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vincentarelbundock · Jul 16, 2023 · 08981ab · 08981ab
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Showing 16 changed files with 75 additions and 22 deletions.
diff --git a/R/comparisons.R b/R/comparisons.R
@@ -234,7 +234,7 @@ comparisons <- function(model,
                         p_adjust = NULL,
                         df = Inf,
                         eps = NULL,
-                        numderiv = "richardson",
+                        numderiv = "fdforward",
                         ...) {
 
 
@@ -646,7 +646,7 @@ avg_comparisons <- function(model,
                             p_adjust = NULL,
                             df = Inf,
                             eps = NULL,
-                            numderiv = "richardson",
+                            numderiv = "fdforward",
                             ...) {
 
     # order of the first few paragraphs is important

diff --git a/R/hypotheses.R b/R/hypotheses.R
@@ -127,7 +127,7 @@ hypotheses <- function(
     joint = FALSE,
     joint_test = "f",
     FUN = NULL,
-    numderiv = "richardson",
+    numderiv = "fdforward",
     ...) {
 
     if (!isFALSE(joint)) {

diff --git a/R/marginal_means.R b/R/marginal_means.R
@@ -146,7 +146,7 @@ marginal_means <- function(model,
                            df = Inf,
                            wts = "equal",
                            by = NULL,
-                           numderiv = "richardson",
+                           numderiv = "fdforward",
                            ...) {
 
 

diff --git a/R/predictions.R b/R/predictions.R
@@ -199,7 +199,7 @@ predictions <- function(model,
                         equivalence = NULL,
                         p_adjust = NULL,
                         df = Inf,
-                        numderiv = "richardson",
+                        numderiv = "fdforward",
                         ...) {
 
 
@@ -690,7 +690,7 @@ avg_predictions <- function(model,
                             equivalence = NULL,
                             p_adjust = NULL,
                             df = Inf,
-                            numderiv = "richardson",
+                            numderiv = "fdforward",
                             ...) {
 
     # order of the first few paragraphs is important

diff --git a/R/sanitize_numderiv.R b/R/sanitize_numderiv.R
@@ -16,7 +16,7 @@ sanitize_numderiv <- function(numderiv) {
         } else if (numderiv[[1]] == "richardson") {
             valid <- c("eps", "d", "zero_tol", "size", "r", "v")
             if (any(!names(numderiv)[2:length(numderiv)] %in% valid)) {
-                stop(sprintf("The only valid arguments for this numeric differentiation method are: %s", paste(valid, collapse = ", ")), call. = FALSE)
+                stop(sprintf("The only valid arguments for this numeric differentiation method are: %s. See `?numDeriv::grad` for details.", paste(valid, collapse = ", ")), call. = FALSE)
             }
         }
     }

diff --git a/R/slopes.R b/R/slopes.R
@@ -88,6 +88,11 @@
 #' the maximum and minimum values of the variable with respect to which we
 #' are taking the derivative. Changing `eps` may be necessary to avoid
 #' numerical problems in certain models.
+#' @param numderiv string or list of strings indicating the method to use to for the numeric differentiation used in to compute delta method standard errors.
+#' + "fdforward": finite difference method with forward differences
+#' + "fdcenter": finite difference method with central differences (default)
+#' + "richardson": Richardson extrapolation method
+#' + Extra arguments can be specified by passing a list to the `numDeriv` argument, with the name of the method first and named arguments following, ex: `numderiv=list("fdcenter", eps = 1e-5)`. When an unknown argument is used, `marginaleffects` prints the list of valid arguments for each method.
 #' @param ... Additional arguments are passed to the `predict()` method
 #' supplied by the modeling package.These arguments are particularly useful
 #' for mixed-effects or bayesian models (see the online vignettes on the
@@ -211,7 +216,7 @@ slopes <- function(model,
                    p_adjust = NULL,
                    df = Inf,
                    eps = NULL,
-                   numderiv = "richardson",
+                   numderiv = "fdforward",
                    ...) {
 
 
@@ -359,7 +364,7 @@ avg_slopes <- function(model,
                        p_adjust = NULL,
                        df = Inf,
                        eps = NULL,
-                       numderiv = "richardson",
+                       numderiv = "fdforward",
                        ...) {
 
     # order of the first few paragraphs is important

diff --git a/inst/tinytest/test-eps.R b/inst/tinytest/test-eps.R
@@ -32,7 +32,7 @@ expect_error(slopes(mod, eps = 0))
 # Issue #840
 df <- causaldata::restaurant_inspections
 m1 <- glm(Weekend ~ Year, data = df, family = binomial)
-z <- avg_slopes(m1, variables = "Year")$statistic
+z <- avg_slopes(m1, variables = "Year", numderiv = "richardson")$statistic
 expect_equivalent(z, -2.06834167185815, tol = 1e-5)
 
 

diff --git a/man/comparisons.Rd b/man/comparisons.Rd
diff --git a/man/deltamethod.Rd b/man/deltamethod.Rd
diff --git a/man/hypotheses.Rd b/man/hypotheses.Rd
diff --git a/man/marginal_means.Rd b/man/marginal_means.Rd
diff --git a/man/marginaleffects.Rd b/man/marginaleffects.Rd
diff --git a/man/marginalmeans.Rd b/man/marginalmeans.Rd
diff --git a/man/meffects.Rd b/man/meffects.Rd
diff --git a/man/predictions.Rd b/man/predictions.Rd
diff --git a/man/slopes.Rd b/man/slopes.Rd