`R/estimate_smooth.R`

`estimate_smooth.Rd`

This function summarises the smooth term trend in terms of linear segments. Using the aproximative derivative, it separates a non-linear vector into quasi-linear segments (in which the trend is either positive or negative). Each of this segment its characterized by its beginning, end, size (in proportion, relative to the total size) trend (the linear regression coefficient) and linearity (the R2 of the linear regression).

estimate_smooth(model, smooth = NULL, levels = NULL, ...)

model | A Bayesian model. |
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smooth | A character indicating the name of the "smooth" term |

levels | A character vector indicating the variables over which the slope will be computed. If NULL (default), it will select all the remaining predictors. |

... | Arguments passed to or from other methods. |

A dataframe of linear description of non-linear terms.

library(modelbased) # \donttest{ if (require("rstanarm")) { model <- stan_gamm4(Sepal.Width ~ s(Petal.Length), data = iris, refresh = 0) estimate_smooth(model) model <- stan_glm(Sepal.Width ~ poly(Petal.Length, 2), data = iris) estimate_smooth(model) model <- stan_gamm4(Sepal.Width ~ Species + s(Petal.Length), data = iris) estimate_smooth(model) model <- stan_glm(Sepal.Width ~ Species * poly(Petal.Length, 2), data = iris) estimate_smooth(model) estimate_smooth(model, levels = "Species") } #> No numeric variable was specified for smooth analysis. Selecting `smooth = "Petal.Length"`. #> #> SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1). #> Chain 1: #> Chain 1: Gradient evaluation took 2.4e-05 seconds #> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.24 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: 0.053597 seconds (Warm-up) #> Chain 1: 0.067017 seconds (Sampling) #> Chain 1: 0.120614 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2). #> Chain 2: #> Chain 2: Gradient evaluation took 1.4e-05 seconds #> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.14 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: 0.053366 seconds (Warm-up) #> Chain 2: 0.066255 seconds (Sampling) #> Chain 2: 0.119621 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3). #> Chain 3: #> Chain 3: Gradient evaluation took 1.3e-05 seconds #> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.13 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: 0.051518 seconds (Warm-up) #> Chain 3: 0.065962 seconds (Sampling) #> Chain 3: 0.11748 seconds (Total) #> Chain 3: #> #> SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4). #> Chain 4: #> Chain 4: Gradient evaluation took 1.3e-05 seconds #> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.13 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: 0.055439 seconds (Warm-up) #> Chain 4: 0.065808 seconds (Sampling) #> Chain 4: 0.121247 seconds (Total) #> Chain 4: #> No numeric variable was specified for smooth analysis. Selecting `smooth = "Petal.Length"`. #> #> SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1). #> Chain 1: #> Chain 1: Gradient evaluation took 2.9e-05 seconds #> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.29 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: 1.18212 seconds (Warm-up) #> Chain 1: 0.797304 seconds (Sampling) #> Chain 1: 1.97942 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2). #> Chain 2: #> Chain 2: Gradient evaluation took 1.7e-05 seconds #> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.17 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: 1.16491 seconds (Warm-up) #> Chain 2: 1.11407 seconds (Sampling) #> Chain 2: 2.27899 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3). #> Chain 3: #> Chain 3: Gradient evaluation took 1.7e-05 seconds #> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.17 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: 1.08878 seconds (Warm-up) #> Chain 3: 1.13334 seconds (Sampling) #> Chain 3: 2.22213 seconds (Total) #> Chain 3: #> #> SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4). #> Chain 4: #> Chain 4: Gradient evaluation took 1.8e-05 seconds #> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.18 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: 1.16016 seconds (Warm-up) #> Chain 4: 1.41319 seconds (Sampling) #> Chain 4: 2.57335 seconds (Total) #> Chain 4: #> No numeric variable was specified for smooth analysis. Selecting `smooth = "Petal.Length"`. #> #> SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1). #> Chain 1: #> Chain 1: Gradient evaluation took 2.5e-05 seconds #> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.25 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: 1.44984 seconds (Warm-up) #> Chain 1: 1.62203 seconds (Sampling) #> Chain 1: 3.07187 seconds (Total) #> Chain 1: #> #> SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2). #> Chain 2: #> Chain 2: Gradient evaluation took 1.3e-05 seconds #> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.13 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: 1.37103 seconds (Warm-up) #> Chain 2: 1.13734 seconds (Sampling) #> Chain 2: 2.50836 seconds (Total) #> Chain 2: #> #> SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3). #> Chain 3: #> Chain 3: Gradient evaluation took 1.5e-05 seconds #> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.15 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: 1.56589 seconds (Warm-up) #> Chain 3: 1.47395 seconds (Sampling) #> Chain 3: 3.03984 seconds (Total) #> Chain 3: #> #> SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4). #> Chain 4: #> Chain 4: Gradient evaluation took 1.4e-05 seconds #> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.14 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: 1.39898 seconds (Warm-up) #> Chain 4: 1.4297 seconds (Sampling) #> Chain 4: 2.82867 seconds (Total) #> Chain 4: #> No numeric variable was specified for smooth analysis. Selecting `smooth = "Petal.Length"`. #> No numeric variable was specified for smooth analysis. Selecting `smooth = "Petal.Length"`. #> Species | Part | Start | End | Size | Trend | Linearity #> ------------------------------------------------------------- #> setosa | 1 | 1.00 | 2.31 | 30.00% | 0.14 | 0.99 #> setosa | 2 | 2.31 | 6.90 | 70.00% | -0.13 | 0.76 #> versicolor | 1 | 1.00 | 6.90 | 100% | 0.26 | 0.92 #> virginica | 1 | 1.00 | 5.59 | 80.00% | 0.52 | 0.96 #> virginica | 2 | 5.59 | 6.90 | 20.00% | | # }