predict.moult: Predict method for moult models

In moult: Models for Analysing Moult in Birds

Predict method for moult models

Description

Predict either the proportion of birds in a certain moult stage (as defined in intervals) on a specified day, the average moult score on a specified day, or start and/or duration of moult for given covariate patterns

Usage

  ## S3 method for class 'moult'
predict(object, newdata, predict.type = "prob", intervals = 0.1, ...)

Arguments

object	moult model objects
newdata	optional dataframe with explanatory variables for which to make predictions. The first column must contain the days (as used when fitting) for which to make predictions.
predict.type	specifies form of predictions, see details.
intervals	length of moult categories for which probabilities/proportions should be calculated. The default (= 0.1) will calculate the probability that a bird will fall in this moult category on the specified day for each of the following categories: 0, (0, 0.1), [0.1, 0.2), [0.2, 0.3), ..., [0.9, 1.0), 1.
...	other arguments passed to the predict method

Details

predict.type has the following options:

"response"

the average moult index (proportion of feather mass grown) for each of the days specified.

"prob"

default, the proportion of birds in each of the moult categories as defined by intervals is predicted.

"duration"

predicts the duration of moult for the covariate combinations defined in newdata, with standard errors. If newdata is not supplied, returns duration of baseline covariate set.

"start"

predicts the mean start date of moult for the covariate combinations defined in newdata, with standard errors. If newdata is not supplied, returns mean start date of baseline covariate set.

"both"

predicts both mean start date of moult and duration of moult for the covariate combinations defined in newdata, with standard errors. Also, covariance of duration and start date estimates is given.

Value

If newdata is missing, the expected moult scores at the observed days are returned.

If predict.type = "response", the expected moult scores at the specified days are returned.

If predict.type = "prob" a matrix of predicted probabilities for being in each of the moult categories defined by intervals.

If predict.type equals "start" or "duration" or "both", the corresponding estimates (with standard errors) for each of the covariate patterns are returned.

Author(s)

[e-mail]

References

Erni, B., Bonnevie, B. T., Oschadleus, H.-D., Altwegg, R. and Underhill, L. G. (2013) moult: An R package to analyze moult in birds. Journal of Statistical Software, 52(8), 1–23. https://www.jstatsoft.org/v52/i08/

Underhill, L. G. and Zucchini, W. (1988) A model for avian primary moult. Ibis 130, 358–372.

Underhill, L. G. and Zucchini, W. and Summers, R. W. (1990) A model for avian primary moult-data types based on migration strategies and an example using the Redshank Tringa totanus. Ibis 132, 118–123.

See Also

moult

Examples

data(weavers)

## convert moult scores to PFMG (proportion feather mass grown)
mscores <- substr(weavers$Moult, 1, 9)
feather.mass <- c(10.4, 10.8, 11.5, 12.8, 14.4, 15.6, 16.3, 15.7, 15.7)
weavers$pfmg <- ms2pfmg(mscores, feather.mass)

## day of year starting 1 August
weavers$day <- date2days(weavers$RDate, dateformat = "yyyy-mm-dd", startmonth = 8)
weavers$ssex <- ifelse(weavers$Sex == 1 | weavers$Sex == 3, "male",
  ifelse(weavers$Sex == 2 | weavers$Sex == 4, "female", NA))
  
mmf <- moult(pfmg ~ day | ssex | ssex, data = weavers, type = 3)
summary(mmf)

## predict duration and start of moult (then both) for males and females
ssex <- c("male", "female")
day <- 150

(p1 <- predict.moult(mmf, newdata = data.frame(day, ssex), predict.type = "duration"))
(p2 <- predict.moult(mmf, newdata = data.frame(day, ssex), predict.type = "start"))
(p3 <- predict.moult(mmf, newdata = data.frame(day, ssex), predict.type = "both"))

moult documentation built on Aug. 30, 2022, 9:06 a.m.