make sure we have uniform get_predicted methods

easystats · Oct 2, 2023 · 7080574 · 7080574
1 parent ea13b35
commit 7080574
Show file tree

Hide file tree

Showing 22 changed files with 354 additions and 48 deletions.
diff --git a/R/bci.R b/R/bci.R
@@ -257,14 +257,19 @@ bci.BFBayesFactor <- function(x, ci = 0.95, verbose = TRUE, ...) {
 }
 
 
+#' @rdname bci
 #' @export
-bci.get_predicted <- function(x, ...) {
-  if ("iterations" %in% names(attributes(x))) {
-    out <- bci(as.data.frame(t(attributes(x)$iterations)), ...)
+bci.get_predicted <- function(x, ci = 0.95, use_iterations = FALSE, verbose = TRUE, ...) {
+  if (isTRUE(use_iterations)) {
+    if ("iterations" %in% names(attributes(x))) {
+      out <- bci(as.data.frame(t(attributes(x)$iterations)), ci = ci, verbose = verbose, ...)
+    } else {
+      insight::format_error("No iterations present in the output.")
+    }
+    attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
   } else {
-    insight::format_error("No iterations present in the output.")
+    out <- bci(as.numeric(x), ci = ci, verbose = verbose, ...)
   }
-  attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
   out
 }
 

diff --git a/R/eti.R b/R/eti.R
@@ -249,17 +249,23 @@ eti.BFBayesFactor <- function(x, ci = 0.95, verbose = TRUE, ...) {
 }
 
 
+#' @rdname eti
 #' @export
-eti.get_predicted <- function(x, ...) {
-  if ("iterations" %in% names(attributes(x))) {
-    out <- eti(as.data.frame(t(attributes(x)$iterations)), ...)
+eti.get_predicted <- function(x, ci = 0.95, use_iterations = FALSE, verbose = TRUE, ...) {
+  if (isTRUE(use_iterations)) {
+    if ("iterations" %in% names(attributes(x))) {
+      out <- eti(as.data.frame(t(attributes(x)$iterations)), ci = ci, verbose = verbose, ...)
+    } else {
+      insight::format_error("No iterations present in the output.")
+    }
+    attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
   } else {
-    insight::format_error("No iterations present in the output.")
+    out <- eti(as.numeric(x), ci = ci, verbose = verbose, ...)
   }
-  attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
   out
 }
 
+
 # Helper ------------------------------------------------------------------
 
 

diff --git a/R/hdi.R b/R/hdi.R
@@ -22,6 +22,10 @@
 #'   filtered by default, so only parameters that typically appear in the
 #'   `summary()` are returned. Use `parameters` to select specific parameters
 #'   for the output.
+#' @param 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).
 #' @param verbose Toggle off warnings.
 #' @param ... Currently not used.
 #'
@@ -353,14 +357,19 @@ hdi.BFBayesFactor <- function(x, ci = 0.95, verbose = TRUE, ...) {
 }
 
 
+#' @rdname hdi
 #' @export
-hdi.get_predicted <- function(x, ...) {
-  if ("iterations" %in% names(attributes(x))) {
-    out <- hdi(as.data.frame(t(attributes(x)$iterations)), ...)
+hdi.get_predicted <- function(x, ci = 0.95, use_iterations = FALSE, verbose = TRUE, ...) {
+  if (isTRUE(use_iterations)) {
+    if ("iterations" %in% names(attributes(x))) {
+      out <- hdi(as.data.frame(t(attributes(x)$iterations)), ci = ci, verbose = verbose, ...)
+    } else {
+      insight::format_error("No iterations present in the output.")
+    }
+    attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
   } else {
-    insight::format_error("No iterations present in the output.")
+    out <- hdi(as.numeric(x), ci = ci, verbose = verbose, ...)
   }
-  attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
   out
 }
 

diff --git a/R/map_estimate.R b/R/map_estimate.R
@@ -51,7 +51,6 @@ map_estimate.numeric <- function(x, precision = 2^10, method = "kernel", ...) {
     precision,
     method = method, ...
   )
-  out[[1]] <- NULL
   attr(out, "data") <- x
   out
 }
@@ -174,13 +173,36 @@ map_estimate.emmGrid <- function(x, precision = 2^10, method = "kernel", ...) {
 map_estimate.emm_list <- map_estimate.emmGrid
 
 
+#' @rdname map_estimate
 #' @export
-map_estimate.get_predicted <- function(x, ...) {
-  if ("iterations" %in% names(attributes(x))) {
-    map_estimate(as.data.frame(t(attributes(x)$iterations)), ...)
+map_estimate.get_predicted <- function(x,
+                                       precision = 2^10,
+                                       method = "kernel",
+                                       use_iterations = FALSE,
+                                       verbose = TRUE,
+                                       ...) {
+  if (isTRUE(use_iterations)) {
+    if ("iterations" %in% names(attributes(x))) {
+      out <- map_estimate(
+        as.data.frame(t(attributes(x)$iterations)),
+        precision = precision,
+        method = method,
+        verbose = verbose,
+        ...
+      )
+    } else {
+      insight::format_error("No iterations present in the output.")
+    }
+    attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
   } else {
-    insight::format_error("No iterations present in the output.")
+    out <- map_estimate(as.numeric(x),
+      precision = precision,
+      method = method,
+      verbose = verbose,
+      ...
+    )
   }
+  out
 }
 
 

diff --git a/R/p_direction.R b/R/p_direction.R
@@ -433,14 +433,35 @@ p_direction.BFBayesFactor <- function(x, method = "direct", null = 0, ...) {
   out
 }
 
+#' @rdname p_direction
 #' @export
-p_direction.get_predicted <- function(x, ...) {
-  if ("iterations" %in% names(attributes(x))) {
-    out <- p_direction(as.data.frame(t(attributes(x)$iterations)), ...)
+p_direction.get_predicted <- function(x,
+                                      method = "direct",
+                                      null = 0,
+                                      use_iterations = FALSE,
+                                      verbose = TRUE,
+                                      ...) {
+  if (isTRUE(use_iterations)) {
+    if ("iterations" %in% names(attributes(x))) {
+      out <- p_direction(
+        as.data.frame(t(attributes(x)$iterations)),
+        method = method,
+        null = null,
+        verbose = verbose,
+        ...
+      )
+    } else {
+      insight::format_error("No iterations present in the output.")
+    }
+    attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
   } else {
-    insight::format_error("No iterations present in the output.")
+    out <- p_direction(as.numeric(x),
+      method = method,
+      null = null,
+      verbose = verbose,
+      ...
+    )
   }
-  attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
   out
 }
 

diff --git a/R/p_map.R b/R/p_map.R
@@ -86,9 +86,39 @@ p_map.numeric <- function(x, null = 0, precision = 2^10, method = "kernel", ...)
 }
 
 
+#' @rdname p_map
 #' @export
-p_map.get_predicted <- function(x, null = 0, precision = 2^10, method = "kernel", ...) {
-  p_map(as.numeric(x), null = null, precision = precision, method = method, ...)
+p_map.get_predicted <- function(x,
+                                null = 0,
+                                precision = 2^10,
+                                method = "kernel",
+                                use_iterations = FALSE,
+                                verbose = TRUE,
+                                ...) {
+  if (isTRUE(use_iterations)) {
+    if ("iterations" %in% names(attributes(x))) {
+      out <- p_map(
+        as.data.frame(t(attributes(x)$iterations)),
+        null = null,
+        precision = precision,
+        method = method,
+        verbose = verbose,
+        ...
+      )
+    } else {
+      insight::format_error("No iterations present in the output.")
+    }
+    attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
+  } else {
+    out <- p_map(as.numeric(x),
+      null = null,
+      precision = precision,
+      method = method,
+      verbose = verbose,
+      ...
+    )
+  }
+  out
 }
 
 

diff --git a/R/p_significance.R b/R/p_significance.R
@@ -63,9 +63,30 @@ p_significance.numeric <- function(x, threshold = "default", ...) {
   out
 }
 
+
+#' @rdname p_significance
 #' @export
-p_significance.get_predicted <- function(x, threshold = "default", ...) {
-  p_significance(as.numeric(x), threshold = threshold, ...)
+p_significance.get_predicted <- function(x, threshold = "default", use_iterations = FALSE, verbose = TRUE, ...) {
+  if (isTRUE(use_iterations)) {
+    if ("iterations" %in% names(attributes(x))) {
+      out <- p_significance(
+        as.data.frame(t(attributes(x)$iterations)),
+        threshold = threshold,
+        verbose = verbose,
+        ...
+      )
+    } else {
+      insight::format_error("No iterations present in the output.")
+    }
+    attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
+  } else {
+    out <- p_significance(as.numeric(x),
+      threshold = threshold,
+      verbose = verbose,
+      ...
+    )
+  }
+  out
 }
 
 

diff --git a/R/point_estimate.R b/R/point_estimate.R
@@ -338,13 +338,36 @@ point_estimate.matrix <- function(x, ...) {
 }
 
 
+#' @rdname point_estimate
 #' @export
-point_estimate.get_predicted <- function(x, ...) {
-  if ("iterations" %in% names(attributes(x))) {
-    point_estimate(as.data.frame(t(attributes(x)$iterations)), ...)
+point_estimate.get_predicted <- function(x,
+                                         centrality = "all",
+                                         dispersion = FALSE,
+                                         use_iterations = FALSE,
+                                         verbose = TRUE,
+                                         ...) {
+  if (isTRUE(use_iterations)) {
+    if ("iterations" %in% names(attributes(x))) {
+      out <- point_estimate(
+        as.data.frame(t(attributes(x)$iterations)),
+        centrality = centrality,
+        dispersion = dispersion,
+        verbose = verbose,
+        ...
+      )
+    } else {
+      insight::format_error("No iterations present in the output.")
+    }
+    attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
   } else {
-    as.numeric(x)
+    out <- point_estimate(as.numeric(x),
+      centrality = centrality,
+      dispersion = dispersion,
+      verbose = verbose,
+      ...
+    )
   }
+  out
 }
 
 

diff --git a/R/rope.R b/R/rope.R
@@ -185,8 +185,31 @@ rope.numeric <- function(x, range = "default", ci = 0.95, ci_method = "ETI", ver
 
 
 #' @export
-rope.get_predicted <- function(x, range = "default", ci = 0.95, ci_method = "ETI", verbose = TRUE, ...) {
-  rope(as.numeric(x), range = range, ci = ci, ci_method = ci_method, verbose = verbose, ...)
+rope.get_predicted <- function(x,
+                               range = "default",
+                               ci = 0.95,
+                               ci_method = "ETI",
+                               use_iterations = FALSE,
+                               verbose = TRUE,
+                               ...) {
+  if (isTRUE(use_iterations)) {
+    if ("iterations" %in% names(attributes(x))) {
+      out <- rope(
+        as.data.frame(t(attributes(x)$iterations)),
+        range = range,
+        ci = ci,
+        ci_method = ci_method,
+        verbose = verbose,
+        ...
+      )
+    } else {
+      insight::format_error("No iterations present in the output.")
+    }
+    attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
+  } else {
+    out <- rope(as.numeric(x), range = range, ci = ci, ci_method = ci_method, verbose = verbose, ...)
+  }
+  out
 }
 
 

diff --git a/R/si.R b/R/si.R
@@ -189,10 +189,26 @@ si.stanfit <- function(posterior, prior = NULL, BF = 1, verbose = TRUE, effects
   out
 }
 
+
+#' @rdname si
 #' @export
-si.get_predicted <- function(posterior, ...) {
-  out <- si(as.data.frame(t(posterior)), ...)
-  attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(posterior))
+si.get_predicted <- function(posterior, prior = NULL, BF = 1, use_iterations = FALSE, verbose = TRUE, ...) {
+  if (isTRUE(use_iterations)) {
+    if ("iterations" %in% names(attributes(posterior))) {
+      out <- si(
+        as.data.frame(t(attributes(posterior)$iterations)),
+        prior = prior,
+        BF = BF,
+        verbose = verbose,
+        ...
+      )
+    } else {
+      insight::format_error("No iterations present in the output.")
+    }
+    attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(posterior))
+  } else {
+    out <- si(insight::get_parameters(posterior), prior = prior, BF = BF, verbose = verbose, ...)
+  }
   out
 }
 

diff --git a/R/spi.R b/R/spi.R
@@ -223,14 +223,19 @@ spi.BFBayesFactor <- function(x, ci = 0.95, verbose = TRUE, ...) {
 }
 
 
+#' @rdname spi
 #' @export
-spi.get_predicted <- function(x, ...) {
-  if ("iterations" %in% names(attributes(x))) {
-    out <- spi(as.data.frame(t(attributes(x)$iterations)), ...)
+spi.get_predicted <- function(x, ci = 0.95, use_iterations = FALSE, verbose = TRUE, ...) {
+  if (isTRUE(use_iterations)) {
+    if ("iterations" %in% names(attributes(x))) {
+      out <- spi(as.data.frame(t(attributes(x)$iterations)), ci = ci, verbose = verbose, ...)
+    } else {
+      insight::format_error("No iterations present in the output.")
+    }
+    attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
   } else {
-    insight::format_error("No iterations present in the output.")
+    out <- spi(as.numeric(x), ci = ci, verbose = verbose, ...)
   }
-  attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
   out
 }