fix merge conflicts

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: equatiomatic
-Title: Transform Models into LaTeX Equations
+Title: Transform Models into 'LaTeX' Equations
 Version: 0.1.0
 Authors@R: c(
     person(given = "Daniel",
@@ -24,14 +24,13 @@ Authors@R: c(
            comment = c(ORCID = "https://orcid.org/0000-0002-4222-1819"))
     )
 Description: The goal of equatiomatic is to reduce the pain associated with
-             writing LaTeX formulas from fitted models. The primary function of
-             the package, extract_eq, takes a fitted model object as its input
-             and returns the corresponding LaTeX code for the model.
+             writing 'LaTeX' formulas from fitted models. The primary function of
+             the package, extract_eq(), takes a fitted model object as its input
+             and returns the corresponding 'LaTeX' code for the model.
 License: MIT + file LICENSE
 Depends: R (>= 3.3.0)
 Imports: 
     broom (>= 0.7.0), 
-    palmerpenguins,
     stats
 Suggests: 
     texPreview,

R/create_eq.R

@@ -13,6 +13,7 @@ create_eq <- function(lhs,...) {
 #'   \code{extract_rhs}.
 #'
 #' @inheritParams extract_eq
+#' @noRd
 
 create_eq.default <- function(lhs, rhs, ital_vars, use_coefs, coef_digits,
                               fix_signs, model, intercept, greek, raw_tex) {
@@ -34,6 +35,7 @@ create_eq.default <- function(lhs, rhs, ital_vars, use_coefs, coef_digits,
 }
 
 #' @export
+#' @noRd
 create_eq.polr <- function(lhs, rhs, ital_vars, use_coefs, coef_digits,
                            fix_signs, model, ...) {
   rhs$final_terms <- create_term(rhs, ital_vars)
@@ -53,6 +55,7 @@ create_eq.polr <- function(lhs, rhs, ital_vars, use_coefs, coef_digits,
 }
 
 #' @export
+#' @noRd
 create_eq.clm <- function(lhs, rhs, ital_vars, use_coefs, coef_digits,
                           fix_signs, model, ...) {
   rhs$final_terms <- create_term(rhs, ital_vars)
@@ -80,6 +83,7 @@ create_eq.clm <- function(lhs, rhs, ital_vars, use_coefs, coef_digits,
 #'   \code{extract_rhs}.
 #'
 #' @inheritParams extract_eq
+#' @noRd
 
 create_term <- function(rhs, ital_vars) {
   prim_escaped <- lapply(rhs$primary, function(x) {
@@ -112,6 +116,7 @@ create_term <- function(rhs, ital_vars) {
 #' @param term A character string to escape
 #'
 #' @return A character string
+#' @noRd
 
 escape_tex <- function(term) {
   unescaped <- c(" ", "&", "%", "$", "#", "_", "{", "}", "~", "^", "\\")
@@ -143,6 +148,7 @@ escape_tex <- function(term) {
 #' @param ital_vars Passed from \code{extract_eq}
 #'
 #' @return A character string
+#' @noRd
 
 add_tex_ital <- function(term, ital_vars) {
   if (any(nchar(term) == 0, ital_vars)) {
@@ -160,6 +166,7 @@ add_tex_ital <- function(term, ital_vars) {
 #' @keywords internal
 #'
 #' @return A vector of characters
+#' @noRd
 
 add_tex_ital_v <- function(term_v, ital_vars) {
   vapply(term_v, add_tex_ital, ital_vars, FUN.VALUE = character(1))
@@ -175,6 +182,7 @@ add_tex_ital_v <- function(term_v, ital_vars) {
 #' @param term A character string to TeXify
 #'
 #' @return A character string
+#' @noRd
 
 add_tex_subscripts <- function(term) {
   if (any(nchar(term) == 0)) {
@@ -191,6 +199,7 @@ add_tex_subscripts <- function(term) {
 #' @keywords internal
 #'
 #' @return A vector of characters
+#' @noRd
 
 add_tex_subscripts_v <- function(term_v) {
   vapply(term_v, add_tex_subscripts, FUN.VALUE = character(1))
@@ -200,6 +209,7 @@ add_tex_subscripts_v <- function(term_v) {
 #' Add multiplication symbol for interaction terms
 #'
 #' @keywords internal
+#' @noRd
 
 add_tex_mult <- function(term) {
   paste(term, collapse = " \\times ")
@@ -214,6 +224,7 @@ add_coefs <- function(rhs, ...) {
 #'
 #' @export
 #' @keywords internal
+#' @noRd
 
 add_coefs.default <- function(rhs, term, coef_digits) {
   ests <- round(rhs$estimate, coef_digits)
@@ -226,6 +237,7 @@ add_coefs.default <- function(rhs, term, coef_digits) {
 
 #' @export
 #' @keywords internal
+#' @noRd
 
 add_coefs.polr <- function(rhs, term, coef_digits) {
   ests <- round(rhs$estimate, coef_digits)
@@ -238,6 +250,7 @@ add_coefs.polr <- function(rhs, term, coef_digits) {
 
 #' @export
 #' @keywords internal
+#' @noRd
 
 add_coefs.clm <- function(rhs, term, coef_digits) {
   ests <- round(rhs$estimate, coef_digits)
@@ -256,6 +269,8 @@ add_greek <- function(rhs, ...) {
 #'
 #' @export
 #' @keywords internal
+#' @noRd
+
 add_greek.default <- function(rhs, terms, greek = "beta", intercept = "alpha",
                               raw_tex = FALSE) {
   int <- switch(intercept,
@@ -273,6 +288,7 @@ add_greek.default <- function(rhs, terms, greek = "beta", intercept = "alpha",
 
 #' @export
 #' @keywords internal
+#' @noRd
 
 add_greek.polr <- function(rhs, terms, ...) {
   rhs$idx <- unlist(lapply(split(rhs, rhs$coef.type), function(x) {
@@ -287,6 +303,7 @@ add_greek.polr <- function(rhs, terms, ...) {
 
 #' @export
 #' @keywords internal
+#' @noRd
 
 add_greek.clm <- function(rhs, terms, ...) {
   rhs$idx <- unlist(lapply(split(rhs, rhs$coef.type), function(x) {
@@ -302,6 +319,7 @@ add_greek.clm <- function(rhs, terms, ...) {
 #' Intermediary function to wrap text in `\\beta_{}`
 #'
 #' @keywords internal
+#' @noRd
 
 anno_greek <- function(greek, nums, terms = NULL, raw_tex = FALSE) {
   if (raw_tex) {
@@ -323,8 +341,8 @@ anno_greek <- function(greek, nums, terms = NULL, raw_tex = FALSE) {
 #' @keywords internal
 #'
 #' @param eq String containing a LaTeX equation
-#'
-#'
+#' @noRd
+
 fix_coef_signs <- function(eq) {
   # Side-by-side + -
   eq_clean <- gsub("\\+ -", "- ", eq)

R/extract_eq.R

@@ -54,7 +54,6 @@
 #' extract_eq(mod2)
 #'
 #' # Works for categorical variables too, putting levels as subscripts
-#' library(palmerpenguins)
 #' mod3 <- lm(body_mass_g ~ bill_length_mm + species, penguins)
 #' extract_eq(mod3)
 #'

R/extract_lhs.R

@@ -4,6 +4,7 @@
 #'
 #' @param model A fitted model
 #' @param \dots additional arguments passed to the specific extractor
+#' @noRd
 
 extract_lhs <- function(model, ...) {
   UseMethod("extract_lhs", model)
@@ -15,6 +16,7 @@ extract_lhs <- function(model, ...) {
 #'
 #' @param model A fitted model
 #' @param \dots additional arguments passed to the specific extractor
+#' @noRd
 
 extract_lhs2 <- function(model, ...) {
   UseMethod("extract_lhs2", model)
@@ -31,6 +33,7 @@ extract_lhs2 <- function(model, ...) {
 #' @inheritParams extract_eq
 #'
 #' @return A character string
+#' @noRd
 
 extract_lhs.lm <- function(model, ital_vars, ...) {
   lhs <- rownames(attr(model$terms, "factors"))[1]
@@ -51,6 +54,7 @@ extract_lhs.lm <- function(model, ital_vars, ...) {
 #' @inheritParams extract_eq
 #'
 #' @return A character string
+#' @noRd
 
 extract_lhs.glm <- function(model, ital_vars, show_distribution, ...) {
   if (show_distribution) {
@@ -80,6 +84,8 @@ extract_lhs.glm <- function(model, ital_vars, show_distribution, ...) {
 
 #' @export
 #' @keywords internal
+#' @noRd
+
 extract_lhs2.glm <- function(model, ital_vars, ...) {
   outcome <- all.vars(formula(model))[1]
   n <- unique(model$model$`(weights)`)
@@ -136,7 +142,7 @@ extract_lhs2.glm <- function(model, ital_vars, ...) {
 #' @inheritParams extract_eq
 #'
 #' @return A character string
-#'
+#' @noRd
 
 extract_lhs.polr <- function(model, ital_vars, ...) {
   tidied <- broom::tidy(model)
@@ -164,6 +170,7 @@ extract_lhs.polr <- function(model, ital_vars, ...) {
 #' @inheritParams extract_eq
 #'
 #' @return A character string
+#' @noRd
 
 extract_lhs.clm <- function(model, ital_vars, ...) {
   tidied <- broom::tidy(model)
@@ -182,12 +189,14 @@ extract_lhs.clm <- function(model, ital_vars, ...) {
 
 #' modifies lhs of equations that include a link function
 #' @keywords internal
+#' @noRd
 modify_lhs_for_link <- function(model, ...) {
   UseMethod("modify_lhs_for_link", model)
 }
 
 #' @export
 #' @keywords internal
+#' @noRd
 modify_lhs_for_link.glm <- function(model, lhs) {
   if (!(any(grepl(model$family$link, link_function_df$link_name)))) { # is this logical operator not ideal?
     message("This link function is not presently supported; using an identity
@@ -201,6 +210,7 @@ modify_lhs_for_link.glm <- function(model, lhs) {
 
 #' @export
 #' @keywords internal
+#' @noRd
 modify_lhs_for_link.polr <- function(model, lhs) {
   matched_row_bool <- grepl(model$method, link_function_df$link_name)
   filtered_link_formula <- link_function_df[matched_row_bool, "link_formula"]
@@ -210,6 +220,7 @@ modify_lhs_for_link.polr <- function(model, lhs) {
 
 #' @export
 #' @keywords internal
+#' @noRd
 modify_lhs_for_link.clm <- function(model, lhs) {
   if (!(any(grepl(model$info$link, link_function_df$link_name)))) {
     message("This link function is not presently supported; using an identity

R/extract_rhs.R

@@ -60,7 +60,7 @@
 #' #>   ..$ : Named chr  "Gentoo" ""
 #' #>   .. ..- attr(*, "names")= chr [1:2] "species" "flipper_length_mm"
 #' }
-#'
+#' @noRd
 
 extract_rhs <- function(model) {
   # Extract RHS from formula
@@ -101,6 +101,7 @@ extract_rhs <- function(model) {
 #'
 #' extract_primary_term(primaries, full_terms)
 #' }
+#' @noRd
 
 extract_primary_term <- function(primary_term_v, all_terms) {
   detected <- lapply(all_terms, detect_primary, primary_term_v)
@@ -125,6 +126,7 @@ extract_primary_term <- function(primary_term_v, all_terms) {
 #' detect_primary("age", c("partyid", "age", "race"))
 #' detect_primary("raceBlack", c("partyid", "age", "race"))
 #' }
+#' @noRd
 
 detect_primary <- function(full_term, primary_term_v) {
   vapply(primary_term_v, function(indiv_term) {
@@ -158,6 +160,7 @@ detect_primary <- function(full_term, primary_term_v) {
 #'
 #' extract_all_subscripts(p_list, ft_list)
 #' }
+#' @noRd
 
 extract_all_subscripts <- function(primary_list, full_term_list) {
   Map(extract_subscripts, primary_list, full_term_list)
@@ -177,6 +180,7 @@ extract_all_subscripts <- function(primary_list, full_term_list) {
 #'                    c("partyidDon't know", "partyidOther party",
 #'                      "partyidNot str democrat"))
 #' }
+#' @noRd
 
 extract_subscripts <- function(primary, full_term_v) {
   out <- switch(as.character(length(primary)),
@@ -198,19 +202,22 @@ extract_subscripts <- function(primary, full_term_v) {
 #' @param tex The TeX version of the RHS of the model (as character), built as
 #'   \code{rhs_combined} or \code{eq_raw$rhs} in \code{extract_eq()}
 #' @param \dots additional arguments passed to the specific extractor
+#' @noRd
 
 wrap_rhs <- function(model, tex, ...) {
   UseMethod("wrap_rhs", model)
 }
 
 #' @export
 #' @keywords internal
+#' @noRd
 wrap_rhs.default <- function(model, tex, ...) {
   return(tex)
 }
 
 #' @export
 #' @keywords internal
+#' @noRd
 wrap_rhs.glm <- function(model, tex, ...) {
   if (model$family$link == "probit") {
     rhs <- probitify(tex)
@@ -223,6 +230,7 @@ wrap_rhs.glm <- function(model, tex, ...) {
 
 #' @export
 #' @keywords internal
+#' @noRd
 wrap_rhs.polr <- function(model, tex, ...) {
   if (model$method == "probit") {
     rhs <- probitify(tex)
@@ -235,6 +243,7 @@ wrap_rhs.polr <- function(model, tex, ...) {
 
 #' @export
 #' @keywords internal
+#' @noRd
 wrap_rhs.clm <- function(model, tex, ...) {
   if (model$info$link == "probit") {
     rhs <- probitify(tex)
@@ -246,6 +255,7 @@ wrap_rhs.clm <- function(model, tex, ...) {
 }
 
 #' @keywords internal
+#' @noRd
 probitify <- function(tex) {
   # Replace existing beginning-of-line \quad space with `\\qquad\` to account for \Phi
   tex <- gsub("&\\\\quad", "&\\\\qquad\\\\", tex)

R/penguins.R

@@ -0,0 +1,23 @@
+#' Size measurements for adult foraging penguins near Palmer Station, Antarctica
+#'
+#' Data originally from \code{\link[palmerpenguins]{penguins}}. Includes
+#' measurements for penguin species, island in Palmer Archipelago,
+#' size (flipper length, body mass, bill dimensions), and sex.
+#' This is a subset of \code{\link[palmerpenguins]{penguins_raw}}.
+#'
+#' @format A tibble with 344 rows and 8 variables:
+#' \describe{
+#'   \item{species}{a factor denoting penguin species (Adélie, Chinstrap and Gentoo)}
+#'   \item{island}{a factor denoting island in Palmer Archipelago, Antarctica (Biscoe, Dream or Torgersen)}
+#'   \item{bill_length_mm}{a number denoting bill length (millimeters)}
+#'   \item{bill_depth_mm}{a number denoting bill depth (millimeters)}
+#'   \item{flipper_length_mm}{an integer denoting flipper length (millimeters)}
+#'   \item{body_mass_g}{an integer denoting body mass (grams)}
+#'   \item{sex}{a factor denoting penguin sex (female, male)}
+#'   \item{year}{an integer denoting the study year (2007, 2008, or 2009)}
+#' }
+#' @source {Adélie penguins: Palmer Station Antarctica LTER and K. Gorman. 2020. Structural size measurements and isotopic signatures of foraging among adult male and female Adélie penguins (Pygoscelis adeliae) nesting along the Palmer Archipelago near Palmer Station, 2007-2009 ver 5. Environmental Data Initiative} \url{https://doi.org/10.6073/pasta/98b16d7d563f265cb52372c8ca99e60f}
+#' @source {Gentoo penguins: Palmer Station Antarctica LTER and K. Gorman. 2020. Structural size measurements and isotopic signatures of foraging among adult male and female Gentoo penguin (Pygoscelis papua) nesting along the Palmer Archipelago near Palmer Station, 2007-2009 ver 5. Environmental Data Initiative} \url{https://doi.org/10.6073/pasta/7fca67fb28d56ee2ffa3d9370ebda689}
+#' @source {Chinstrap penguins: Palmer Station Antarctica LTER and K. Gorman. 2020. Structural size measurements and isotopic signatures of foraging among adult male and female Chinstrap penguin (Pygoscelis antarcticus) nesting along the Palmer Archipelago near Palmer Station, 2007-2009 ver 6. Environmental Data Initiative} \url{https://doi.org/10.6073/pasta/c14dfcfada8ea13a17536e73eb6fbe9e}
+#' @source {Originally published in: Gorman KB, Williams TD, Fraser WR (2014) Ecological Sexual Dimorphism and Environmental Variability within a Community of Antarctic Penguins (Genus Pygoscelis). PLoS ONE 9(3): e90081. doi:10.1371/journal.pone.0090081}
+"penguins"

R/utils.R

@@ -8,7 +8,7 @@
 #'
 #' @return A vector of the corresponding type, \code{chr} = character,
 #'   \code{dbl} = double, \code{lgl} = logical, and \code{int} = logical
-#'
+#' @noRd
 mapply_chr <- function(...) {
 	out <- mapply(...)
 	stopifnot(is.character(out))