fixing docs

DESCRIPTION

@@ -4,7 +4,7 @@ Title: Marginal Effects for Model Objects
 Description: An R port of the margins command from 'Stata', which can be used to
     calculate marginal (or partial) effects from model objects.
 License: MIT + file LICENSE
-Version: 0.3.27
+Version: 0.3.28
 Authors@R: c(person("Thomas J.", "Leeper",
                     role = c("aut"), 
                     comment = c(ORCID = "0000-0003-4097-6326")),
@@ -47,4 +47,5 @@ Enhances:
     survey
 ByteCompile: true
 VignetteBuilder: knitr
-RoxygenNote: 7.1.0
+Encoding: UTF-8
+RoxygenNote: 7.3.2

NAMESPACE

@@ -12,6 +12,10 @@ S3method(dydx,default)
 S3method(dydx,factor)
 S3method(dydx,logical)
 S3method(dydx,ordered)
+S3method(find_terms_in_model,default)
+S3method(find_terms_in_model,lmerMod)
+S3method(find_terms_in_model,merMod)
+S3method(gradient_factory,default)
 S3method(image,glm)
 S3method(image,lm)
 S3method(image,loess)
@@ -44,6 +48,12 @@ S3method(persp,loess)
 S3method(plot,margins)
 S3method(print,margins)
 S3method(print,summary.margins)
+S3method(reset_coefs,betareg)
+S3method(reset_coefs,default)
+S3method(reset_coefs,glm)
+S3method(reset_coefs,lm)
+S3method(reset_coefs,lmerMod)
+S3method(reset_coefs,merMod)
 S3method(summary,margins)
 S3method(vcov,margins)
 export(cplot)

NEWS.md

@@ -1,3 +1,7 @@
+## margins 0.3.28
+
+* CRAN issues only (documentation, vignette support)
+
 ## margins 0.3.27
 
 * version bump and resubmission to recover from `prediction` archive cascade

R/cplot.R

@@ -10,7 +10,7 @@
 #' @param vcov A matrix containing the variance-covariance matrix for estimated model coefficients, or a function to perform the estimation with \code{model} as its only argument.
 #' @param at Currently ignored.
 #' @param n An integer specifying the number of points across \code{x} at which to calculate the predicted value or marginal effect, when \code{x} is numeric. Ignored otherwise.
-#' @param xvals A numeric vector of values at which to calculate predictions or marginal effects, if \code{x} is numeric. By default, it is calculated from the data using \code{\link{seq_range}}. If \code{x} is a factor, this is ignored, as is \code{n}.
+#' @param xvals A numeric vector of values at which to calculate predictions or marginal effects, if \code{x} is numeric. By default, it is calculated from the data using \code{\link[prediction]{seq_range}}. If \code{x} is a factor, this is ignored, as is \code{n}.
 #' @param level The confidence level required (used to draw uncertainty bounds).
 #' @param draw A logical (default \code{TRUE}), specifying whether to draw the plot. If \code{FALSE}, the data used in drawing are returned as a list of data.frames. This might be useful if you want to plot using an alternative plotting package (e.g., ggplot2). Also, if set to value \dQuote{add}, then the resulting data is added to the existing plot.
 #' @param xlab A character string specifying the value of \code{xlab} in \code{\link[graphics]{plot}}. 

R/find_terms_in_model.R

@@ -7,6 +7,7 @@ find_terms_in_model <- function(model, variables = NULL) {
     UseMethod("find_terms_in_model")
 }
 
+#' @export
 find_terms_in_model.default <- function(model, variables = NULL) {
 
     # identify classes of terms in `model`
@@ -71,6 +72,7 @@ find_terms_in_model.default <- function(model, variables = NULL) {
     return(vars)
 }
 
+#' @export
 find_terms_in_model.merMod <- function(model, variables = NULL) {
 
     # require lme4 package in order to identify random effects terms
@@ -85,6 +87,7 @@ find_terms_in_model.merMod <- function(model, variables = NULL) {
     varslist
 }
 
+#' @export
 find_terms_in_model.lmerMod <- find_terms_in_model.merMod
 
 # call gsub_bracket on all common formula operations

R/gradient_factory.R

@@ -4,6 +4,7 @@ gradient_factory <- function(data, model, variables = NULL, type = "response", w
     UseMethod("gradient_factory", model)
 }
 
+#' @export
 gradient_factory.default <- function(data, model, variables = NULL, type = "response", weights = NULL, eps = 1e-7, varslist = NULL, ...) {
 
     # identify classes of terms in `model`

R/reset_coefs.R

@@ -3,18 +3,21 @@ reset_coefs <- function(model, coefs) {
     UseMethod("reset_coefs")
 }
 
+#' @export
 reset_coefs.default <- function(model, coefs) {
     # in basic model classes coefficients are named vector
     model[["coefficients"]][names(coefs)] <- coefs
     model
 }
 
+#' @export
 reset_coefs.lm <- function(model, coefs) {
     # in lm coefficients are named vector
     model[["coefficients"]][names(coefs)] <- coefs
     model
 }
 
+#' @export
 reset_coefs.glm <- function(model, coefs) {
     # in glm coefficients are named vector
     model[["coefficients"]][names(coefs)] <- coefs
@@ -25,12 +28,14 @@ reset_coefs.glm <- function(model, coefs) {
     model
 }
 
+#' @export
 reset_coefs.betareg <- function(model, coefs) {
     # in betareg, coefficients are a two-element list. We want to substitute the first element!
     model[["coefficients"]]$mean[names(coefs)] <- coefs
     model
 }
 
+#' @export
 reset_coefs.merMod <- function(model, coefs) {
     # in 'merMod', predictions work the slot called "beta", which is unnamed
     # `fixef(model)` returns the same thing named
@@ -41,4 +46,5 @@ reset_coefs.merMod <- function(model, coefs) {
     model
 }
 
+#' @export
 reset_coefs.lmerMod <- reset_coefs.merMod