prodist {distributions3}R Documentation

Extracting fitted or predicted probability distributions from models


Generic function with methods for various model classes for extracting fitted (in-sample) or predicted (out-of-sample) probability distributions3 objects.


prodist(object, ...)

## S3 method for class 'lm'
prodist(object, ..., sigma = "ML")

## S3 method for class 'glm'
prodist(object, ..., dispersion = NULL)



A model object.


Arguments passed on to methods, typically for calling the underlying predict methods, e.g., newdata for lm or glm objects or n.ahead for arima objects.


character or numeric or NULL. Specification of the standard deviation sigma to be used for the Normal distribution in the lm method. The default "ML" (or equivalently "MLE" or NULL) uses the maximum likelihood estimate based on the residual sum of squares divided by the number of observations, n. Alternatively, sigma = "OLS" uses the least-squares estimate (divided by the residual degrees of freedom, n - k). Finally, a concrete numeric value can also be specified in sigma.


character or numeric or NULL. Specification of the dispersion parameter in the glm method. The default NULL (or equivalently "deviance") is to use the deviance divided by the number of observations, n. Alternatively, dispersion = "Chisquared" uses the Chi-squared statistic divided by the residual degrees of freedom, n - k. Finally, a concrete numeric value can also be specified in dispersion.


To facilitate making probabilistic forecasts based on regression and time series model objects, the function prodist extracts fitted or predicted probability distribution objects. Currently, methods are provided for objects fitted by lm, glm, and arima in base R as well as glm.nb from the MASS package and hurdle/zeroinfl/zerotrunc from the pscl or countreg packages.

All methods essentially proceed in two steps: First, the standard predict method for these model objects is used to compute fitted (in-sample, default) or predicted (out-of-sample) distribution parameters. Typically, this includes the mean plus further parameters describing scale, dispersion, shape, etc.). Second, the distributions objects are set up using the generator functions from distributions3.

Note that these probability distributions only reflect the random variation in the dependent variable based on the model employed (and its associated distributional assumpation for the dependent variable). This does not capture the uncertainty in the parameter estimates.

For both linear regression models and generalized linear models, estimated by lm and glm respectively, there is some ambiguity as to which estimate for the dispersion parameter of the model is to be used. While the logLik methods use the maximum-likelihood (ML) estimate implicitly, the summary methods report an estimate that is standardized with the residual degrees of freedom, n - k (rather than the number of observations, n). The prodist methods for these objects follow the logLik method by default but the summary behavior can be mimicked by setting the sigma or dispersion arguments accordingly.


An object inheriting from distribution.

See Also

predict, lm, glm, arima


## Model: Linear regression
## Fit: lm
## Data: 1920s cars data
data("cars", package = "datasets")

## Stopping distance (ft) explained by speed (mph)
reg <- lm(dist ~ speed, data = cars)

## Extract fitted normal distributions (in-sample, with constant variance)
pd <- prodist(reg)

## Extract log-likelihood from model object

## Replicate log-likelihood via distributions object
sum(log_pdf(pd, cars$dist))
log_likelihood(pd, cars$dist)

## Compute corresponding medians and 90% interval
qd <- quantile(pd, c(0.05, 0.5, 0.95))

## Visualize observations with predicted quantiles
plot(dist ~ speed, data = cars)
matplot(cars$speed, qd, add = TRUE, type = "l", col = 2, lty = 1)

## Sigma estimated by maximum-likelihood estimate (default, used in logLik)
## vs. least-squares estimate (used in summary)
nd <- data.frame(speed = 50)
prodist(reg, newdata = nd, sigma = "ML")
prodist(reg, newdata = nd, sigma = "OLS")

## Model: Poisson generalized linear model
## Fit: glm
## Data: FIFA 2018 World Cup data
data("FIFA2018", package = "distributions3")

## Number of goals per team explained by ability differences
poisreg <- glm(goals ~ difference, data = FIFA2018, family = poisson)
## Interpretation: When the ratio of abilities increases by 1 percent,
## the expected number of goals increases by around 0.4 percent

## Predict fitted Poisson distributions for teams with equal ability (out-of-sample)
nd <- data.frame(difference = 0)
prodist(poisreg, newdata = nd)

## Extract fitted Poisson distributions (in-sample)
pd <- prodist(poisreg)

## Extract log-likelihood from model object

## Replicate log-likelihood via distributions object
sum(log_pdf(pd, FIFA2018$goals))
log_likelihood(pd, FIFA2018$goals)

## Model: Autoregressive integrated moving average model
## Fit: arima
## Data: Quarterly approval ratings of U.S. presidents (1945-1974)
data("presidents", package = "datasets")

## ARMA(2,1) model
arma21 <- arima(presidents, order = c(2, 0, 1))

## Extract predicted normal distributions for next two years
p <- prodist(arma21, n.ahead = 8)

## Compute median (= mean) forecast along with 80% and 95% interval
quantile(p, c(0.5, 0.1, 0.9, 0.025, 0.975))

[Package distributions3 version 0.2.1 Index]