 124)
z <- predict(fit, x = c(0.5, 1, 1.5), shape = "wide", include_data = FALSE)
head(z, 3)

# Case 1: x as values, linearly interpolated, test sample (n = 76)
z <- predict(fit, test, x = c(0.5, 1, 1.5), shape = "wide", include_data = FALSE)
head(z, 3)

# Case 1: x, not possible for light object
z <- predict(fit_light, x = "knots")

# -- Case 2: x, y, -group

# Case 2: form one new group with id = 0
predict(fit, x = "knots", y = c(1, 1, 0.5, 0), shape = "wide")

# Case 2: works also for a light object
predict(fit_light, x = "knots", y = c(1, 1, 0.5, 0), shape = "wide")


# -- Case 3: -x, -y, group

# Case 3: Predict at observed age for subset of groups, training sample
pred <- predict(fit, group = c(10001, 10005, 10022))
head(pred, 3)

# Case 3: Of course, we cannot do this for light objects
pred_light <- predict(fit_light, group = c(10001, 10005, 10022))

# Case 3: We can use another sample. Note there is no child 999
pred <- predict(fit, test, group = c(11045, 11120, 999))
tail(pred, 3)

# Case 3: Works also for a light object
pred_light <- predict(fit_light, test, group = c(11045, 11120, 999))
identical(pred, pred_light)

# -- Case 4: x, -y, group

# Case 4: Predict at specified x, only in selected groups, train sample
pred <- predict(fit, x = c(0.5, 1, 1.25), group = c(10001, 10005, 10022),
        include_data = FALSE)
pred

# Case 4: Same, but include observed data and sort
pred_all <- predict(fit,
  x = c(0.5, 1, 1.25), group = c(10001, 10005, 10022)) %>%
  dplyr::arrange(id, age)

# Case 4: Applies also to test sample
pred <- predict(fit, test, x = c(0.5, 1, 1.25), group = c(11045, 11120, 999),
 include_data = FALSE)
pred

# Case 4: Works also with light object
pred_light <- predict(fit_light, test, x = c(0.5, 1, 1.25),
  group = c(11045, 11120, 999), include_data = FALSE)
identical(pred_light, pred)

# -- Case 5: x, y, group

# Case 5: Add new data to training sample, and refreshes broken stick
# estimate at age x.
# Note that novel child (not in train) 999 has one data point
predict(fit,
  x = c(0.9, 0.9, 0.9), y = c(1, 1, 1),
  group = c(10001, 10005, 999), include_data = FALSE)

# Case 5: Same, but now for test sample. Novel child 899 has two data points
predict(fit, test,
  x = c(0.5, 0.9, 0.6, 0.9),
  y = c(0, 0.5, 0.5, 0.6), group = c(11045, 11120, 899, 899),
  include_data = FALSE)

# Case 5: Also works for light object
predict(fit_light, test,
  x = c(0.5, 0.9, 0.6, 0.9),
  y = c(0, 0.5, 0.5, 0.6), group = c(11045, 11120, 899, 899),
  include_data = FALSE)


# -- Case 6: As Case 5, but without previous data

# Case 6: Same call as last, but now without newdata = test
# All children are de facto novel as they do not occur in the training
# or test samples.
# Note: Predictions for 11045 and 11120 differ from prediction in Case 5.
predict(fit,
  x = c(0.5, 0.9, 0.6, 0.9),
  y = c(0, 0.5, 0.5, 0.6), group = c(11045, 11120, 899, 899))

# This also work for the light brokenstick object
predict(fit_light,
  x = c(0.5, 0.9, 0.6, 0.9),
  y = c(0, 0.5, 0.5, 0.6), group = c(11045, 11120, 899, 899))
} # }