predict.BTm {BradleyTerry2} | R Documentation |

## Predict Method for Bradley-Terry Models

### Description

Obtain predictions and optionally standard errors of those predictions from a fitted Bradley-Terry model.

### Usage

```
## S3 method for class 'BTm'
predict(
object,
newdata = NULL,
level = ifelse(is.null(object$random), 0, 1),
type = c("link", "response", "terms"),
se.fit = FALSE,
dispersion = NULL,
terms = NULL,
na.action = na.pass,
...
)
```

### Arguments

`object` |
a fitted object of class |

`newdata` |
(optional) a data frame in which to look for variables with which to predict. If omitted, the fitted linear predictors are used. |

`level` |
for models with random effects: an integer vector giving the
level(s) at which predictions are required. Level zero corresponds to
population-level predictions (fixed effects only), whilst level one
corresponds to the player-level predictions (full model) which are NA for
contests involving players not in the original data. By default, |

`type` |
the type of prediction required. The default is on the scale of
the linear predictors; the alternative |

`se.fit` |
logical switch indicating if standard errors are required. |

`dispersion` |
a value for the dispersion, not used for models with
random effects. If omitted, that returned by |

`terms` |
with |

`na.action` |
function determining what should be done with missing
values in |

`...` |
further arguments passed to or from other methods. |

### Details

If `newdata`

is omitted the predictions are based on the data used for
the fit. In that case how cases with missing values in the original fit are
treated is determined by the `na.action`

argument of that fit. If
`na.action = na.omit`

omitted cases will not appear in the residuals,
whereas if `na.action = na.exclude`

they will appear (in predictions
and standard errors), with residual value `NA`

. See also
`napredict`

.

### Value

If `se.fit = FALSE`

, a vector or matrix of predictions. If
`se = TRUE`

, a list with components

`fit` |
Predictions |

`se.fit` |
Estimated standard errors |

### Author(s)

Heather Turner

### See Also

`predict.glm()`

, `predict.glmmPQL()`

### Examples

```
## The final model in example(flatlizards)
result <- rep(1, nrow(flatlizards$contests))
Whiting.model3 <- BTm(1, winner, loser, ~ throat.PC1[..] + throat.PC3[..] +
head.length[..] + SVL[..] + (1|..),
family = binomial(link = "probit"),
data = flatlizards, trace = TRUE)
## `new' data for contests between four of the original lizards
## factor levels must correspond to original levels, but unused levels
## can be dropped - levels must match rows of predictors
newdata <- list(contests = data.frame(
winner = factor(c("lizard048", "lizard060"),
levels = c("lizard006", "lizard011",
"lizard048", "lizard060")),
loser = factor(c("lizard006", "lizard011"),
levels = c("lizard006", "lizard011",
"lizard048", "lizard060"))
),
predictors = flatlizards$predictors[c(3, 6, 27, 33), ])
predict(Whiting.model3, level = 1, newdata = newdata)
## same as
predict(Whiting.model3, level = 1)[1:2]
## introducing a new lizard
newpred <- rbind(flatlizards$predictors[c(3, 6, 27),
c("throat.PC1","throat.PC3", "SVL", "head.length")],
c(-5, 1.5, 1, 0.1))
rownames(newpred)[4] <- "lizard059"
newdata <- list(contests = data.frame(
winner = factor(c("lizard048", "lizard059"),
levels = c("lizard006", "lizard011",
"lizard048", "lizard059")),
loser = factor(c("lizard006", "lizard011"),
levels = c("lizard006", "lizard011",
"lizard048", "lizard059"))
),
predictors = newpred)
## can only predict at population level for contest with new lizard
predict(Whiting.model3, level = 0:1, se.fit = TRUE, newdata = newdata)
## predicting at specific levels of covariates
## consider a model from example(CEMS)
table6.model <- BTm(outcome = cbind(win1.adj, win2.adj),
player1 = school1, player2 = school2,
formula = ~ .. +
WOR[student] * Paris[..] +
WOR[student] * Milano[..] +
WOR[student] * Barcelona[..] +
DEG[student] * St.Gallen[..] +
STUD[student] * Paris[..] +
STUD[student] * St.Gallen[..] +
ENG[student] * St.Gallen[..] +
FRA[student] * London[..] +
FRA[student] * Paris[..] +
SPA[student] * Barcelona[..] +
ITA[student] * London[..] +
ITA[student] * Milano[..] +
SEX[student] * Milano[..],
refcat = "Stockholm",
data = CEMS)
## estimate abilities for a combination not seen in the original data
## same schools
schools <- levels(CEMS$preferences$school1)
## new student data
students <- data.frame(STUD = "other", ENG = "good", FRA = "good",
SPA = "good", ITA = "good", WOR = "yes", DEG = "no",
SEX = "female", stringsAsFactors = FALSE)
## set levels to be the same as original data
for (i in seq_len(ncol(students))){
students[,i] <- factor(students[,i], levels(CEMS$students[,i]))
}
newdata <- list(preferences =
data.frame(student = factor(500), # new id matching with `students[1,]`
school1 = factor("London", levels = schools),
school2 = factor("Paris", levels = schools)),
students = students,
schools = CEMS$schools)
## warning can be ignored as model specification was over-parameterized
predict(table6.model, newdata = newdata)
## if treatment contrasts are use (i.e. one player is set as the reference
## category), then predicting the outcome of contests against the reference
## is equivalent to estimating abilities with specific covariate values
## add student with all values at reference levels
students <- rbind(students,
data.frame(STUD = "other", ENG = "good", FRA = "good",
SPA = "good", ITA = "good", WOR = "no", DEG = "no",
SEX = "female", stringsAsFactors = FALSE))
## set levels to be the same as original data
for (i in seq_len(ncol(students))){
students[,i] <- factor(students[,i], levels(CEMS$students[,i]))
}
newdata <- list(preferences =
data.frame(student = factor(rep(c(500, 502), each = 6)),
school1 = factor(schools, levels = schools),
school2 = factor("Stockholm", levels = schools)),
students = students,
schools = CEMS$schools)
predict(table6.model, newdata = newdata, se.fit = TRUE)
## the second set of predictions (elements 7-12) are equivalent to the output
## of BTabilities; the first set are adjust for `WOR` being equal to "yes"
BTabilities(table6.model)
```

*BradleyTerry2*version 1.1-2 Index]