updated documentation and gh pages

DESCRIPTION

@@ -7,6 +7,8 @@ Authors@R: c(
         person("Matthew", "Kay", role = "aut", email = "mjskay@northwestern.edu"),
         person("Michael", "Moon", role = "ctb", email = "moon@utstat.toronto.edu"),
         person("Mark", "Miller", role = "ctb", email = "725mrm@gmail.com"),
+        person("Kyle", "Hwang", role = "ctb", email = "kyle.sg.hwang@gmail.com"),
+        person("Hadley", "Wickham", role = "ctb", email = "hadley@posit.co"),
         person("Alex", "Kale", role = "ctb", email = "kalea@uw.edu"),
         person("Nathan", "Taback", role = "ctb", email = "nathan.taback@utoronto.ca"),
         person("Fanny", "Chevalier", role = "ctb", email = "fanny@dgp.toronto.edu"),
@@ -29,6 +31,7 @@ Description: Implement 'multiverse' style analyses (Steegen S., Tuerlinckx F, Ge
      analysis options by interacting with the paper itself.
 License: GPL (>= 3)
 Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 Depends:
     R (>= 3.5.0),

NAMESPACE

@@ -20,9 +20,10 @@ export(conditions)
 export(execute_multiverse)
 export(execute_universe)
 export(expand)
-export(export_2_json)
 export(export_code_json)
-export(export_dist_2_json)
+export(export_data_json)
+export(export_results_dist_json)
+export(export_results_json)
 export(extract_variable_from_universe)
 export(extract_variables)
 export(inside)
@@ -47,11 +48,13 @@ importFrom(dplyr,rename)
 importFrom(dplyr,select)
 importFrom(formatR,tidy_source)
 importFrom(furrr,future_map)
+importFrom(htmltools,includeCSS)
 importFrom(htmltools,tagList)
 importFrom(htmltools,tags)
 importFrom(jsonlite,write_json)
 importFrom(knitr,knit_engines)
 importFrom(knitr,knit_global)
+importFrom(knitr,opts_chunk)
 importFrom(magrittr,"%>%")
 importFrom(magrittr,extract2)
 importFrom(magrittr,inset)
@@ -61,6 +64,7 @@ importFrom(purrr,map)
 importFrom(purrr,map2)
 importFrom(purrr,map_chr)
 importFrom(purrr,reduce)
+importFrom(readr,guess_parser)
 importFrom(rlang,as_name)
 importFrom(rlang,caller_env)
 importFrom(rlang,enexpr)
@@ -77,6 +81,7 @@ importFrom(rlang,is_empty)
 importFrom(rlang,is_missing)
 importFrom(rlang,is_null)
 importFrom(rlang,is_symbol)
+importFrom(rlang,is_true)
 importFrom(rlang,parse_expr)
 importFrom(rlang,quo)
 importFrom(rlang,quo_text)

R/engine_multiverse.R

@@ -114,7 +114,7 @@ multiverse_default_block_exec <- function(.code, options, knit = FALSE) {
 
         temp_options$label = paste0(temp_options$label, "-universe-", x) 
 
-        .assignment = expand(M)[[".parameter_assignment"]][[x]]
+        .assignment = expand(.multiverse)[[".parameter_assignment"]][[x]]
         class_name = paste(names(.assignment), .assignment, sep="---", collapse=" ")
 
         # assuming default is the first universe,

R/export_json.R

@@ -16,14 +16,16 @@ globalVariables(c(".max", ".min", "cdf.x", "cdf.y", "limits", "universe"))
 #' @param filename filename on disk (as a character string)
 #' 
 #' @return a JSON file or (if a filepath is not specified) a dataframe for the results file and a list for the code file
-#' @format ## `results` JSON file schema
+#' 
+#' @details
+#' ## results JSON file schema
 #' It consists of a list of objects (where each object corresponds to one analysis in the multiverse). 
 #' Within this object, the results attribute contains a(nother) list of objects corresponding to each outcome variable. 
 #' For e.g., here we have four coefficients (see the results of the regression model), and thus the results attribute will contain four objects. 
 #' Each object has the following attributes:
 #' - `term`: name of the outcome variable
-#' - `estimate`: mean / median point estimate i.e., $\mathbb{E}(\mu)$ for any parameter $\mu$.
-#' - `std.error`: standard error for the point estimate i.e., $\sqrt{\text{var}(\mu)}$
+#' - `estimate`: mean / median point estimate i.e., \eqn{\mathbb{E}(\mu)} for any parameter \eqn{\mu}.
+#' - `std.error`: standard error for the point estimate i.e., \eqn{\sqrt{\text{var}(\mu)}}
 #' - `cdf.x`: a list of quantiles
 #' - `cdf.y`: a list of cumulative probability density estimates corresponding to the quantiles
 #' 
@@ -34,13 +36,13 @@ globalVariables(c(".max", ".min", "cdf.x", "cdf.y", "limits", "universe"))
 #' - `conf.high`
 #' 
 #' 
-#' @format ## `code` JSON file schema
+#' ## code JSON file schema
 #' It consists of two attributes: `code` and `parameters`. 
 #' `code` is a list of strings consisting of the R and multiverse syntax used to implement the analysis. For readability, we
 #' use [styler] to break up the declared code.
 #' `parameters` is an object listing the parameter names and the corresponding options for each of the parameters declared in the analysis.
 #' 
-#' @format ## `data` JSON file schema
+#' ## data JSON file schema
 #' It consists of a list of objects, each with two attributes: `field` and `values`. 
 #' `field` is the name of a column corresponding to a variable in the dataset. 
 #' `values` are a list of values for that variable in the dataset.