predict.DI {DImodels}  R Documentation 
Predict Method for DiversityInteractions (DI) Models
Description
Generates predictions for a fitted DI models object and, optionally, the associated standard errors for those predictions.
Usage
## S3 method for class 'DI'
predict(object, newdata, se.fit = FALSE,
interval = c("none", "confidence", "prediction"),
level = 0.95, weights = 1,
type = c("link", "response", "terms"), ...)
Arguments
object 

newdata 
optionally, a data frame in which to look for variables with which to predict. If omitted, predictions will be made for data used to fit the model. 
se.fit 
A logical switch indicating whether to calculate the associated standard errors. 
interval 
The type of interval to be calculated. Accepts one of "none", "confidence" or "prediction", with "none"" being the default. 
level 
The level (1  
weights 
The variance weights for calculating the prediction intervals. By default all values get the same weight of 1. Can also specify a numeric vector of same length as number of rows in 
type 
the type of prediction required. One of "link", "response" or "terms". The default "link" is on the scale of the linear predictors while "response" is on the scale of the response variable. The "terms" option returns a matrix giving the fitted values of each term in the model formula on the linear predictor scale. 
... 
further arguments passed to or from other methods. For eg: 
Details
If newdata
doesn't contain all predictors from the model, necessary numeric predictors will be added in with a value of 0, while categorical predictors will be added in with their baseline value. See examples for more information.
Value
if se.fit = FALSE
, a vector of predictions is returned.
if se.fit = TRUE
, a list with the following components is returned.
fit 
Predictions, as for 
se.fit 
Estimated standard error for each prediction 
residual.scale 
A scalar giving the square root of the dispersion used in computing the standard errors. 
Author(s)
Rafael A. Moral, John Connolly, Rishabh Vishwakarma and Caroline Brophy
References
Connolly J, T Bell, T Bolger, C Brophy, T Carnus, JA Finn, L Kirwan, F Isbell, J Levine, A Luescher, V Picasso, C Roscher, MT Sebastia, M Suter and A Weigelt (2013) An improved model to predict the effects of changing biodiversity levels on ecosystem function. Journal of Ecology, 101, 344355.
Kirwan L, J Connolly, JA Finn, C Brophy, A Luescher, D Nyfeler and MT Sebastia (2009) Diversityinteraction modelling  estimating contributions of species identities and interactions to ecosystem function. Ecology, 90, 20322038.
See Also
Examples
## Load the Switzerland data
data(Switzerland)
## Summarise the Switzerland data
summary(Switzerland)
## Fit a DI model
m1 < DI(y = "yield", prop = 4:7, treat = 'nitrogen', DImodel = 'AV',
density = 'density', estimate_theta = TRUE, data = Switzerland)
summary(m1)
## Prediction without newdata, full dataset from model fit will be used
predict(m1, se.fit = TRUE)
## Prediction with newdata
newdata1 < data.frame('p1' = c(1,0), 'p2' = c(0,1), 'p3' = c(0,0), 'p4' = c(0,0),
'nitrogen' = c(50, 150), 'density' = c('low','high'))
predict(m1, newdata = newdata1, se.fit = TRUE)
## If any categorical variable is missing, the baseline level
## of the variable is used for prediction
newdata2 < newdata1[, 5]
print(newdata2)
predict(m1, newdata = newdata2)
## If a numerical variable is missing, the value 0 is used for it
newdata3 < newdata1[, c(3,4)]
print(newdata3)
predict(m1, newdata = newdata3)