Description Usage Arguments Details Value Note See Also Examples

View source: R/crossvalidation.R

Function `validateFDboost()`

is experimental.
Cross-Validation and bootstrapping over curves to compute the empirical risk for
hyper-parameter selection and to compute resampled coefficients and predictions for
the models.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | ```
applyFolds(object, folds = cv(rep(1, length(unique(object$id))), type =
"bootstrap"), grid = 1:mstop(object), fun = NULL, riskFun = NULL,
numInt = object$numInt, papply = mclapply, mc.preschedule = FALSE,
showProgress = TRUE, ...)
validateFDboost(object, response = NULL, folds = cv(rep(1,
length(unique(object$id))), type = "bootstrap"), grid = 1:mstop(object),
fun = NULL, getCoefCV = TRUE, riskopt = c("mean", "median"),
mrdDelete = 0, refitSmoothOffset = TRUE, showProgress = TRUE, ...)
## S3 method for class 'FDboost'
cvrisk(object, folds = cvLong(id = object$id, weights =
model.weights(object)), grid = 1:mstop(object), papply = mclapply,
fun = NULL, corrected = TRUE, mc.preschedule = FALSE, ...)
cvLong(id, weights = rep(1, l = length(id)), type = c("bootstrap", "kfold",
"subsampling", "curves"), B = ifelse(type == "kfold", 10, 25), prob = 0.5,
strata = NULL)
cvMa(ydim, weights = rep(1, l = ydim[1] * ydim[2]), type = c("bootstrap",
"kfold", "subsampling", "curves"), B = ifelse(type == "kfold", 10, 25),
prob = 0.5, strata = NULL, ...)
``` |

`object` |
fitted FDboost-object |

`folds` |
a weight matrix with number of rows equal to the number of observed trajectories. |

`grid` |
the grid over which the optimal number of boosting iterations (mstop) is searched. |

`fun` |
if |

`riskFun` |
only exists in |

`numInt` |
only exists in |

`papply` |
(parallel) apply function, defaults to |

`mc.preschedule` |
Defaults to |

`showProgress` |
logical, defaults to |

`...` |
further arguments passed to |

`response` |
optional, specify a response vector for the computation of the prediction errors.
Defaults to |

`getCoefCV` |
logical, defaults to |

`riskopt` |
how is the optimal stopping iteration determined. Defaults to the mean, but median is possible as well. |

`mrdDelete` |
Delete values that are |

`refitSmoothOffset` |
logical, should the offset be refitted in each learning sample?
Defaults to |

`corrected` |
see |

`id` |
the id-vector as integers 1, 2, ... specifying which observations belong to the same curve,
deprecated in |

`weights` |
a numeric vector of (integration) weights, defaults to 1. |

`type` |
character argument for specifying the cross-validation method. Currently (stratified) bootstrap, k-fold cross-validation, subsampling and leaving-one-curve-out cross validation (i.e. jack knife on curves) are implemented. |

`B` |
number of folds, per default 25 for |

`prob` |
percentage of observations to be included in the learning samples for subsampling. |

`strata` |
a factor of the same length as |

`ydim` |
dimensions of response-matrix |

The number of boosting iterations is an important hyper-parameter of boosting
and can be chosen using the functions `applyFolds`

, `cvrisk.FDboost`

and
`validateFDboost`

as they compute
honest, i.e., out-of-bag, estimates of the empirical risk for different numbers of boosting iterations.
The weights (zero weights correspond to test cases) are defined via the folds matrix,
see `cvrisk`

in package mboost.

`applyFolds`

is still EXPERIMENTAL!
The function `applyFolds`

is especially suited to models with functional response.
It recomputes the model in each fold using `FDboost`

. Thus, all parameters are recomputed,
including the smooth offset (if present) and the identifiability constraints (if present, only
relevant for bolsc, brandomc and bbsc).
Note, that the function `applyFolds`

expects folds that give weights
per trajectory without considering integration weights.

The function `validateFDboost`

is especially suited to models with functional response.
Using the option `refitSmoothOffset`

the offset is refitted on each fold.
Note, that the function `validateFDboost`

expects folds that give weights
per trajectory without considering integration weights. The integration weights of
`object`

are used to compute the empirical risk as integral. The argument `response`

can be useful in simulation studies where the true value of the response is known but for
the model fit the response is used with noise.

The function `cvrisk.FDboost`

is a wrapper for `cvrisk`

in package mboost.
It overrides the default for the folds, so that the folds are sampled on the level of curves
(not on the level of single observations, which does not make sense for functional response).
Note that the smooth offset and the computation of the identifiability constraints
are not part of the refitting if `cvrisk`

is used.
Per default the integration weights of the model fit are used to compute the prediction errors
(as the integration weights are part of the default folds).
Note that in `cvrisk`

the weights are rescaled to sum up to one.

The functions `cvMa`

and `cvLong`

can be used to build an appropriate
weight matrix for functional response to be used with `cvrisk`

as sampling
is done on the level of curves. The probability for each
trajectory to enter a fold is equal over all trajectories.
The function `cvMa`

takes the dimensions of the response matrix as input argument and thus
can only be used for regularly observed response.
The function `cvLong`

takes the id variable and the weights as arguments and thus can be used
for responses in long format that are potentially observed irregularly.

If `strata`

is defined
sampling is performed in each stratum separately thus preserving
the distribution of the `strata`

variable in each fold.

`cvMa`

and `cvLong`

return a matrix of weights to be used in `cvrisk`

.

The functions `applyFolds`

and `cvrisk.FDboost`

return a `cvrisk`

-object,
which is a matrix of the computed out-of-bag risk. The matrix has the folds in rows and the
number of boosting iteratins in columns. Furhtermore, the matrix has attributes including:

`risk` |
name of the applied risk function |

`call` |
model call of the model object |

`mstop` |
gird of stopping iterations that is used |

`type` |
name for the type of folds |

The function `validateFDboost`

returns a `validateFDboost`

-object,
which is a named list containing:

`response` |
the response |

`yind` |
the observation points of the response |

`id` |
the id variable of the response |

`folds` |
folds that were used |

`grid` |
grid of possible numbers of boosting iterations |

`coefCV` |
if |

`predCV` |
if |

`oobpreds` |
if the type of folds is curves the out-of-bag predictions for each trajectory |

`oobrisk` |
the out-of-bag risk |

`oobriskMean` |
the out-of-bag risk at the minimal mean risk |

`oobmse` |
the out-of-bag mean squared error (MSE) |

`oobrelMSE` |
the out-of-bag relative mean squared error (relMSE) |

`oobmrd` |
the out-of-bag mean relative deviation (MRD) |

`oobrisk0` |
the out-of-bag risk without consideration of integration weights |

`oobmse0` |
the out-of-bag mean squared error (MSE) without consideration of integration weights |

`oobmrd0` |
the out-of-bag mean relative deviation (MRD) without consideration of integration weights |

`format` |
one of "FDboostLong" or "FDboost" depending on the class of the object |

`fun_ret` |
list of what fun returns if fun was specified |

Use argument `mc.cores = 1L`

to set the numbers of cores that is used in
parallel computation. On Windows only 1 core is possible, `mc.cores = 1`

, which is the default.

`cvrisk`

to perform cross-validation with scalar response.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 | ```
Ytest <- matrix(rnorm(15), ncol = 3) # 5 trajectories, each with 3 observations
Ylong <- as.vector(Ytest)
## 4-folds for bootstrap for the response in long format without integration weights
cvMa(ydim = c(5,3), type = "bootstrap", B = 4)
cvLong(id = rep(1:5, times = 3), type = "bootstrap", B = 4)
if(require(fda)){
## load the data
data("CanadianWeather", package = "fda")
## use data on a daily basis
canada <- with(CanadianWeather,
list(temp = t(dailyAv[ , , "Temperature.C"]),
l10precip = t(dailyAv[ , , "log10precip"]),
l10precip_mean = log(colMeans(dailyAv[ , , "Precipitation.mm"]), base = 10),
lat = coordinates[ , "N.latitude"],
lon = coordinates[ , "W.longitude"],
region = factor(region),
place = factor(place),
day = 1:365, ## corresponds to t: evaluation points of the fun. response
day_s = 1:365)) ## corresponds to s: evaluation points of the fun. covariate
## center temperature curves per day
canada$tempRaw <- canada$temp
canada$temp <- scale(canada$temp, scale = FALSE)
rownames(canada$temp) <- NULL ## delete row-names
## fit the model
mod <- FDboost(l10precip ~ 1 + bolsc(region, df = 4) +
bsignal(temp, s = day_s, cyclic = TRUE, boundary.knots = c(0.5, 365.5)),
timeformula = ~ bbs(day, cyclic = TRUE, boundary.knots = c(0.5, 365.5)),
data = canada)
mod <- mod[75]
## Not run:
#### create folds for 3-fold bootstrap: one weight for each curve
set.seed(123)
folds_bs <- cv(weights = rep(1, mod$ydim[1]), type = "bootstrap", B = 3)
## compute out-of-bag risk on the 3 folds for 1 to 75 boosting iterations
cvr <- applyFolds(mod, folds = folds_bs, grid = 1:75)
## compute out-of-bag risk and coefficient estimates on folds
cvr2 <- validateFDboost(mod, folds = folds_bs, grid = 1:75)
## weights per observation point
folds_bs_long <- folds_bs[rep(1:nrow(folds_bs), times = mod$ydim[2]), ]
attr(folds_bs_long, "type") <- "3-fold bootstrap"
## compute out-of-bag risk on the 3 folds for 1 to 75 boosting iterations
cvr3 <- cvrisk(mod, folds = folds_bs_long, grid = 1:75)
## End(Not run)
## Not run:
## plot the out-of-bag risk
par(mfrow = c(1,3))
plot(cvr); legend("topright", lty=2, paste(mstop(cvr)))
plot(cvr2)
plot(cvr3); legend("topright", lty=2, paste(mstop(cvr3)))
## End(Not run)
## Not run:
## plot the estimated coefficients per fold
## more meaningful for higher number of folds, e.g., B = 100
par(mfrow = c(2,2))
plotPredCoef(cvr2, terms = FALSE, which = 2)
plotPredCoef(cvr2, terms = FALSE, which = 3)
## End(Not run)
## Not run:
## compute out-of-bag risk and predictions for leaving-one-curve-out cross-validation
cvr_jackknife <- validateFDboost(mod, folds = cvLong(unique(mod$id),
type = "curves"), grid = 1:75)
plot(cvr_jackknife)
## plot oob predictions per fold for 3rd effect
plotPredCoef(cvr_jackknife, which = 3)
## plot coefficients per fold for 2nd effect
plotPredCoef(cvr_jackknife, which = 2, terms = FALSE)
## End(Not run)
}
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.