Description Usage Arguments Details Value Note See Also Examples

View source: R/crossvalidation.R

Cross-validation and bootstrapping over curves to compute the empirical risk for hyper-parameter selection.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ```
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, compress = FALSE, ...)
## 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 |

`compress` |
logical, defaults to |

`...` |
further arguments passed 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.
It be chosen using the functions `applyFolds`

or `cvrisk.FDboost`

. Those functions
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.

In case of functional response, we recommend to use `applyFolds`

.
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 curve without considering integration weights.

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
curve to enter a fold is equal over all curves.
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 sampling 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 |

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 | ```
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)
## 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(cvr3); legend("topright", lty=2, paste(mstop(cvr3)))
## End(Not run)
}
``` |

FDboost documentation built on May 11, 2018, 1:04 a.m.

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