source commit: c536d2a

CODE_OF_CONDUCT.md

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+---
+title: "Contributor Code of Conduct"
+---
+
+As contributors and maintainers of this project,
+we pledge to follow the [The Epiverse-TRACE Code of Conduct][coc].
+
+<!--
+Instances of abusive, harassing, or otherwise unacceptable behavior
+may be reported by following our [reporting guidelines][coc-reporting].
+-->
+
+[coc-reporting]: https://forms.gle/guKqVXPk6K43jPn59
+[coc]: https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md
+

LICENSE.md

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+---
+title: "Licenses"
+---
+
+## Instructional Material
+
+The tutorials in this repository are developed by Epiverse-TRACE, based on the [lesson template from the Carpentries](https://github.com/carpentries/workbench-template-rmd) (template under CC BY license).
+
+All Epiverse-TRACE
+instructional material is made available under the [Creative Commons
+Attribution license][cc-by-human]. The following is a human-readable summary of
+(and not a substitute for) the [full legal text of the CC BY 4.0
+license][cc-by-legal].
+
+You are free:
+
+- to **Share**---copy and redistribute the material in any medium or format
+- to **Adapt**---remix, transform, and build upon the material
+
+for any purpose, even commercially.
+
+The licensor cannot revoke these freedoms as long as you follow the license
+terms.
+
+Under the following terms:
+
+- **Attribution**---You must give appropriate credit (mentioning that your work
+  is derived from work that is Copyright (c) Epiverse-TRACE, where
+  practical, linking to <https://epiverse-trace.github.io/>), provide a [link to the
+  license][cc-by-human], and indicate if changes were made. You may do so in
+  any reasonable manner, but not in any way that suggests the licensor endorses
+  you or your use.
+
+- **No additional restrictions**---You may not apply legal terms or
+  technological measures that legally restrict others from doing anything the
+  license permits.  With the understanding that:
+
+Notices:
+
+* You do not have to comply with the license for elements of the material in
+  the public domain or where your use is permitted by an applicable exception
+  or limitation.
+* No warranties are given. The license may not give you all of the permissions
+  necessary for your intended use. For example, other rights such as publicity,
+  privacy, or moral rights may limit how you use the material.
+
+## Software
+
+Except where otherwise noted, the example programs and other software provided
+by Epiverse-TRACE are made available under the [OSI][osi]-approved [MIT
+license][mit-license].
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+[cc-by-human]: https://creativecommons.org/licenses/by/4.0/
+[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
+[mit-license]: https://opensource.org/licenses/mit-license.html
+[osi]: https://opensource.org

config.yaml

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+#------------------------------------------------------------
+# Values for this lesson.
+#------------------------------------------------------------
+
+# Which carpentry is this (swc, dc, lc, or cp)?
+# swc: Software Carpentry
+# dc: Data Carpentry
+# lc: Library Carpentry
+# cp: Carpentries (to use for instructor training for instance)
+# incubator: The Carpentries Incubator
+carpentry: 'epiverse-trace'
+
+# Overall title for pages.
+title: 'Outbreak analytics with R'
+
+# Date the lesson was created (YYYY-MM-DD, this is empty by default)
+created:
+
+# Comma-separated list of keywords for the lesson
+keywords: 'forecasts, epidemic models, interventions'
+
+# Life cycle stage of the lesson
+# possible values: pre-alpha, alpha, beta, stable
+life_cycle: 'pre-alpha'
+
+# License of the lesson materials (recommended CC-BY 4.0)
+license: 'CC-BY 4.0'
+
+# Link to the source repository for this lesson
+source: 'https://github.com/epiverse-trace/tutorials'
+
+# Default branch of your lesson
+branch: 'main'
+
+# Who to contact if there are any issues
+contact: 'andree.valle-campos@lshtm.ac.uk'
+
+# Navigation ------------------------------------------------
+#
+# Use the following menu items to specify the order of
+# individual pages in each dropdown section. Leave blank to
+# include all pages in the folder.
+#
+# Example -------------
+#
+# episodes:
+# - introduction.md
+# - first-steps.md
+#
+# learners:
+# - setup.md
+#
+# instructors:
+# - instructor-notes.md
+#
+# profiles:
+# - one-learner.md
+# - another-learner.md
+
+# Order of episodes in your lesson
+episodes:
+# - template.Rmd
+- introduction.Rmd
+
+# Information for Learners
+learners:
+
+# Information for Instructors
+instructors:
+
+# Learner Profiles
+profiles:
+
+# Customisation ---------------------------------------------
+#
+# This space below is where custom yaml items (e.g. pinning
+# sandpaper and varnish versions) should live
+
+varnish: epiverse-trace/varnish@epiversetheme
+# this is carpentries/sandpaper#533 in our fork so we can keep it up to date with main
+sandpaper: epiverse-trace/sandpaper@patch-renv-github-bug

data/ebola_cases.csv

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+"date","confirm"
+2014-05-18,1
+2014-05-20,2
+2014-05-21,4
+2014-05-22,6
+2014-05-23,1
+2014-05-24,2
+2014-05-26,10
+2014-05-27,8
+2014-05-28,2
+2014-05-29,12
+2014-05-30,7
+2014-05-31,2
+2014-06-01,5
+2014-06-02,2
+2014-06-03,1
+2014-06-05,3
+2014-06-06,7
+2014-06-07,4
+2014-06-08,6
+2014-06-09,1
+2014-06-10,29
+2014-06-11,1
+2014-06-12,10
+2014-06-13,20
+2014-06-14,17
+2014-06-15,4
+2014-06-16,1
+2014-06-17,4
+2014-06-18,8
+2014-06-19,11
+2014-06-20,9
+2014-06-21,3
+2014-06-22,3
+2014-06-23,2
+2014-06-24,9
+2014-06-25,9
+2014-06-26,14
+2014-06-27,15
+2014-06-28,21
+2014-06-29,9
+2014-06-30,15
+2014-07-01,12
+2014-07-02,11
+2014-07-03,4
+2014-07-04,11
+2014-07-05,17
+2014-07-06,9
+2014-07-07,18
+2014-07-08,11
+2014-07-09,8
+2014-07-10,14
+2014-07-11,8
+2014-07-12,7
+2014-07-13,4
+2014-07-14,7
+2014-07-15,5
+2014-07-16,7
+2014-07-17,8
+2014-07-18,10
+2014-07-19,13
+2014-07-20,13
+2014-07-21,18
+2014-07-22,9
+2014-07-23,13
+2014-07-24,10
+2014-07-25,40
+2014-07-26,8
+2014-07-27,7
+2014-07-28,14
+2014-07-29,9
+2014-07-30,14
+2014-07-31,12
+2014-08-01,12
+2014-08-02,15
+2014-08-03,14
+2014-08-04,5
+2014-08-05,13
+2014-08-06,8
+2014-08-07,8
+2014-08-08,13
+2014-08-09,8
+2014-08-10,13
+2014-08-11,4
+2014-08-12,9
+2014-08-13,6
+2014-08-14,8
+2014-08-15,5
+2014-08-16,1
+2014-08-17,5
+2014-08-18,17
+2014-08-19,18
+2014-08-20,35
+2014-08-21,18
+2014-08-22,16
+2014-08-23,18
+2014-08-24,38
+2014-08-25,25
+2014-08-26,42
+2014-08-27,16
+2014-08-28,26
+2014-08-29,30
+2014-08-30,23
+2014-08-31,24
+2014-09-01,29
+2014-09-02,29
+2014-09-03,43
+2014-09-04,41
+2014-09-05,15
+2014-09-06,44
+2014-09-07,30
+2014-09-08,42
+2014-09-09,38
+2014-09-10,21
+2014-09-11,39
+2014-09-12,37
+2014-09-13,38
+2014-09-14,49
+2014-09-15,68
+2014-09-16,84
+2014-09-17,56

index.md

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+---
+site: sandpaper::sandpaper_site
+---
+
+This is an [Epiverse-TRACE][epiversetrace] tutorial built with [The Carpentries Workbench][workbench]. 
+
+[epiversetrace]: https://epiverse-trace.github.io/
+[workbench]: https://carpentries.github.io/workbench/

instructor-notes.md

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+---
+title: 'Instructor Notes'
+---
+
+Instructor notes