Title: | Diagnostic Tools for INLA Models |
---|---|
Description: | Several functions which can be useful to choose sensible priors and diagnose the fitted model. |
Authors: | Thierry Onkelinx [aut, cre] (<https://orcid.org/0000-0001-8804-4216>, Research Institute for Nature and Forest (INBO)), Research Institute for Nature and Forest (INBO) [cph, fnd] |
Maintainer: | Thierry Onkelinx <[email protected]> |
License: | GPL-3 |
Version: | 0.0.3 |
Built: | 2024-11-03 05:52:51 UTC |
Source: | https://github.com/inbo/inlatools |
The generalised Poisson distribution
dgpoisson(y, mu, phi) rgpoisson(n, mu, phi)
dgpoisson(y, mu, phi) rgpoisson(n, mu, phi)
y |
a vector of positive integers for which to calculate the density |
mu |
a vector of averages for which to calculate the density |
phi |
a single overdispersion parameter |
n |
the number of simulated values |
a matrix with the density for each combination of y
(rows) and mu
(cols)
Other statistics:
dispersion()
,
fitted,inla-method
,
get_observed()
,
residuals,inla-method
Other statistics:
dispersion()
,
fitted,inla-method
,
get_observed()
,
residuals,inla-method
The measure is calculated as the average of the squared Pearson residuals
dispersion(observed, fitted, variance)
dispersion(observed, fitted, variance)
observed |
the observed values |
fitted |
the fitted values |
variance |
the variance of the fitted values |
Other statistics:
dgpoisson()
,
fitted,inla-method
,
get_observed()
,
residuals,inla-method
library(INLA) set.seed(20181202) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) dispersion( observed = get_observed(model), fitted = fitted(model), variance = fitted(model) )
library(INLA) set.seed(20181202) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) dispersion( observed = get_observed(model), fitted = fitted(model), variance = fitted(model) )
Use simulations to check for overdispersion or underdispersion
dispersion_check(object, nsim = 1000) ## S4 method for signature 'inla' dispersion_check(object, nsim = 1000)
dispersion_check(object, nsim = 1000) ## S4 method for signature 'inla' dispersion_check(object, nsim = 1000)
object |
the INLA model |
nsim |
the number of simulation |
Other checks:
distribution_check()
,
fast_aggregation_check()
,
fast_distribution_check()
,
get_anomaly()
library(INLA) set.seed(20181202) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) dc <- dispersion_check(model) str(dc)
library(INLA) set.seed(20181202) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) dc <- dispersion_check(model) str(dc)
Use simulations to compare the observed distribution with the modelled distribution
distribution_check(object, nsim = 1000, seed = 0L) ## S4 method for signature 'inla' distribution_check(object, nsim = 1000, seed = 0L)
distribution_check(object, nsim = 1000, seed = 0L) ## S4 method for signature 'inla' distribution_check(object, nsim = 1000, seed = 0L)
object |
the INLA model |
nsim |
the number of simulation |
seed |
See the same argument in |
Other checks:
dispersion_check()
,
fast_aggregation_check()
,
fast_distribution_check()
,
get_anomaly()
library(INLA) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE), control.compute = list(config = TRUE) ) distribution_check(model, seed = 20181202)
library(INLA) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE), control.compute = list(config = TRUE) ) distribution_check(model, seed = 20181202)
Fast aggregation check Compare the observed and modelled aggregated values.
fast_aggregation_check( object, grouping_vars, fun = sum, remove_na = TRUE, nsim = 1000 ) ## S4 method for signature 'inla' fast_aggregation_check( object, grouping_vars, fun = sum, remove_na = TRUE, nsim = 1000 )
fast_aggregation_check( object, grouping_vars, fun = sum, remove_na = TRUE, nsim = 1000 ) ## S4 method for signature 'inla' fast_aggregation_check( object, grouping_vars, fun = sum, remove_na = TRUE, nsim = 1000 )
object |
the INLA model |
grouping_vars |
character vector of variable names to group by. |
fun |
function to apply to the aggregated values. |
remove_na |
logical. Indicated whether to remove observations where the response variable is a missing values. |
nsim |
the number of simulation |
Other checks:
dispersion_check()
,
distribution_check()
,
fast_distribution_check()
,
get_anomaly()
This check uses the fitted values and thus ignores the uncertainty on the predictions
fast_distribution_check(object, nsim = 1000) ## S4 method for signature 'inla' fast_distribution_check(object, nsim = 1000) ## S4 method for signature 'list' fast_distribution_check(object, nsim = 1000)
fast_distribution_check(object, nsim = 1000) ## S4 method for signature 'inla' fast_distribution_check(object, nsim = 1000) ## S4 method for signature 'list' fast_distribution_check(object, nsim = 1000)
object |
the INLA model |
nsim |
the number of simulation |
Other checks:
dispersion_check()
,
distribution_check()
,
fast_aggregation_check()
,
get_anomaly()
library(INLA) set.seed(20181202) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) fast_distribution_check(model)
library(INLA) set.seed(20181202) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) fast_distribution_check(model)
Extract the fitted values from an INLA model
## S4 method for signature 'inla' fitted(object, ...)
## S4 method for signature 'inla' fitted(object, ...)
object |
an object for which the extraction of model fitted values is meaningful. |
... |
other arguments. |
Other statistics:
dgpoisson()
,
dispersion()
,
get_observed()
,
residuals,inla-method
library(INLA) set.seed(20181202) model <- inla(#' poisson ~ 1, poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) fitted(model)
library(INLA) set.seed(20181202) model <- inla(#' poisson ~ 1, poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) fitted(model)
All distributions share the same latent variable
with
.
generate_data( a = 0, sigma_random = 0.5, n_random = 20, n_replicate = 10, nb_size = 1, b_size = 5, zero_inflation = 0.5 )
generate_data( a = 0, sigma_random = 0.5, n_random = 20, n_replicate = 10, nb_size = 1, b_size = 5, zero_inflation = 0.5 )
a |
the intercept of the latent variable |
sigma_random |
The standard error for the random effect |
n_random |
the number of random effect levels (groups). |
n_replicate |
the number of observation per random effect level. |
nb_size |
the size parameter of the negative binomial distribution.
Passed to the |
b_size |
the size parameter of the binomial distribution. Passed to the
|
zero_inflation |
the probability the the observed value stems for the a point mass in zero. |
The Poisson distribution uses .
The negation binomial distribution uses .
The binomial distribution uses
.
A data.frame
ìd
the id of the random effect.
eta
the latent variable.
zero_inflation
use the point mass in zero.
poisson
the Poisson distributed variable.
zipoisson
the zero-inflated Poisson distributed variable.
negbin
the negative binomial distributed variable.
zinegbin
the zero-inflated negative binomial distributed variable.
binom
the binomial distributed variable.
Other utils:
plot.dispersion_check()
,
plot.distribution_check()
set.seed(20181202) head(generate_data())
set.seed(20181202) head(generate_data())
Returns a named list with an element called observations
and one element
for every random effect.
The random effect components use the name of the random effect.
get_anomaly(object, n = 10) ## S4 method for signature 'inla' get_anomaly(object, n = 20)
get_anomaly(object, n = 10) ## S4 method for signature 'inla' get_anomaly(object, n = 20)
object |
the INLA model |
n |
the number of anomalies per criterion.
Defaults to |
observations
is a subset of the original data.frame.
It contains the rows with the n
largest and n
smallest values of the
Pearson residuals.
The random effect components contain a subset of the random effects.
Here we select the rows with the n
largest and n
lowest values of the
mean.
Other checks:
dispersion_check()
,
distribution_check()
,
fast_aggregation_check()
,
fast_distribution_check()
library(INLA) set.seed(20181202) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) dc <- get_anomaly(model, n = 2) str(dc)
library(INLA) set.seed(20181202) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) dc <- get_anomaly(model, n = 2) str(dc)
get the observed values from the model object
get_observed(object)
get_observed(object)
object |
the INLA model |
Other statistics:
dgpoisson()
,
dispersion()
,
fitted,inla-method
,
residuals,inla-method
library(INLA) set.seed(20181202) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) get_observed(model)
library(INLA) set.seed(20181202) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) get_observed(model)
Plot the results from a dispersion check
## S3 method for class 'dispersion_check' plot(x, y, ...)
## S3 method for class 'dispersion_check' plot(x, y, ...)
x |
a dispersion_check object. Which is the output of
|
y |
currently ignored |
... |
currently ignored |
A \link[ggplot2]{ggplot}
object.
Other utils:
generate_data()
,
plot.distribution_check()
library(INLA) set.seed(20181202) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) dc <- dispersion_check(model) plot(dc)
library(INLA) set.seed(20181202) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) dc <- dispersion_check(model) plot(dc)
Plot the results from a distribution check
## S3 method for class 'distribution_check' plot(x, y, ..., n = FALSE, scales = "fixed")
## S3 method for class 'distribution_check' plot(x, y, ..., n = FALSE, scales = "fixed")
x |
a distribution_check object. Which is the output of
|
y |
currently ignored |
... |
currently ignored |
n |
display the number of observations |
scales |
Should scales be fixed ( |
A \link[ggplot2]{ggplot}
object.
Other utils:
generate_data()
,
plot.dispersion_check()
library(INLA) set.seed(20181202) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) fdc <- fast_distribution_check(model) plot(fdc)
library(INLA) set.seed(20181202) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) fdc <- fast_distribution_check(model) plot(fdc)
Plot Simulated Random Intercepts
## S3 method for class 'sim_iid' plot( x, y, ..., link = c("identity", "log", "logit"), baseline, center = c("mean", "bottom", "top"), quantiles = c(0.025, 0.1, 0.5, 0.9, 0.975) )
## S3 method for class 'sim_iid' plot( x, y, ..., link = c("identity", "log", "logit"), baseline, center = c("mean", "bottom", "top"), quantiles = c(0.025, 0.1, 0.5, 0.9, 0.975) )
x |
A |
y |
Currently ignored. |
... |
Currently ignored. |
link |
Which link to use for back transformation. |
baseline |
Optional baseline for the time series. |
center |
Defines how to centre the time series to the baseline.
Options are: |
quantiles |
Which quantiles are shown on the plot. |
A \link[ggplot2]{ggplot}
object.
Other priors:
plot.sim_rw()
,
select_change()
,
select_divergence()
,
select_poly()
,
select_quantile()
,
simulate_iid()
,
simulate_rw()
set.seed(20181202) x <- simulate_iid(sigma = 0.25) plot(x) plot(x, link = "log") plot(x, link = "logit")
set.seed(20181202) x <- simulate_iid(sigma = 0.25) plot(x) plot(x, link = "log") plot(x, link = "logit")
Plot Simulated Random Walks
## S3 method for class 'sim_rw' plot( x, y, ..., link = c("identity", "log", "logit"), baseline, center = c("start", "mean", "bottom", "top") )
## S3 method for class 'sim_rw' plot( x, y, ..., link = c("identity", "log", "logit"), baseline, center = c("start", "mean", "bottom", "top") )
x |
An |
y |
Currently ignored. |
... |
Currently ignored. |
link |
Which link to use for back transformation. |
baseline |
Optional baseline for the time series. |
center |
Defines how to centre the time series to the baseline.
Options are: |
A \link[ggplot2]{ggplot}
object.
Other priors:
plot.sim_iid()
,
select_change()
,
select_divergence()
,
select_poly()
,
select_quantile()
,
simulate_iid()
,
simulate_rw()
set.seed(20181202) x <- simulate_rw(sigma = 0.05, start = -10, length = 40) plot(x) plot(select_quantile(x)) plot(select_quantile(x), link = "log") plot(select_quantile(x), link = "logit") x <- simulate_rw(sigma = 0.001, start = -10, length = 40, order = 2) plot(x) plot(select_quantile(x)) plot(select_quantile(x), link = "log") plot(select_quantile(x), link = "logit")
set.seed(20181202) x <- simulate_rw(sigma = 0.05, start = -10, length = 40) plot(x) plot(select_quantile(x)) plot(select_quantile(x), link = "log") plot(select_quantile(x), link = "logit") x <- simulate_rw(sigma = 0.001, start = -10, length = 40, order = 2) plot(x) plot(select_quantile(x)) plot(select_quantile(x), link = "log") plot(select_quantile(x), link = "logit")
Convert the posterior marginal of a precision to a standard deviation
prec2sd(marg)
prec2sd(marg)
marg |
A matrix with columns "y" and "x" where "y" is the marginal of the precision. |
A data.frame
with the mean, standard deviation and 2.5%, 25%, 50%,
75% and 97.5% quantiles of the posterior of the standard deviation.
stopifnot(require(INLA)) model <- inla(Sepal.Length ~ Species, data = iris, family = "gaussian") marg <- model$marginals.hyperpar[["Precision for the Gaussian observations"]] prec2sd(marg)
stopifnot(require(INLA)) model <- inla(Sepal.Length ~ Species, data = iris, family = "gaussian") marg <- model$marginals.hyperpar[["Precision for the Gaussian observations"]] prec2sd(marg)
Calculate the Residuals From an INLA Model
## S4 method for signature 'inla' residuals( object, type = c("pearson", "deviance", "working", "response", "partial"), ... )
## S4 method for signature 'inla' residuals( object, type = c("pearson", "deviance", "working", "response", "partial"), ... )
object |
An |
type |
Currently only Pearson residuals are available.
Other types are only listed for compatibility with the default |
... |
Currently ignored. |
Other statistics:
dgpoisson()
,
dispersion()
,
fitted,inla-method
,
get_observed()
library(INLA) set.seed(20181202) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) residuals(model)
library(INLA) set.seed(20181202) model <- inla( poisson ~ 1, family = "poisson", data = data.frame( poisson = rpois(20, lambda = 10), base = 1 ), control.predictor = list(compute = TRUE) ) residuals(model)
Zero altered negative binomial
rzanbinom(n, mu, size, prob, tol = 2e-10)
rzanbinom(n, mu, size, prob, tol = 2e-10)
n |
number of random values to return. |
mu |
alternative parametrization via mean: see ‘Details’. |
size |
target for number of successful trials, or dispersion parameter (the shape parameter of the gamma mixing distribution). Must be strictly positive, need not be integer. |
prob |
the point mass of zero |
tol |
the tolerance for low numbers |
Generate random numbers from a zero-altered Poisson distribution
rzapois(n, lambda, prob, tol = 2e-10)
rzapois(n, lambda, prob, tol = 2e-10)
n |
number of random values to return. |
lambda |
vector of (non-negative) means. |
prob |
the point mass of zero |
tol |
the tolerance for low numbers |
Zero inflated negative binomial
rzinbinom(n, mu, size, prob)
rzinbinom(n, mu, size, prob)
n |
number of random values to return. |
mu |
alternative parametrization via mean: see ‘Details’. |
size |
target for number of successful trials, or dispersion parameter (the shape parameter of the gamma mixing distribution). Must be strictly positive, need not be integer. |
prob |
the mass of extra zero's |
Generate random numbers from a zero-inflated Poisson distribution
rzipois(n, lambda, prob)
rzipois(n, lambda, prob)
n |
number of random values to return. |
lambda |
vector of (non-negative) means. |
prob |
the mass of extra zero's |
sim_rw
ObjectThis functions count the number of changes in direction in each simulation. It returns the subset with the highest number of direction changes
select_change(x, n = 10)
select_change(x, n = 10)
x |
An |
n |
The number of simulations to plot when only a subset is shown. |
Other priors:
plot.sim_iid()
,
plot.sim_rw()
,
select_divergence()
,
select_poly()
,
select_quantile()
,
simulate_iid()
,
simulate_rw()
sim_rw
ObjectThe selection will contain the most extreme simulations base on either the minimum effect or the maximum effect within the simulation.
select_divergence(x, n = 10)
select_divergence(x, n = 10)
x |
An |
n |
The number of simulations to plot when only a subset is shown. |
Other priors:
plot.sim_iid()
,
plot.sim_rw()
,
select_change()
,
select_poly()
,
select_quantile()
,
simulate_iid()
,
simulate_rw()
The target coefficients will be rescaled to have norm 1. The coefficients of the simulations will be rescaled by the largest norm over all simulations.
select_poly(x, coefs = c(0, -1), n = 10)
select_poly(x, coefs = c(0, -1), n = 10)
x |
An |
coefs |
The polynomial coefficients. |
n |
The number of simulations to plot when only a subset is shown. |
Other priors:
plot.sim_iid()
,
plot.sim_rw()
,
select_change()
,
select_divergence()
,
select_quantile()
,
simulate_iid()
,
simulate_rw()
sim_rw
objectselect the quantiles from an sim_rw
object
select_quantile(x, quantiles = c(0.025, 0.1, 0.25, 0.5, 0.75, 0.975))
select_quantile(x, quantiles = c(0.025, 0.1, 0.25, 0.5, 0.75, 0.975))
x |
An |
quantiles |
a vector of quantiles |
Other priors:
plot.sim_iid()
,
plot.sim_rw()
,
select_change()
,
select_divergence()
,
select_poly()
,
simulate_iid()
,
simulate_rw()
simulate data from a second order random walk
simulate_iid(sigma = NULL, tau = NULL, n_sim = 1000)
simulate_iid(sigma = NULL, tau = NULL, n_sim = 1000)
sigma |
the standard deviation of the random intercept |
tau |
the precision of the random intercept |
n_sim |
the number of simulations |
a data.frame with simulated time series from the random walk
Other priors:
plot.sim_iid()
,
plot.sim_rw()
,
select_change()
,
select_divergence()
,
select_poly()
,
select_quantile()
,
simulate_rw()
set.seed(20181202) x <- simulate_iid(sigma = 0.25) head(x)
set.seed(20181202) x <- simulate_iid(sigma = 0.25) head(x)
simulate data from a second order random walk
simulate_rw( sigma = NULL, tau = NULL, length = 10, start = 1, order = 1, n_sim = 1000 )
simulate_rw( sigma = NULL, tau = NULL, length = 10, start = 1, order = 1, n_sim = 1000 )
sigma |
the standard deviation of the random walk process |
tau |
the precision of the random walk process |
length |
the length of the time series |
start |
the starting values of the time series |
order |
1 for first order random walk or 2 for second order random walk |
n_sim |
the number of simulations |
a data.frame with simulated time series from the random walk
Other priors:
plot.sim_iid()
,
plot.sim_rw()
,
select_change()
,
select_divergence()
,
select_poly()
,
select_quantile()
,
simulate_iid()
set.seed(20181202) x <- simulate_rw(sigma = 0.1, start = -10, length = 40) head(x) y <- simulate_rw(sigma = 0.001, start = -10, length = 40, order = 2) head(y)
set.seed(20181202) x <- simulate_rw(sigma = 0.1, start = -10, length = 40) head(x) y <- simulate_rw(sigma = 0.001, start = -10, length = 40, order = 2) head(y)
The type 1 zero-inflated negative binomial distribution is a standard negative binomial distribution with an additional point mass at zero.
The type 1 zero-inflated poisson is a standard Poisson distribution with an additional point mass at zero.
var_nbinom(mu, size) var_zinbinom1(mu, size, zero) var_zipois1(mu, zero)
var_nbinom(mu, size) var_zinbinom1(mu, size, zero) var_zipois1(mu, zero)
mu |
mean of the distribution. Must be on the original scale. |
size |
Size of the negative binomial distribution. Must be strict positive. |
zero |
Probability of the point mass at zero. |