vignettes/posterior.Rmd
posterior.RmdThe posterior R package is intended to provide useful tools for both users and developers of packages for fitting Bayesian models or working with output from Bayesian models. The primary goals of the package are to:
You can install the latest official release version via
install.packages("posterior")or the latest development version from GitHub via
# install.packages("remotes")
remotes::install_github("stan-dev/posterior")## This is posterior version 1.6.0##
## Attaching package: 'posterior'## The following objects are masked from 'package:stats':
##
## mad, sd, var## The following objects are masked from 'package:base':
##
## %in%, matchTo demonstrate how to work with the posterior package, throughout the
rest of this vignette we will use example posterior draws obtained from
the eight schools hierarchical meta-analysis model described in Gelman
et al. (2013). The variables are an estimate per school
(theta[1] through theta[8]) as well as an
overall mean (mu) and standard deviation across schools
(tau).
eight_schools_array <- example_draws("eight_schools")
print(eight_schools_array, max_variables = 3)## # A draws_array: 100 iterations, 4 chains, and 10 variables
## , , variable = mu
##
## chain
## iteration 1 2 3 4
## 1 2.0 3.0 1.79 6.5
## 2 1.5 8.2 5.99 9.1
## 3 5.8 -1.2 2.56 0.2
## 4 6.8 10.9 2.79 3.7
## 5 1.8 9.8 -0.03 5.5
##
## , , variable = tau
##
## chain
## iteration 1 2 3 4
## 1 2.8 2.80 8.7 3.8
## 2 7.0 2.76 2.9 6.8
## 3 9.7 0.57 8.4 5.3
## 4 4.8 2.45 4.4 1.6
## 5 2.8 2.80 11.0 3.0
##
## , , variable = theta[1]
##
## chain
## iteration 1 2 3 4
## 1 3.96 6.26 13.3 5.78
## 2 0.12 9.32 6.3 2.09
## 3 21.25 -0.97 10.6 15.72
## 4 14.70 12.45 5.4 2.69
## 5 5.96 9.75 8.2 -0.91
##
## # ... with 95 more iterations, and 7 more variablesThe structure of this object is explained in the next section.
Because different formats are preferable in different situations, posterior supports multiple formats and easy conversion between them. The currently supported formats are:
draws_array: An iterations by chains by variables
array.draws_matrix: A draws (iterations x chains) by
variables array.draws_df: A draws by variables data frame with addition
meta columns .chain, .iteration,
.draw.draws_list: A list with one sublist per chain. Each
sublist is a named list with one vector of iterations per variable.draws_rvars: A list of random variable
rvar objects, one per variable. See
vignette("rvar") for an introduction to this new data
type.These formats are essentially base R object classes and can be used
as such. For example, a draws_matrix object is just a
matrix with a little more consistency (e.g., no dropping of
dimensions with one level when indexing) and additional methods. The
exception to this is the draws_rvars format, which contains
rvar objects that behave somewhat like arrays but are
really a unique data type. See the separate vignette on the
rvar and draws_rvars data types for
details.
The draws for our example come as a draws_array object
with 100 iterations, 4 chains, and 10 variables:
str(eight_schools_array)## 'draws_array' num [1:100, 1:4, 1:10] 2.01 1.46 5.81 6.85 1.81 ...
## - attr(*, "dimnames")=List of 3
## ..$ iteration: chr [1:100] "1" "2" "3" "4" ...
## ..$ chain : chr [1:4] "1" "2" "3" "4"
## ..$ variable : chr [1:10] "mu" "tau" "theta[1]" "theta[2]" ...Each of the formats has a method as_draws_<format>
(e.g., as_draws_list()) for creating an object of the class
from any of the other formats. As a demonstration we can convert the
example draws_array to a draws_df, a data
frame with additional meta information. To convert to a
draws_df we use as_draws_df().
eight_schools_df <- as_draws_df(eight_schools_array)
str(eight_schools_df)## draws_df [400 × 13] (S3: draws_df/draws/tbl_df/tbl/data.frame)
## $ mu : num [1:400] 2.01 1.46 5.81 6.85 1.81 ...
## $ tau : num [1:400] 2.77 6.98 9.68 4.79 2.85 ...
## $ theta[1] : num [1:400] 3.962 0.124 21.251 14.7 5.96 ...
## $ theta[2] : num [1:400] 0.271 -0.069 14.931 8.586 1.156 ...
## $ theta[3] : num [1:400] -0.743 0.952 1.829 2.675 3.109 ...
## $ theta[4] : num [1:400] 2.1 7.28 1.38 4.39 1.99 ...
## $ theta[5] : num [1:400] 0.923 -0.062 0.531 4.758 0.769 ...
## $ theta[6] : num [1:400] 1.65 11.26 7.16 8.1 4.66 ...
## $ theta[7] : num [1:400] 3.32 9.62 14.8 9.49 1.21 ...
## $ theta[8] : num [1:400] 4.85 -8.64 -1.74 5.28 -4.54 ...
## $ .chain : int [1:400] 1 1 1 1 1 1 1 1 1 1 ...
## $ .iteration: int [1:400] 1 2 3 4 5 6 7 8 9 10 ...
## $ .draw : int [1:400] 1 2 3 4 5 6 7 8 9 10 ...
print(eight_schools_df)## # A draws_df: 100 iterations, 4 chains, and 10 variables
## mu tau theta[1] theta[2] theta[3] theta[4] theta[5] theta[6]
## 1 2.01 2.8 3.96 0.271 -0.74 2.1 0.923 1.7
## 2 1.46 7.0 0.12 -0.069 0.95 7.3 -0.062 11.3
## 3 5.81 9.7 21.25 14.931 1.83 1.4 0.531 7.2
## 4 6.85 4.8 14.70 8.586 2.67 4.4 4.758 8.1
## 5 1.81 2.8 5.96 1.156 3.11 2.0 0.769 4.7
## 6 3.84 4.1 5.76 9.909 -1.00 5.3 5.889 -1.7
## 7 5.47 4.0 4.03 4.151 10.15 6.6 3.741 -2.2
## 8 1.20 1.5 -0.28 1.846 0.47 4.3 1.467 3.3
## 9 0.15 3.9 1.81 0.661 0.86 4.5 -1.025 1.1
## 10 7.17 1.8 6.08 8.102 7.68 5.6 7.106 8.5
## # ... with 390 more draws, and 2 more variables
## # ... hidden reserved variables {'.chain', '.iteration', '.draw'}draws formats
The example draws already come in a format natively supported by posterior, but we can of course also import the draws from other sources like common base R objects.
In addition to converting other draws objects to the
draws_matrix format, the as_draws_matrix()
function will convert a regular matrix to a
draws_matrix.
x <- matrix(rnorm(50), nrow = 10, ncol = 5)
colnames(x) <- paste0("V", 1:5)
x <- as_draws_matrix(x)
print(x)## # A draws_matrix: 10 iterations, 1 chains, and 5 variables
## variable
## draw V1 V2 V3 V4 V5
## 1 -1.14 -1.386 0.54 -0.83 0.700
## 2 -1.52 2.124 -0.35 0.64 1.078
## 3 -2.01 -1.062 0.40 0.94 -0.071
## 4 0.31 -0.032 1.69 0.55 -0.071
## 5 -0.63 -1.580 0.83 0.69 -0.870
## 6 0.12 0.687 1.76 -0.25 -0.448
## 7 -0.25 0.278 0.79 0.68 2.251
## 8 0.98 0.932 -1.02 0.45 2.170
## 9 -0.30 -0.384 -0.12 1.34 0.434
## 10 -0.38 -0.872 -2.81 -0.36 -0.379Because the matrix was converted to a draws_matrix, all
of the methods for working with draws objects described in
subsequent sections of this vignette will now be available.
Instead of as_draws_matrix() we also could have just
used as_draws(), which attempts to find the closest
available format to the input object. In this case the result would be a
draws_matrix object either way.
In addition to the as_draws_matrix() converter function
there is also a draws_matrix() constructor function that
can be used to create draws matrix from multiple vectors.
x <- draws_matrix(alpha = rnorm(50), beta = rnorm(50))
print(x)## # A draws_matrix: 50 iterations, 1 chains, and 2 variables
## variable
## draw alpha beta
## 1 -0.044 -0.885
## 2 -1.048 1.247
## 3 0.983 0.725
## 4 1.390 1.201
## 5 -1.002 -0.693
## 6 0.247 -1.470
## 7 1.265 -0.074
## 8 0.113 -0.132
## 9 -0.094 0.310
## 10 -0.794 -0.014
## # ... with 40 more drawsAnalogous functions exist for the other draws formats and are used similarly.
draws objects
The posterior package provides many methods for manipulating draws objects in useful ways. In this section we demonstrate several of the most commonly used methods. These methods, like the other methods in posterior, are available for every supported draws format.
Subsetting draws objects can be done according to
various aspects of the draws (iterations, chains, or variables). The
posterior package provides a convenient interface for this purpose via
subset_draws(). For example, here is the code to extract
the first five iterations of the first two chains of the variable
mu.
sub_df <- subset_draws(eight_schools_df, variable = "mu", chain = 1:2, iteration = 1:5)
str(sub_df)## draws_df [10 × 4] (S3: draws_df/draws/tbl_df/tbl/data.frame)
## $ mu : num [1:10] 2.01 1.46 5.81 6.85 1.81 ...
## $ .chain : int [1:10] 1 1 1 1 1 2 2 2 2 2
## $ .iteration: int [1:10] 1 2 3 4 5 1 2 3 4 5
## $ .draw : int [1:10] 1 2 3 4 5 6 7 8 9 10The same call to subset_draws() can be used regardless
of the draws format. For example, here is the same code except replacing
the draws_df object with the draws_array
object.
sub_arr <- subset_draws(eight_schools_array, variable = "mu", chain = 1:2, iteration = 1:5)
str(sub_arr)## 'draws_array' num [1:5, 1:2, 1] 2.01 1.46 5.81 6.85 1.81 ...
## - attr(*, "dimnames")=List of 3
## ..$ iteration: chr [1:5] "1" "2" "3" "4" ...
## ..$ chain : chr [1:2] "1" "2"
## ..$ variable : chr "mu"We can check that these two calls to subset_draws() (the
first with the data frame, the second with the array) produce the same
result.
identical(sub_df, as_draws_df(sub_arr))
identical(as_draws_array(sub_df), sub_arr)## [1] TRUE
## [1] TRUEIt is also possible to use standard R subsetting syntax with
draws objects. The following is equivalent to the use of
subset_draws() with the array above.
eight_schools_array[1:5, 1:2, "mu"]## # A draws_array: 5 iterations, 2 chains, and 1 variables
## , , variable = mu
##
## chain
## iteration 1 2
## 1 2.0 3.0
## 2 1.5 8.2
## 3 5.8 -1.2
## 4 6.8 10.9
## 5 1.8 9.8The major difference between how posterior behaves when indexing and
how base R behaves is that posterior will not drop dimensions
with only one level. That is, even though there is only one variable
left after subsetting, the result of the subsetting above is still a
draws_array and not a draws_matrix.
The magic of having obtained draws from the joint posterior (or
prior) distribution of a set of variables is that these draws can also
be used to obtain draws from any other variable that is a function of
the original variables. That is, if we are interested in the posterior
distribution of, say, phi = (mu + tau)^2 all we have to do
is to perform the transformation for each of the individual draws to
obtain draws from the posterior distribution of the transformed
variable. This procedure is handled by
mutate_variables().
x <- mutate_variables(eight_schools_df, phi = (mu + tau)^2)
x <- subset_draws(x, c("mu", "tau", "phi"))
print(x)## # A draws_df: 100 iterations, 4 chains, and 3 variables
## mu tau phi
## 1 2.01 2.8 22.8
## 2 1.46 7.0 71.2
## 3 5.81 9.7 240.0
## 4 6.85 4.8 135.4
## 5 1.81 2.8 21.7
## 6 3.84 4.1 62.8
## 7 5.47 4.0 88.8
## 8 1.20 1.5 7.1
## 9 0.15 3.9 16.6
## 10 7.17 1.8 79.9
## # ... with 390 more draws
## # ... hidden reserved variables {'.chain', '.iteration', '.draw'}To rename variables use rename_variables(). Here we
rename the scalar mu to mean and the vector
theta to alpha.
# mu is a scalar, theta is a vector
x <- rename_variables(eight_schools_df, mean = mu, alpha = theta)
variables(x)## [1] "mean" "tau" "alpha[1]" "alpha[2]" "alpha[3]" "alpha[4]"
## [7] "alpha[5]" "alpha[6]" "alpha[7]" "alpha[8]"In the call to rename_variables() above, mu
and theta can be quoted or unquoted.
It is also possible to rename individual elements of non-scalar
parameters, for example we can rename just the first element of
alpha:
x <- rename_variables(x, a1 = `alpha[1]`)
variables(x)## [1] "mean" "tau" "a1" "alpha[2]" "alpha[3]" "alpha[4]"
## [7] "alpha[5]" "alpha[6]" "alpha[7]" "alpha[8]"The bind_draws() method can be used to combine
draws objects along different dimensions. As an example,
suppose we have several different draws_matrix objects:
x1 <- draws_matrix(alpha = rnorm(5), beta = rnorm(5))
x2 <- draws_matrix(alpha = rnorm(5), beta = rnorm(5))
x3 <- draws_matrix(theta = rexp(5))We can bind x1 and x3 together along the
'variable' dimension to get a single
draws_matrix with the variables from both x1
and x3:
x4 <- bind_draws(x1, x3, along = "variable")
print(x4)## # A draws_matrix: 5 iterations, 1 chains, and 3 variables
## variable
## draw alpha beta theta
## 1 0.793 -0.073 0.22
## 2 0.483 0.267 0.19
## 3 0.331 0.238 6.60
## 4 -0.837 1.301 0.47
## 5 0.066 0.722 1.33Because x1 and x2 have the same variables,
we can bind them along the 'draw' dimension to create a
single draws_matrix with more draws:
x5 <- bind_draws(x1, x2, along = "draw")
print(x5)## # A draws_matrix: 10 iterations, 1 chains, and 2 variables
## variable
## draw alpha beta
## 1 0.793 -0.073
## 2 0.483 0.267
## 3 0.331 0.238
## 4 -0.837 1.301
## 5 0.066 0.722
## 6 1.374 1.284
## 7 -0.061 -0.212
## 8 -0.386 -0.052
## 9 -1.356 0.061
## 10 0.627 -0.815As with all posterior methods, bind_draws() can be used
with all draws formats and depending on the format different dimensions
are available to bind on. For example, we can bind
draws_array objects together by iteration,
chain, or variable, but a 2-D
draws_matrix with the chains combined can only by bound by
draw and variable.
Computing summaries of posterior or prior draws and convergence
diagnostics for posterior draws are some of the most common tasks when
working with Bayesian models fit using Markov Chain Monte Carlo (MCMC)
methods. The posterior package provides a flexible interface for this
purpose via summarise_draws() (or
summarize_draws()), which can be passed any of the formats
supported by the package.
# summarise_draws or summarize_draws
summarise_draws(eight_schools_df)## # A tibble: 10 × 10
## variable mean median sd mad q5 q95 rhat ess_bulk ess_tail
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 mu 4.18 4.16 3.40 3.57 -0.854 9.39 1.02 558. 322.
## 2 tau 4.16 3.07 3.58 2.89 0.309 11.0 1.01 246. 202.
## 3 theta[1] 6.75 5.97 6.30 4.87 -1.23 18.9 1.01 400. 254.
## 4 theta[2] 5.25 5.13 4.63 4.25 -1.97 12.5 1.02 564. 372.
## 5 theta[3] 3.04 3.99 6.80 4.94 -10.3 11.9 1.01 312. 205.
## 6 theta[4] 4.86 4.99 4.92 4.51 -3.57 12.2 1.02 695. 252.
## 7 theta[5] 3.22 3.72 5.08 4.38 -5.93 10.8 1.01 523. 306.
## 8 theta[6] 3.99 4.14 5.16 4.81 -4.32 11.5 1.02 548. 205.
## 9 theta[7] 6.50 5.90 5.26 4.54 -1.19 15.4 1.00 434. 308.
## 10 theta[8] 4.57 4.64 5.25 4.89 -3.79 12.2 1.02 355. 146.The result is a data frame with one row per variable and one column
per summary statistic or convergence diagnostic. The summaries
rhat, ess_bulk, and ess_tail are
described in Vehtari et al. (2020). We can choose which summaries to
compute by passing additional arguments, either functions or names of
functions. For instance, if we only wanted the mean and its
corresponding Monte Carlo Standard Error (MCSE) we could use either of
these options:
# the function mcse_mean is provided by the posterior package
s1 <- summarise_draws(eight_schools_df, "mean", "mcse_mean")
s2 <- summarise_draws(eight_schools_df, mean, mcse_mean)
identical(s1, s2)## [1] TRUE
print(s1)## # A tibble: 10 × 3
## variable mean mcse_mean
## <chr> <dbl> <dbl>
## 1 mu 4.18 0.150
## 2 tau 4.16 0.213
## 3 theta[1] 6.75 0.319
## 4 theta[2] 5.25 0.202
## 5 theta[3] 3.04 0.447
## 6 theta[4] 4.86 0.189
## 7 theta[5] 3.22 0.232
## 8 theta[6] 3.99 0.222
## 9 theta[7] 6.50 0.250
## 10 theta[8] 4.57 0.273The column names in the output can be changed by providing the
functions as name-value pairs, where the name is the name to use in the
output and the value is a function name or definition. For example, here
we change the names mean and sd to
posterior_mean and posterior_sd.
summarise_draws(eight_schools_df, posterior_mean = mean, posterior_sd = sd)## # A tibble: 10 × 3
## variable posterior_mean posterior_sd
## <chr> <dbl> <dbl>
## 1 mu 4.18 3.40
## 2 tau 4.16 3.58
## 3 theta[1] 6.75 6.30
## 4 theta[2] 5.25 4.63
## 5 theta[3] 3.04 6.80
## 6 theta[4] 4.86 4.92
## 7 theta[5] 3.22 5.08
## 8 theta[6] 3.99 5.16
## 9 theta[7] 6.50 5.26
## 10 theta[8] 4.57 5.25For a function to work with summarise_draws(), it needs
to take a vector or matrix of numeric values and return a single numeric
value or a named vector of numeric values. Additional arguments to the
function can be specified in a list passed to the .args
argument.
weighted_mean <- function(x, wts) {
sum(x * wts)/sum(wts)
}
summarise_draws(
eight_schools_df,
weighted_mean,
.args = list(wts = rexp(ndraws(eight_schools_df)))
)## # A tibble: 10 × 2
## variable weighted_mean
## <chr> <dbl>
## 1 mu 4.13
## 2 tau 4.07
## 3 theta[1] 6.93
## 4 theta[2] 5.54
## 5 theta[3] 3.35
## 6 theta[4] 5.03
## 7 theta[5] 3.23
## 8 theta[6] 3.52
## 9 theta[7] 6.59
## 10 theta[8] 4.58It is also possible to specify a summary function using a one-sided
formula that follows the conventions supported by
rlang::as_function(). For example, the function
can be simplified to
# for multiple arguments `.x` and `.y` can be used, see ?rlang::as_function
~quantile(., probs = c(0.4, 0.6))Both can be used with summarise_draws() and produce the
same output:
summarise_draws(eight_schools_df, function(x) quantile(x, probs = c(0.4, 0.6)))## # A tibble: 10 × 3
## variable `40%` `60%`
## <chr> <dbl> <dbl>
## 1 mu 3.41 5.35
## 2 tau 2.47 3.96
## 3 theta[1] 4.95 7.01
## 4 theta[2] 4.32 6.13
## 5 theta[3] 2.54 5.33
## 6 theta[4] 3.78 6.11
## 7 theta[5] 2.69 4.69
## 8 theta[6] 2.92 5.47
## 9 theta[7] 4.81 7.33
## 10 theta[8] 3.50 5.92
summarise_draws(eight_schools_df, ~quantile(.x, probs = c(0.4, 0.6)))## # A tibble: 10 × 3
## variable `40%` `60%`
## <chr> <dbl> <dbl>
## 1 mu 3.41 5.35
## 2 tau 2.47 3.96
## 3 theta[1] 4.95 7.01
## 4 theta[2] 4.32 6.13
## 5 theta[3] 2.54 5.33
## 6 theta[4] 3.78 6.11
## 7 theta[5] 2.69 4.69
## 8 theta[6] 2.92 5.47
## 9 theta[7] 4.81 7.33
## 10 theta[8] 3.50 5.92See help("as_function", "rlang") for details on
specifying these functions.
In addition to the default diagnostic functions used by
summarise_draws() (rhat(),
ess_bulk(), ess_tail()), posterior also
provides additional diagnostics like effective sample sizes and Monte
Carlo standard errors for quantiles and standard deviations, an
experimental new diagnostic called R*, and others. For a list of
available diagnostics and links to their individual help pages see
help("diagnostics", "posterior").
If you have suggestions for additional diagnostics that should be implemented in posterior, please open an issue at https://github.com/stan-dev/posterior/issues.
draws objects
In addition to the methods demonstrated in this vignette, posterior
has various other methods available for working with draws
objects. The following is a (potentially incomplete) list.
| Method | Description |
|---|---|
order_draws() |
Order draws objects according to iteration
and chain number |
repair_draws() |
Repair indices of draws objects so that
iterations chains, and draws are continuously and consistently
numbered |
resample_draws() |
Resample draws objects according to
provided weights |
thin_draws() |
Thin draws objects to reduce size and
autocorrelation |
weight_draws() |
Add weights to draws objects, with one weight per draw, for use in subsequent weighting operations |
extract_variable() |
Extract a vector of draws of a single variable |
extract_variable_matrix() |
Extract an iterations x chains matrix of draws of a single variable |
merge_chains() |
Merge chains of draws objects into a
single chain. |
split_chains() |
Split chains of draws objects by halving
the number of iterations per chain and doubling the number of
chains. |
If you have suggestions for additional methods that would be useful
for working with draws objects, please open an issue at https://github.com/stan-dev/posterior/issues.
Gelman A., Carlin J. B., Stern H. S., David B. Dunson D. B., Vehtari, A., & Rubin D. B. (2013). Bayesian Data Analysis, Third Edition. Chapman and Hall/CRC.
Vehtari A., Gelman A., Simpson D., Carpenter B., & Bürkner P. C. (2020). Rank-normalization, folding, and localization: An improved Rhat for assessing convergence of MCMC. Bayesian Analysis, 16(2):667-718.