Got vignette compiling, needs R not Rscript.

.Rbuildignore

@@ -1,4 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.travis\.yml$
-^vignettes/\.env$
+^\.env$

.gitignore

@@ -1,7 +1,3 @@
-.Rproj.user
 .Rhistory
-.RData
 .env
-
-/vignettes/piwikr.md
-/vignettes/figure/
+inst/doc

DESCRIPTION

@@ -17,6 +17,10 @@ Imports:
     RMySQL,
     DBI
 RoxygenNote: 5.0.1
-Suggests:
+Suggests: 
     covr,
-    testthat
+    testthat,
+    knitr,
+    rmarkdown,
+    pander
+VignetteBuilder: knitr

NAMESPACE

@@ -1,9 +1,19 @@
 # Generated by roxygen2: do not edit by hand
 
+export(compute_days)
+export(compute_pages)
+export(compute_sources)
+export(compute_visitors)
+export(get_actions)
+export(get_visits)
+export(graph_browser_resolutions)
+export(graph_site_structure)
+export(graph_visitors_vs_date)
+export(src_mysql)
+import(DBI)
+import(RMySQL)
 import(dplyr)
 import(ggplot2)
-importFrom(DBI,dbGetQuery)
-importFrom(RMySQL,dbGetStatement)
 importFrom(igraph,E)
 importFrom(igraph,V)
 importFrom(igraph,graph_from_data_frame)

R/data_retrieval.R

@@ -1,7 +1,7 @@
 #' @import dplyr
+#' @import DBI
+#' @import RMySQL
 #' @importFrom lubridate ymd_hms floor_date
-#' @importFrom DBI dbGetQuery
-#' @importFrom RMySQL dbGetStatement
 
 globalVariables(c(
     "time_spent_ref_action",
@@ -15,6 +15,9 @@ globalVariables(c(
     "idaction"
 ))
 
+#' @export
+dplyr::src_mysql
+
 describe_database <- function(db) {
     ## TODO: Use RMySQL function instead of DBI
     table_names <- dbGetQuery(db$con, "show tables")[, 1]
@@ -43,6 +46,7 @@ describe_database <- function(db) {
     return(x)
 }
 
+#' @export
 get_actions <- function(db) {
     actions <- .get(db, "piwik_log_link_visit_action")
 
@@ -79,6 +83,7 @@ get_actions <- function(db) {
     return(actions)
 }
 
+#' @export
 get_visits <- function(db) {
     visits <- .get(db, "piwik_log_visit")
     visits <- .remove_empty_columns(visits)

R/graphs.R

@@ -15,6 +15,7 @@ globalVariables(c(
     "config_resolution"
 ))
 
+#' @export
 graph_visitors_vs_date <- function(days) {
     g <- (
         ggplot(days, aes(x = day_of_first_visit, y = new_visitors)) +
@@ -28,6 +29,7 @@ graph_visitors_vs_date <- function(days) {
     return(g)
 }
 
+#' @export
 graph_browser_resolutions <- function(visits) {
     resolutions <- visits %>%
         separate(config_resolution, c("width", "height"), sep = "x", convert = TRUE) %>%
@@ -48,6 +50,7 @@ graph_browser_resolutions <- function(visits) {
     )
 }
 
+#' @export
 graph_site_structure <- function(actions) {
     views <- actions %>%
         filter(grepl("amarder.github.io", url)) %>%

R/munging.R

@@ -1,3 +1,5 @@
+#' @importFrom lubridate floor_date
+
 globalVariables(c(
     "day",
     "visitor_id",
@@ -10,15 +12,17 @@ globalVariables(c(
     "Page"
 ))
 
+#' @export
 compute_visitors <- function(actions) {
     visitors <- actions %>%
-        mutate(day = lubridate::floor_date(actions$datetime, "day")) %>%
+        mutate(day = floor_date(actions$datetime, "day")) %>%
         group_by(visitor_id) %>%
         summarise(day_of_first_visit = min(day))
 
     return(visitors)
 }
 
+#' @export
 compute_pages <- function(actions) {
     pages <- actions %>%
         group_by(url) %>%
@@ -31,6 +35,7 @@ compute_pages <- function(actions) {
     return(pages)
 }
 
+#' @export
 compute_days <- function(actions) {
     visitors <- compute_visitors(actions)
 
@@ -48,6 +53,7 @@ compute_days <- function(actions) {
     return(days)
 }
 
+#' @export
 compute_sources <- function(visits) {
     visitors <- visits %>%
         group_by(idvisitor) %>%

vignettes/piwikr.Rmd

@@ -1,6 +1,12 @@
 ---
 title: "Custom Web Analytics"
+author: "Andrew Marder"
 date: "2016-02-17"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Custom Web Analytics}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
 ---
 
 ```{r, echo=FALSE, warning=FALSE}