Description Usage Arguments Details Value Examples

View source: R/crossvalidation.R

DEPRECATED!
The function `validateFDboost()`

is deprecated,
use `applyFolds`

and `bootstrapCI`

instead.

1 2 3 4 |

`object` |
fitted FDboost-object |

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

`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 |

`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 |

`showProgress` |
logical, defaults to |

`...` |
further arguments passed to |

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

as they compute
honest, i.e., out-of-bag, estimates of the empirical risk for different numbers of boosting iterations.

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 curve 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 `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 |

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 | ```
## Not run:
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$temp) <- NULL ## delete row-names
## fit the model
mod <- FDboost(l10precip ~ 1 + bolsc(region, df = 4) +
bsignal(temp, s = day_s, cyclic = TRUE, boundary.knots = c(0.5, 365.5)),
timeformula = ~ bbs(day, cyclic = TRUE, boundary.knots = c(0.5, 365.5)),
data = canada)
mod <- mod[75]
#### create folds for 3-fold bootstrap: one weight for each curve
set.seed(123)
folds_bs <- cv(weights = rep(1, mod$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$ydim[2]), ]
attr(folds_bs_long, "type") <- "3-fold bootstrap"
## compute out-of-bag risk on the 3 folds for 1 to 75 boosting iterations
cvr3 <- cvrisk(mod, folds = folds_bs_long, grid = 1:75)
## plot the out-of-bag risk
par(mfrow = c(1,3))
plot(cvr); legend("topright", lty=2, paste(mstop(cvr)))
plot(cvr2)
plot(cvr3); legend("topright", lty=2, paste(mstop(cvr3)))
## plot the estimated coefficients per fold
## more meaningful for higher number of folds, e.g., B = 100
par(mfrow = c(2,2))
plotPredCoef(cvr2, terms = FALSE, which = 2)
plotPredCoef(cvr2, terms = FALSE, which = 3)
## compute out-of-bag risk and predictions for leaving-one-curve-out cross-validation
cvr_jackknife <- validateFDboost(mod, folds = cvLong(unique(mod$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)
``` |

FDboost documentation built on Aug. 6, 2018, 9:04 a.m.

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