Update docs (#104)

.Rbuildignore

@@ -7,3 +7,8 @@ README.html
 ^.*\.Rproj$
 ^\.Rproj\.user$
 docs/
+^\.github$
+^data-raw$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

@@ -0,0 +1,42 @@
+on:
+  push:
+    branches: master
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: macOS-r-3.6-${{ hashFiles('depends.Rds') }}
+          restore-keys: macOS-r-3.6-
+
+      - name: Install dependencies
+        run: |
+          install.packages("remotes")
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_dev("pkgdown")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        run: pkgdown::deploy_to_branch(new_process = FALSE)
+        shell: Rscript {0}

DESCRIPTION

@@ -10,15 +10,16 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Suggests:
-  outbreaks,
-  incidence,
-  testthat,
-  knitr,
-  roxygen2,
-  covr,
-  tibble,
-  dplyr,
-  magrittr
+    outbreaks,
+    incidence,
+    testthat,
+    knitr,
+    roxygen2,
+    covr,
+    tibble,
+    dplyr,
+    magrittr,
+    rmarkdown
 RoxygenNote: 7.0.2
 Imports:
   matchmaker (>= 0.1.0),

R/linelist-package.R

@@ -0,0 +1,8 @@
+#' @keywords internal
+"_PACKAGE"
+
+# The following block is used by usethis to automatically manage
+# roxygen namespace tags. Modify with care!
+## usethis namespace: start
+## usethis namespace: end
+NULL

README.Rmd

@@ -23,7 +23,7 @@ knitr::opts_chunk$set(
 [![Codecov test coverage](https://codecov.io/gh/reconhub/linelist/branch/master/graph/badge.svg)](https://codecov.io/gh/reconhub/linelist?branch=master)
 
 This package is dedicated to simplifying the cleaning and standardisation of
-linelist data. Considering a case linelist `data.frame`, it aims to:
+[line list](https://outbreaktools.ca/background/line-lists/) data. Considering a case line list `data.frame`, it aims to:
 
 - standardise the variables names, replacing all non-ascii characters with their
   closest latin equivalent, removing blank spaces and other separators,
@@ -54,10 +54,24 @@ devtools::install_github("reconhub/linelist")
 
 Note that this requires the package *devtools* installed.
 
+# Quick example
 
-# What does it do?
+Let us consider a messy `data.frame` as an example: 
 
-## Data cleaning
+```{r toy_data}
+library(linelist)
+example_data <- messy_data(10)
+example_data
+```
+
+We then use the `clean_data()` command to get nice, clean data!
+
+```{r clean_data}
+clean_data(example_data, guess_dates = TRUE)
+```
+
+
+# What does it do?
 
 Procedures to clean data, first and foremost aimed at `data.frame` formats,
 include:
@@ -78,47 +92,6 @@ include:
 - `guess_dates()`: find dates in various, unspecified formats in a messy
   `character` vector
 
-
-
-# Worked example
-
-Let us consider some messy `data.frame` as a toy example: 
-
-```{r toy_data}
-
-## make toy data
-onsets <- as.Date("2018-01-01") + sample(1:10, 20, replace = TRUE)
-discharge <- format(as.Date(onsets) + 10, "%d/%m/%Y")
-genders <- c("male", "female", "FEMALE", "Male", "Female", "MALE")
-gender <- sample(genders, 20, replace = TRUE)
-case_types <- c("confirmed", "probable", "suspected", "not a case",
-                "Confirmed", "PROBABLE", "suspected  ", "Not.a.Case")
-messy_dates <- sample(
-                 c("01-12-2001", "male", "female", "2018-10-18", "2018_10_17",
-                   "2018 10 19", "// 24//12//1989", NA, "that's 24/12/1989!"),
-                 20, replace = TRUE)
-case <- factor(sample(case_types, 20, replace = TRUE))
-toy_data <- data.frame("Date of Onset." = onsets,
-                       "DisCharge.." = discharge,
-                       "SeX_ " = gender,
-                       "Épi.Case_définition" = case,
-                       "messy/dates" = messy_dates)
-## show data
-toy_data
-
-```
-
-We start by cleaning these data:
-
-```{r clean_data}
-## load library
-library(linelist)
-
-## clean data with defaults
-x <- clean_data(toy_data)
-x
-
-```