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insight: A Unified Interface to Access Information from Model Objects in R |
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05 June 2019 |
paper.bib |
When fitting any statistical model, there are many useful pieces of information that are simultaneously calculated and stored beyond coefficient estimates and general model fit statistics. Although there exist some generic functions to obtain model information and data, many package-specific modeling functions do not provide such methods to allow users to access such valuable information.
insight is an R-package [@rcore] that fills this important gap by providing a suite of functions to support almost any model (see a list of the many models supported below in the Supported Models section). The goal of insight, then, is to offer tools that provide easy, intuitive, and consistent access to information contained in model objects. These tools aid applied researchers in virtually any field who fit, diagnose, and present statistical models by streamlining access to every aspect of model objects via consistent syntax and output.
Ultimately, the development of insight is in line with the philosophy of the easystats project, which is to facilitate and streamline the process of statistical analysis, interpreting and reporting the results in the R programming language.
Built with non-programmers in mind, insight offers a broad toolbox for making model and data information easily accessible. While insight offers many useful functions for working with and understanding model objects (discussed below), we suggest users start with model_info(), as this function provides a clean and consistent overview of model objects (e.g., functional form of the model, the model family, link function, number of observations, variables included in the specification, etc.). With a clear understanding of the model introduced, users are able to adapt other insight functions for more nuanced exploration of and interaction with virtually any model object.
Building on this starting place, the remainder of the package revolves around two key prefixes: get_* and find_*. The get_* prefix extracts values (or data) associated with model-specific objects (e.g., parameters or variables), while the find_* prefix lists model-specific objects (e.g., priors or predictors). These are powerful families of functions allowing for great flexibility in use, whether at a high, descriptive level (find_*) or narrower level of statistical inspection and reporting (get_*).
\pagebreak
In total, the insight package includes 16 core functions (see Figure 1): get_data(), get_priors(), get_variance(), get_parameters(), get_predictors(), get_random(), get_response(), find_algorithm(), find_formula(), find_variables(), find_terms(), find_parameters(), find_predictors(), find_random(), find_response(), and model_info(). In all cases, users must supply at a minimum, the name of the fitted model object. In several functions, there are additional arguments that allow for more targeted returns of model information. For example, the find_variables() function's effects argument allows for the extraction of "fixed effects" terms, "random effects" terms, or by default, "all" terms in the model object. We point users to the package documentation or the complementary package website, https://easystats.github.io/insight/, for a detailed list of the arguments associated with each function as well as the returned values from each function.
\pagebreak
The functions from insight address different components of models. In an effort to avoid confusion about specific "targets" of each function, in this section we provide a short explanation of insight's definitions of regression model components (see Figures 2 and 3). For detailed examples, we point users to the accompanying package website.
The dataset used to fit the model.
Values estimated or learned from data that capture the relationship between variables. In regression models, these are usually referred to as coefficients.
- response: the outcome or response variable (dependent variable) of a regression model.
- predictors: independent variables of (the fixed part of) a regression model. For mixed models, variables that are only in the random effects part (i.e. grouping factors) of the model are not returned as predictors by default. However, these can be included using additional arguments in the function call, treating predictors as "unique". As such, if a variable appears as a fixed effect and a random slope, it is treated as one (the same) predictor.
Any unique variable names that appear in a regression model, e.g., response variable, predictors or random effects. A "variable" only relates to the unique occurence of a term, or the term name. For instance, the expression x + poly(x, 2) has only the variable x.
\pagebreak
Terms themselves consist of variable and factor names separated by operators, or involve arithmetic expressions. For instance, the expression x + poly(x, 2) has one variable x, but two terms x and poly(x, 2).
- random slopes: variables that are specified as random slopes in a mixed effects model.
- random or grouping factors: variables that are specified as grouping variables in a mixed effects model.
For a more intuitive introduction, consider the following examples for three major types of models: ordinary least squares (OLS) regression, linear mixed effects models, and Bayesian models. Importantly, though only a few functions are included below for the sake of space, users are encouraged to inspect the package documentation for an exhaustive list of package functionality with accompanying examples.
# Load the "insight" package
install.packages("insight")
library(insight)
# Sample model 1: OLS
sample1 <- lm(mpg ~ cyl + wt + hp, data = mtcars)
get_parameters(sample1)
#> parameter estimate
#> 1 (Intercept) 38.7517874
#> 2 cyl -0.9416168
#> 3 wt -3.1669731
#> 4 hp -0.0180381
find_algorithm(sample1)
#> $algorithm
#> [1] "OLS"
find_formula(sample1)
#> $conditional
#> mpg ~ cyl + wt + hp
# Sample model 2: Linear Mixed Effects (via lme4)
sample2 <- lme4::lmer(
Reaction ~ Days + (Days | Subject),
data = sleepstudy
)
get_parameters(sample2)
#> parameter estimate
#> 1 (Intercept) 251.40510
#> 2 Days 10.46729
find_algorithm(sample2)
#> $algorithm
#> [1] "REML"
#>
#> $optimizer
#> [1] "nloptwrap"
find_formula(sample2)
#> $conditional
#> Reaction ~ Days
#>
#> $random
#> ~Days | Subject
# Sample model 3: Bayesian (via rstanarm)
sample3 <- rstanarm::stan_glm(
Sepal.Width ~ Species * Petal.Length,
data = iris
)
get_priors(sample3)
#> parameter distribution location scale
#> 1 (Intercept) normal 0 10.0
#> 2 Speciesversicolor normal 0 2.5
#> 3 Speciesvirginica normal 0 2.5
#> 4 Petal.Length normal 0 2.5
#> 5 Speciesversicolor:Petal.Length normal 0 2.5
#> 6 Speciesvirginica:Petal.Length normal 0 2.5
find_algorithm(sample3)
#> $algorithm
#> [1] "sampling"
#>
#> $chains
#> [1] 4
#>
#> $iterations
#> [1] 2000
#>
#> $warmup
#> [1] 1000
find_formula(sample3)
#> $conditional
#> Sepal.Width ~ Species * Petal.Lengthinsight is already used by different packages to solve problems that typically occur when the users' inputs are different model objects of varying complexity, e.g. ggeffects [@ludecke_ggeffects_2018], the sjPlot-package [@pkg_sjPlot], bayestestR [@pkg_bayestestR] and the performance-package [@pkg_performance]. We point users to the get started-vignette for further details and examples.
insight works with many different model-objects (from various packages), such as AER (ivreg, tobit), afex (mixed), aod (betabin, negbin), base (aov, aovlist, lm, glm), BayesFactor (BFBayesFactor), betareg (betareg), biglm (biglm, bigglm), blme (blmer, bglmer), brms (brmsfit), censReg, crch, countreg (zerontrunc), coxme, estimatr (lm_robust, iv_robust), feisr (feis), gam (Gam), gamm4 , gamlss, gbm, gee, geepack (geeglm), GLMMadaptive (MixMod), glmmTMB (glmmTMB), gmnl, HRQoL (BBreg, BBmm), lfe (felm), lme4 (lmer, glmer, nlmer, glmer.nb), MASS (glmmPQL, polr), mgcv (gam, gamm), multgee (LORgee), nnet (multinom), nlme (lme, gls), ordinal (clm, clm2, clmm), panelr (wbm), plm, pscl (zeroinf, hurdle), quantreg (rq, crq, rqss), rms (lsr, ols, psm), robust (glmRob, lmRob), robustbase (glmrob, lmrob), robustlmm (rlmer), rstanarm (stanreg, stanmvreg), speedlm (speedlm, speedglm), survey, survival (coxph, survreg), truncreg (truncreg), VGAM (vgam, vglm), and more.
insight is licensed under the GNU General Public License (v3.0), with all source code stored at GitHub (https://github.com/easystats/insight), with a corresponding issue tracker for bug-reporting and feature enhancements. In the spirit of open science and research, we encourage interaction with our package through requests/tips for fixes, support for additional model objects, feature updates, as well as general questions and concerns via direct interaction with contributors and developers.