Skip to contents

Find the Highest Maximum A Posteriori probability estimate (MAP) of a posterior, i.e., the value associated with the highest probability density (the "peak" of the posterior distribution). In other words, it is an estimation of the mode for continuous parameters. Note that this function relies on estimate_density(), which by default uses a different smoothing bandwidth ("SJ") compared to the legacy default implemented the base R density() function ("nrd0").

## Usage

map_estimate(x, ...)

# S3 method for numeric
map_estimate(x, precision = 2^10, method = "kernel", ...)

# S3 method for stanreg
map_estimate(
x,
precision = 2^10,
method = "kernel",
effects = c("fixed", "random", "all"),
component = c("location", "all", "conditional", "smooth_terms", "sigma",
"distributional", "auxiliary"),
parameters = NULL,
...
)

# S3 method for brmsfit
map_estimate(
x,
precision = 2^10,
method = "kernel",
effects = c("fixed", "random", "all"),
component = c("conditional", "zi", "zero_inflated", "all"),
parameters = NULL,
...
)

# S3 method for data.frame
map_estimate(x, precision = 2^10, method = "kernel", ...)

# S3 method for get_predicted
map_estimate(
x,
precision = 2^10,
method = "kernel",
use_iterations = FALSE,
verbose = TRUE,
...
)

## Arguments

x

Vector representing a posterior distribution, or a data frame of such vectors. Can also be a Bayesian model. bayestestR supports a wide range of models (see, for example, methods("hdi")) and not all of those are documented in the 'Usage' section, because methods for other classes mostly resemble the arguments of the .numeric or .data.framemethods.

...

Currently not used.

precision

Number of points of density data. See the n parameter in density.

method

Density estimation method. Can be "kernel" (default), "logspline" or "KernSmooth".

effects

Should results for fixed effects, random effects or both be returned? Only applies to mixed models. May be abbreviated.

component

Should results for all parameters, parameters for the conditional model or the zero-inflated part of the model be returned? May be abbreviated. Only applies to brms-models.

parameters

Regular expression pattern that describes the parameters that should be returned. Meta-parameters (like lp__ or prior_) are filtered by default, so only parameters that typically appear in the summary() are returned. Use parameters to select specific parameters for the output.

use_iterations

Logical, if TRUE and x is a get_predicted object, (returned by insight::get_predicted()), the function is applied to the iterations instead of the predictions. This only applies to models that return iterations for predicted values (e.g., brmsfit models).

verbose

Toggle off warnings.

## Value

A numeric value if x is a vector. If x is a model-object, returns a data frame with following columns:

• Parameter: The model parameter(s), if x is a model-object. If x is a vector, this column is missing.

• MAP_Estimate: The MAP estimate for the posterior or each model parameter.

## Examples

# \donttest{
library(bayestestR)

posterior <- rnorm(10000)
map_estimate(posterior)
#> MAP Estimate
#>
#> Parameter | MAP_Estimate
#> ------------------------
#> x         |         0.06

plot(density(posterior))
abline(v = as.numeric(map_estimate(posterior)), col = "red")

model <- rstanarm::stan_glm(mpg ~ wt + cyl, data = mtcars)
#>
#> SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
#> Chain 1:
#> Chain 1: Gradient evaluation took 2.1e-05 seconds
#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.21 seconds.
#> Chain 1: Adjust your expectations accordingly!
#> Chain 1:
#> Chain 1:
#> Chain 1: Iteration:    1 / 2000 [  0%]  (Warmup)
#> Chain 1: Iteration:  200 / 2000 [ 10%]  (Warmup)
#> Chain 1: Iteration:  400 / 2000 [ 20%]  (Warmup)
#> Chain 1: Iteration:  600 / 2000 [ 30%]  (Warmup)
#> Chain 1: Iteration:  800 / 2000 [ 40%]  (Warmup)
#> Chain 1: Iteration: 1000 / 2000 [ 50%]  (Warmup)
#> Chain 1: Iteration: 1001 / 2000 [ 50%]  (Sampling)
#> Chain 1: Iteration: 1200 / 2000 [ 60%]  (Sampling)
#> Chain 1: Iteration: 1400 / 2000 [ 70%]  (Sampling)
#> Chain 1: Iteration: 1600 / 2000 [ 80%]  (Sampling)
#> Chain 1: Iteration: 1800 / 2000 [ 90%]  (Sampling)
#> Chain 1: Iteration: 2000 / 2000 [100%]  (Sampling)
#> Chain 1:
#> Chain 1:  Elapsed Time: 0.047 seconds (Warm-up)
#> Chain 1:                0.045 seconds (Sampling)
#> Chain 1:                0.092 seconds (Total)
#> Chain 1:
#>
#> SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
#> Chain 2:
#> Chain 2: Gradient evaluation took 1.1e-05 seconds
#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds.
#> Chain 2: Adjust your expectations accordingly!
#> Chain 2:
#> Chain 2:
#> Chain 2: Iteration:    1 / 2000 [  0%]  (Warmup)
#> Chain 2: Iteration:  200 / 2000 [ 10%]  (Warmup)
#> Chain 2: Iteration:  400 / 2000 [ 20%]  (Warmup)
#> Chain 2: Iteration:  600 / 2000 [ 30%]  (Warmup)
#> Chain 2: Iteration:  800 / 2000 [ 40%]  (Warmup)
#> Chain 2: Iteration: 1000 / 2000 [ 50%]  (Warmup)
#> Chain 2: Iteration: 1001 / 2000 [ 50%]  (Sampling)
#> Chain 2: Iteration: 1200 / 2000 [ 60%]  (Sampling)
#> Chain 2: Iteration: 1400 / 2000 [ 70%]  (Sampling)
#> Chain 2: Iteration: 1600 / 2000 [ 80%]  (Sampling)
#> Chain 2: Iteration: 1800 / 2000 [ 90%]  (Sampling)
#> Chain 2: Iteration: 2000 / 2000 [100%]  (Sampling)
#> Chain 2:
#> Chain 2:  Elapsed Time: 0.055 seconds (Warm-up)
#> Chain 2:                0.052 seconds (Sampling)
#> Chain 2:                0.107 seconds (Total)
#> Chain 2:
#>
#> SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
#> Chain 3:
#> Chain 3: Gradient evaluation took 9e-06 seconds
#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds.
#> Chain 3: Adjust your expectations accordingly!
#> Chain 3:
#> Chain 3:
#> Chain 3: Iteration:    1 / 2000 [  0%]  (Warmup)
#> Chain 3: Iteration:  200 / 2000 [ 10%]  (Warmup)
#> Chain 3: Iteration:  400 / 2000 [ 20%]  (Warmup)
#> Chain 3: Iteration:  600 / 2000 [ 30%]  (Warmup)
#> Chain 3: Iteration:  800 / 2000 [ 40%]  (Warmup)
#> Chain 3: Iteration: 1000 / 2000 [ 50%]  (Warmup)
#> Chain 3: Iteration: 1001 / 2000 [ 50%]  (Sampling)
#> Chain 3: Iteration: 1200 / 2000 [ 60%]  (Sampling)
#> Chain 3: Iteration: 1400 / 2000 [ 70%]  (Sampling)
#> Chain 3: Iteration: 1600 / 2000 [ 80%]  (Sampling)
#> Chain 3: Iteration: 1800 / 2000 [ 90%]  (Sampling)
#> Chain 3: Iteration: 2000 / 2000 [100%]  (Sampling)
#> Chain 3:
#> Chain 3:  Elapsed Time: 0.052 seconds (Warm-up)
#> Chain 3:                0.049 seconds (Sampling)
#> Chain 3:                0.101 seconds (Total)
#> Chain 3:
#>
#> SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
#> Chain 4:
#> Chain 4: Gradient evaluation took 9e-06 seconds
#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.09 seconds.
#> Chain 4: Adjust your expectations accordingly!
#> Chain 4:
#> Chain 4:
#> Chain 4: Iteration:    1 / 2000 [  0%]  (Warmup)
#> Chain 4: Iteration:  200 / 2000 [ 10%]  (Warmup)
#> Chain 4: Iteration:  400 / 2000 [ 20%]  (Warmup)
#> Chain 4: Iteration:  600 / 2000 [ 30%]  (Warmup)
#> Chain 4: Iteration:  800 / 2000 [ 40%]  (Warmup)
#> Chain 4: Iteration: 1000 / 2000 [ 50%]  (Warmup)
#> Chain 4: Iteration: 1001 / 2000 [ 50%]  (Sampling)
#> Chain 4: Iteration: 1200 / 2000 [ 60%]  (Sampling)
#> Chain 4: Iteration: 1400 / 2000 [ 70%]  (Sampling)
#> Chain 4: Iteration: 1600 / 2000 [ 80%]  (Sampling)
#> Chain 4: Iteration: 1800 / 2000 [ 90%]  (Sampling)
#> Chain 4: Iteration: 2000 / 2000 [100%]  (Sampling)
#> Chain 4:
#> Chain 4:  Elapsed Time: 0.05 seconds (Warm-up)
#> Chain 4:                0.053 seconds (Sampling)
#> Chain 4:                0.103 seconds (Total)
#> Chain 4:
map_estimate(model)
#> MAP Estimate
#>
#> Parameter   | MAP_Estimate
#> --------------------------
#> (Intercept) |        39.51
#> wt          |        -3.24
#> cyl         |        -1.39

model <- brms::brm(mpg ~ wt + cyl, data = mtcars)
#> Compiling Stan program...
#> Start sampling
#>
#> SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
#> Chain 1:
#> Chain 1: Gradient evaluation took 7e-06 seconds
#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.07 seconds.
#> Chain 1: Adjust your expectations accordingly!
#> Chain 1:
#> Chain 1:
#> Chain 1: Iteration:    1 / 2000 [  0%]  (Warmup)
#> Chain 1: Iteration:  200 / 2000 [ 10%]  (Warmup)
#> Chain 1: Iteration:  400 / 2000 [ 20%]  (Warmup)
#> Chain 1: Iteration:  600 / 2000 [ 30%]  (Warmup)
#> Chain 1: Iteration:  800 / 2000 [ 40%]  (Warmup)
#> Chain 1: Iteration: 1000 / 2000 [ 50%]  (Warmup)
#> Chain 1: Iteration: 1001 / 2000 [ 50%]  (Sampling)
#> Chain 1: Iteration: 1200 / 2000 [ 60%]  (Sampling)
#> Chain 1: Iteration: 1400 / 2000 [ 70%]  (Sampling)
#> Chain 1: Iteration: 1600 / 2000 [ 80%]  (Sampling)
#> Chain 1: Iteration: 1800 / 2000 [ 90%]  (Sampling)
#> Chain 1: Iteration: 2000 / 2000 [100%]  (Sampling)
#> Chain 1:
#> Chain 1:  Elapsed Time: 0.022 seconds (Warm-up)
#> Chain 1:                0.019 seconds (Sampling)
#> Chain 1:                0.041 seconds (Total)
#> Chain 1:
#>
#> SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 2).
#> Chain 2:
#> Chain 2: Gradient evaluation took 4e-06 seconds
#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.04 seconds.
#> Chain 2: Adjust your expectations accordingly!
#> Chain 2:
#> Chain 2:
#> Chain 2: Iteration:    1 / 2000 [  0%]  (Warmup)
#> Chain 2: Iteration:  200 / 2000 [ 10%]  (Warmup)
#> Chain 2: Iteration:  400 / 2000 [ 20%]  (Warmup)
#> Chain 2: Iteration:  600 / 2000 [ 30%]  (Warmup)
#> Chain 2: Iteration:  800 / 2000 [ 40%]  (Warmup)
#> Chain 2: Iteration: 1000 / 2000 [ 50%]  (Warmup)
#> Chain 2: Iteration: 1001 / 2000 [ 50%]  (Sampling)
#> Chain 2: Iteration: 1200 / 2000 [ 60%]  (Sampling)
#> Chain 2: Iteration: 1400 / 2000 [ 70%]  (Sampling)
#> Chain 2: Iteration: 1600 / 2000 [ 80%]  (Sampling)
#> Chain 2: Iteration: 1800 / 2000 [ 90%]  (Sampling)
#> Chain 2: Iteration: 2000 / 2000 [100%]  (Sampling)
#> Chain 2:
#> Chain 2:  Elapsed Time: 0.021 seconds (Warm-up)
#> Chain 2:                0.019 seconds (Sampling)
#> Chain 2:                0.04 seconds (Total)
#> Chain 2:
#>
#> SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 3).
#> Chain 3:
#> Chain 3: Gradient evaluation took 3e-06 seconds
#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds.
#> Chain 3: Adjust your expectations accordingly!
#> Chain 3:
#> Chain 3:
#> Chain 3: Iteration:    1 / 2000 [  0%]  (Warmup)
#> Chain 3: Iteration:  200 / 2000 [ 10%]  (Warmup)
#> Chain 3: Iteration:  400 / 2000 [ 20%]  (Warmup)
#> Chain 3: Iteration:  600 / 2000 [ 30%]  (Warmup)
#> Chain 3: Iteration:  800 / 2000 [ 40%]  (Warmup)
#> Chain 3: Iteration: 1000 / 2000 [ 50%]  (Warmup)
#> Chain 3: Iteration: 1001 / 2000 [ 50%]  (Sampling)
#> Chain 3: Iteration: 1200 / 2000 [ 60%]  (Sampling)
#> Chain 3: Iteration: 1400 / 2000 [ 70%]  (Sampling)
#> Chain 3: Iteration: 1600 / 2000 [ 80%]  (Sampling)
#> Chain 3: Iteration: 1800 / 2000 [ 90%]  (Sampling)
#> Chain 3: Iteration: 2000 / 2000 [100%]  (Sampling)
#> Chain 3:
#> Chain 3:  Elapsed Time: 0.022 seconds (Warm-up)
#> Chain 3:                0.018 seconds (Sampling)
#> Chain 3:                0.04 seconds (Total)
#> Chain 3:
#>
#> SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 4).
#> Chain 4:
#> Chain 4: Gradient evaluation took 3e-06 seconds
#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.03 seconds.
#> Chain 4: Adjust your expectations accordingly!
#> Chain 4:
#> Chain 4:
#> Chain 4: Iteration:    1 / 2000 [  0%]  (Warmup)
#> Chain 4: Iteration:  200 / 2000 [ 10%]  (Warmup)
#> Chain 4: Iteration:  400 / 2000 [ 20%]  (Warmup)
#> Chain 4: Iteration:  600 / 2000 [ 30%]  (Warmup)
#> Chain 4: Iteration:  800 / 2000 [ 40%]  (Warmup)
#> Chain 4: Iteration: 1000 / 2000 [ 50%]  (Warmup)
#> Chain 4: Iteration: 1001 / 2000 [ 50%]  (Sampling)
#> Chain 4: Iteration: 1200 / 2000 [ 60%]  (Sampling)
#> Chain 4: Iteration: 1400 / 2000 [ 70%]  (Sampling)
#> Chain 4: Iteration: 1600 / 2000 [ 80%]  (Sampling)
#> Chain 4: Iteration: 1800 / 2000 [ 90%]  (Sampling)
#> Chain 4: Iteration: 2000 / 2000 [100%]  (Sampling)
#> Chain 4:
#> Chain 4:  Elapsed Time: 0.024 seconds (Warm-up)
#> Chain 4:                0.021 seconds (Sampling)
#> Chain 4:                0.045 seconds (Total)
#> Chain 4:
map_estimate(model)
#> MAP Estimate
#>
#> Parameter   | MAP_Estimate
#> --------------------------
#> b_Intercept |        39.67
#> b_wt        |        -3.06
#> b_cyl       |        -1.58
# }