Merge branch 'main' into scrutin_test

Author: strengejacke

.github/CODE_OF_CONDUCT.md

@@ -59,7 +59,7 @@ representative at an online or offline event.
 ## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported to the community leaders responsible for enforcement at d.luedecke@uke.de. 
+reported to the community leaders responsible for enforcement at d.luedecke@uke.de.
 All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the
@@ -121,6 +121,6 @@ Community Impact Guidelines were inspired by
 [Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
 
 For answers to common questions about this code of conduct, see the FAQ at
-<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+<https://www.contributor-covenant.org/faq/>. Translations are available at <https://www.contributor-covenant.org/translations/>.
 
 [homepage]: https://www.contributor-covenant.org

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: insight
 Title: Easy Access to Model Information for Various Model Objects
-Version: 1.5.0.1
+Version: 1.5.1.4
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",
@@ -90,6 +90,7 @@ Suggests:
     BayesFactor,
     bayestestR,
     bbmle,
+    BSDA,
     bdsmatrix,
     betareg,
     biglm,
@@ -223,9 +224,9 @@ VignetteBuilder:
     knitr
 Encoding: UTF-8
 Language: en-US
-RoxygenNote: 7.3.3
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 Config/Needs/website: easystats/easystatstemplate
 Config/Needs/check: stan-dev/cmdstanr
+Config/roxygen2/version: 8.0.0

GEMINI.md

@@ -12,18 +12,14 @@ This document outlines the common coding conventions observed in the `easystats`
 
 *   If pull requests include user-visible changes, the "developer" version number should be increased (e.g. from 0.10.1.5 to 0.10.1.6). This ensures that `easystats::install_latest()` will download the latest versions.
 
+* For the NEWS file, the current development version should not be indicated by a version number, but rather with `(devel)`.
+
 ## Code Style & Formatting
 
 *   **Assignment:** Use the `<-` operator for assignment, not `=`.
 *   **Spacing:**
     *   Use spaces around all infix operators (`<-`, `==`, `+`, etc.).
     *   Place a space after a comma, but not before.
-*   **Curly Braces:**
-    *   For function definitions, the opening `{` should be on the same line
-        as the closing `)` of that function definition. That can be on the
-        same line as the function definition itself, but might be on a new
-        line if the argument list is too long for one line.
-    *   For `if`/`else` statements, the opening `{` can be on the same line.
 *   **Line Length:** Keep lines to a reasonable length (e.g., under 80-100 characters) to improve readability.
 
 ## Function Naming
@@ -70,8 +66,9 @@ All exported functions must be documented using `roxygen2`-style comments (`#'`)
 
 *   Use base-R wherever possible (to reduce hard dependencies)
 *   Make sure R-version requirements are not too strict
-*   **Package Functions:** Always use the `::` operator to call functions from other packages (e.g., `stats::shapiro.test`, `insight::model_info`). Do not use `library()` or `require()` at the top of a file (no full import, only selective import of functions).
+*   **Package Functions:** Always use the `::` operator to call functions from other packages (e.g., `stats::shapiro.test`, `insight::model_info`). Do not use `library()` or `require()` at the top of a file (no full import, only selective import of functions). However, in test files, package vignettes (.rmd), or in the package documentation, `::` is not required for core R packages like `stats` or `tools`.
 *   **Conditional Checks:** Use `insight::check_if_installed("pkg_name")` to check if a package is available before using it, especially for optional ("Suggests") dependencies.
+*   **Argument validation:** Use `insight::validate_argument()` instead of `match.arg()` to validate correct input of arguments, unless you need `several.ok`. In this case, rely on `match.arg()`.
 
 ## S3 Object System
 
@@ -83,7 +80,11 @@ All exported functions must be documented using `roxygen2`-style comments (`#'`)
 
 *   Use `tryCatch` for operations that might fail. The internal `.safe()` helper is a good example.
 *   Use the `insight` package's functions for user-facing messages:
-    *   `insight::format_error()`
-    *   `insight::format_warning()`
-    *   `insight::format_alert()`
-    *   `insight::print_color()`
+    *   For errors: `insight::format_error()`
+    *   For warnings: `insight::format_warning()`
+    *   For messages: `insight::format_alert()`
+    *   To highlight messages: `insight::print_color()`
+    Note that character vectors are not pasted together, unlike in `message()`,
+    thus you usually want to use something like `paste()` to concatenate the
+    string. Character vectors will add a new paragraph for each string element,
+    not paste them together.

NAMESPACE

@@ -40,6 +40,7 @@ S3method(ellipsis_info,default)
 S3method(find_algorithm,Arima)
 S3method(find_algorithm,BBmm)
 S3method(find_algorithm,BBreg)
+S3method(find_algorithm,CmdStanFit)
 S3method(find_algorithm,Gam)
 S3method(find_algorithm,LORgee)
 S3method(find_algorithm,MixMod)
@@ -206,6 +207,7 @@ S3method(find_parameters,BBmm)
 S3method(find_parameters,BBreg)
 S3method(find_parameters,BFBayesFactor)
 S3method(find_parameters,BGGM)
+S3method(find_parameters,CmdStanFit)
 S3method(find_parameters,DirichletRegModel)
 S3method(find_parameters,Gam)
 S3method(find_parameters,HLfit)
@@ -503,6 +505,7 @@ S3method(get_data,meta_random)
 S3method(get_data,metaplus)
 S3method(get_data,mhurdle)
 S3method(get_data,mipo)
+S3method(get_data,mira)
 S3method(get_data,mixed)
 S3method(get_data,mixor)
 S3method(get_data,mjoint)
@@ -704,6 +707,7 @@ S3method(get_parameters,BBmm)
 S3method(get_parameters,BBreg)
 S3method(get_parameters,BFBayesFactor)
 S3method(get_parameters,BGGM)
+S3method(get_parameters,CmdStanFit)
 S3method(get_parameters,DirichletRegModel)
 S3method(get_parameters,Gam)
 S3method(get_parameters,HLfit)
@@ -1179,6 +1183,7 @@ S3method(get_varcov,glmx)
 S3method(get_varcov,hglm)
 S3method(get_varcov,hurdle)
 S3method(get_varcov,ivFixed)
+S3method(get_varcov,lavaan)
 S3method(get_varcov,lcmm)
 S3method(get_varcov,list)
 S3method(get_varcov,lmRob)
@@ -1244,6 +1249,10 @@ S3method(get_weights,svycoxph)
 S3method(get_weights,svyglm)
 S3method(get_weights,svyolr)
 S3method(get_weights,svysurvreg)
+S3method(has_intercept,default)
+S3method(has_intercept,felm)
+S3method(has_intercept,fepois)
+S3method(has_intercept,fixest)
 S3method(is_converged,"_glm")
 S3method(is_converged,default)
 S3method(is_converged,glm)
@@ -1881,6 +1890,21 @@ S3method(text_remove_backticks,matrix)
 S3method(trim_ws,data.frame)
 S3method(trim_ws,default)
 S3method(trim_ws,list)
+S3method(vcovFPC,clm)
+S3method(vcovFPC,clm2)
+S3method(vcovFPC,default)
+S3method(vcovFPC,glm)
+S3method(vcovFPC,glmRob)
+S3method(vcovFPC,glmmTMB)
+S3method(vcovFPC,glmrob)
+S3method(vcovFPC,lm)
+S3method(vcovFPC,lmRob)
+S3method(vcovFPC,lm_robust)
+S3method(vcovFPC,merMod)
+S3method(vcovFPC,model_fit)
+S3method(vcovFPC,polr)
+S3method(vcovFPC,speedglm)
+S3method(vcovFPC,speedlm)
 export(all_models_equal)
 export(all_models_same_class)
 export(broom_columns)
@@ -2007,3 +2031,4 @@ export(supported_models)
 export(text_remove_backticks)
 export(trim_ws)
 export(validate_argument)
+export(vcovFPC)

NEWS.md

@@ -2,9 +2,53 @@
 
 ## Changes
 
+* Major performance improvement for `compact_list` on very large, nested list
+  objects.
+
+* `get_varcov()` now explicitly works for `lavaan` objects.
+
+## Bug fixes
+
+* `get_modelmatrix()` now correctly handles *brms* models fitted with
+  `0 + Intercept` formulas.
+
+* `get_priors()` did not return degrees of freedom for Student's t-distribution
+  for *rstanarm* models.
+
+# insight 1.5.1
+
+## Changes
+
+* New support for `CmdStanFit` models from the *cmdstanr* package -
+  `find_algorithm()`, `find_parameters()`, and `get_parameters()` now work with
+  these models.
+
+* `model_info()` now correctly detects t- and z-tests from package *BSDA*.
+
+* `format_bf()` gains a `digits` argument.
+
 * More informative error message when the response variable in `get_response()`
   is not present in the data.
 
+* `format_table()` now also formats columns for tail and bulk ESS from Bayesian
+  models.
+
+* `get_data()` now supports objects of class `mira` from package *mice*.
+
+* `get_varcov()` now supports the option `"fpc"` to apply finite population
+  correction (Lai et al. 2018).
+
+* Added a new function, `vcovFPC()`, to calculate finite-population-adjusted
+  variance-covariance matrices.
+
+## Bug fixes
+
+* `has_intercept()` now correctly detects whether models from packages *fixest*
+  and *lfe* have intercepts or not.
+
+* The `vcov` argument in `get_varcov()` was ignored when `vcov` was of class
+  `"dpoMatrix"` and did not return `TRUE` to `is.matrix()`.
+
 # insight 1.5.0
 
 ## Changes

R/find_algorithm.R

@@ -347,3 +347,13 @@ find_algorithm.brmsfit <- function(x, ...) {
     warmup = info$warmup
   )
 }
+
+#' @export
+find_algorithm.CmdStanFit <- function(x, ...) {
+  check_if_installed("cmdstanr")
+  md <- x$metadata()
+  out <- md[c("method", "num_chains", "iter_sampling", "iter_warmup")]
+  names(out) <- c("algorithm", "chains", "iterations", "warmup")
+  out$chains <- out$chains * length(md$id)
+  out
+}

R/find_parameters_bayesian.R

@@ -557,3 +557,18 @@ find_parameters.stanfit <- function(
     l
   }
 }
+
+#' @export
+find_parameters.CmdStanFit <- function(x, flatten = FALSE, ...) {
+  check_if_installed("cmdstanr")
+  md <- x$metadata()
+
+  v <- md$variables
+  # v <- md$stan_variables
+
+  v <- setdiff(v, "lp__")
+  if (isTRUE(flatten)) {
+    return(v)
+  }
+  list(conditional = v)
+}

R/format_bf.R

@@ -9,6 +9,8 @@
 #' @param inferiority_star String, indicating the symbol that is used to
 #'   indicate inferiority, i.e. when the Bayes Factor is smaller than one third
 #'   (the thresholds are smaller than one third, 1/10 and 1/30).
+#' @param digits Number of significant digits. Can also be `"scientific"` (which
+#' is identical to `exact = TRUE`).
 #' @inheritParams format_p
 #'
 #' @return A formatted string.
@@ -30,10 +32,12 @@ format_bf <- function(
   name = "BF",
   protect_ratio = FALSE,
   na_reference = NA,
-  exact = FALSE
+  exact = FALSE,
+  digits = NULL
 ) {
+  bad_bf <- is.na(bf)
   if (is.na(na_reference)) {
-    bf[bad_bf <- is.na(bf)] <- 1
+    bf[bad_bf] <- 1
   } else {
     bf[is.na(bf)] <- na_reference
   }
@@ -47,16 +51,30 @@ format_bf <- function(
     is_small <- logical(length(bf))
   }
 
-  digits <- ifelse(is.na(bf), 0, ifelse(bf < 1, 3, 2)) # nolint
+  # digis = scientific is the same as exact = TRUE
+  if (identical(digits, "scientific")) {
+    exact <- TRUE
+    digits <- NULL
+  }
+
+  if (is.null(digits) || is.character(digits)) {
+    digits <- ifelse(is.na(bf), 0, ifelse(bf < 1, 3, 2))
+  }
 
   bf_text <- paste0(
     "= ",
     ifelse(is_small, "1/", ""),
     format_value(bf, digits = digits)
   )
 
+  # what is extreme small?
+  extreme_small <- (10^max(digits))
+  if (extreme_small < 1000) {
+    extreme_small <- 1000
+  }
+
   ## Very big/small values
-  is_extreme <- bf_orig > 1000 | bf_orig < 1 / 1000
+  is_extreme <- bf_orig > 1000 | bf_orig < 1 / extreme_small
   if (any(is_extreme)) {
     if (exact) {
       bf_text[is_extreme] <- ifelse(
@@ -65,9 +83,9 @@ format_bf <- function(
         bf_text[is_extreme]
       )
       bf_text[is_extreme] <- ifelse(
-        bf_orig[is_extreme] < 1 / 1000,
+        bf_orig[is_extreme] < 1 / extreme_small,
         ifelse(
-          is_small[is_extreme], # nolint
+          is_small[is_extreme],
           sprintf("= 1/%.2e", bf[is_extreme]),
           sprintf("= %.2e", bf_orig[is_extreme])
         ),
@@ -80,8 +98,15 @@ format_bf <- function(
         bf_text[is_extreme]
       )
       bf_text[is_extreme] <- ifelse(
-        bf_orig[is_extreme] < 1 / 1000,
-        ifelse(is_small[is_extreme], "< 1/1000", "< 0.001"), # nolint
+        bf_orig[is_extreme] < 1 / extreme_small,
+        ifelse(
+          is_small[is_extreme],
+          paste0("< 1/", extreme_small),
+          paste0(
+            "< ",
+            format_value(1 / extreme_small, digits = round(log10(extreme_small)))
+          )
+        ),
         bf_text[is_extreme]
       )
     }
@@ -93,20 +118,20 @@ format_bf <- function(
     paste0(bf_text, "***"),
     ifelse(
       bf_orig > 10,
-      paste0(bf_text, "**"), # nolint
-      ifelse(bf_orig > 3, paste0(bf_text, "*"), bf_text) # nolint
+      paste0(bf_text, "**"),
+      ifelse(bf_orig > 3, paste0(bf_text, "*"), bf_text)
     )
   )
 
   ## Add inferiority stars
   if (!is.null(inferiority_star)) {
     bf_text <- ifelse(
       bf_orig < (1 / 30),
-      paste0(bf_text, paste(rep_len(inferiority_star, 3), collapse = "")), # nolint
+      paste0(bf_text, paste(rep_len(inferiority_star, 3), collapse = "")),
       ifelse(
         bf_orig < 0.1,
-        paste0(bf_text, paste(rep_len(inferiority_star, 2), collapse = "")), # nolint
-        ifelse(bf_orig < (1 / 3), paste0(bf_text, inferiority_star), bf_text) # nolint
+        paste0(bf_text, paste(rep_len(inferiority_star, 2), collapse = "")),
+        ifelse(bf_orig < (1 / 3), paste0(bf_text, inferiority_star), bf_text)
       )
     )
   }

R/format_table.R

@@ -802,6 +802,13 @@ format_table <- function(
   if ("ESS" %in% names(x)) {
     x$ESS <- round(x$ESS)
   }
+  if ("ESS_tail" %in% names(x)) {
+    x$ESS_tail <- round(x$ESS_tail)
+  }
+  if ("ESS_bulk" %in% names(x)) {
+    x$ESS_bulk <- round(x$ESS_bulk)
+  }
+  colnames(x) <- gsub("^ESS_(.*)$", "ESS (\\1)", colnames(x))
 
   if ("ROPE_Equivalence" %in% names(x)) {
     names(x)[names(x) == "ROPE_Equivalence"] <- "Equivalence (ROPE)"