improve CITATION

.mailmap

@@ -1,7 +1,27 @@
-Edmund Hart <edmund.m.hart@gmail.com> <edmund_hart@apple.com> <edmund.m.hart@gmail.com>
-Mark Robinson <markrobinsonuzh@users.noreply.github.com> <mark.robinson@imls.uzh.ch>
+Edmund Hart <edmund.m.hart@gmail.com> <edmund_hart@apple.com>
+Edmund Hart <edmund.m.hart@gmail.com> Ted Hart <edmund.m.hart@gmail.com>
+Mark Robinson <mark.robinson@imls.uzh.ch> markrobinsonuzh <markrobinsonuzh@users.noreply.github.com>
+Mark Robinson <mark.robinson@imls.uzh.ch> markrobinsonuzh <mark.robinson@imls.uzh.ch>
 Tracy Teal <tkteal@gmail.com> <tracyt@idyll.org>
 Francois Michonneau <francois.michonneau@gmail.com> <francois.michonneau@gmail.Com>
 Karen Cranston <karen.cranston@gmail.com>
 Markus J. Akenbrand <iimog@iimog.org>
-Shawn Taylor <sdtaylor@users.noreply.github.com>
+Shawn Taylor <sdtaylor@users.noreply.github.com>
+Mateusz Kuzak <mateusz.kuzak@gmail.com>
+Matthias Grenié <matthias.grenie@hotmail.com>
+Christie Bahlai <cbahlai@msu.edu>
+Meghan Duffy <duffy.ma@gmail.com>
+Zena Lapp <zenalapp@umich.edu>
+Kevin Hall <KWHall@MSU.edu>
+Laurent Gatto <lg390@cam.ac.uk>
+Clara Shaw <claralouise.shaw@gmail.com>
+Eilis Hannon <e.j.hannon@ex.ac.uk>
+Dmytro Fishman <dmytrofishman@gmail.com>
+Joseph Stachelek <jstachelek@utexas.edu>
+Marco Chiapello <mc983.cam@gmail.com>
+Philip Lijnzaad <plijnzaad@users.noreply.github.com>
+Ryan Peek <rapeek@ucdavis.edu>
+Sarah Supp <sarah@weecology.org>
+sfn_brt <kemya@users.noreply.github.com>
+Daniel Stubbs <daniel.stubbs@calculquebec.ca>
+suparee <suparee@uw.edu>

.zenodo.json

@@ -1 +1 @@
-{"creators":[{"name":"Achaz von Hardenberg"},{"name":"Adam Obeng"},{"name":"Aleksandra Pawlik"},{"name":"Alex Pletzer"},{"name":"Alexey Shiklomanov"},{"name":"Anne Fouilloux"},{"name":"Auriel Fournier"},{"name":"Ben Marwick"},{"name":"C. Titus Brown"},{"name":"Carolyn Voter"},{"name":"Catherine Hulshof"},{"name":"Daina Bouquin"},{"name":"Darya Vanichkina"},{"name":"Earle Wilson"},{"name":"Edmund Hart"},{"name":"Elena Sügis"},{"name":"Eli Strauss"},{"name":"Emilia Gan"},{"name":"Erin Becker"},{"name":"Ethan White"},{"name":"Francisco Rodriguez-Sanchez"},{"name":"Francois Michonneau"},{"name":"Fred Boehm"},{"name":"Hao Ye"},{"name":"Harriet Dashnow"},{"name":"Hilmar Lapp"},{"name":"Jaime Ashander"},{"name":"Jarrett Byrnes"},{"name":"Jeffrey W Hollister"},{"name":"Jieming Chen"},{"name":"Jillian Dunic"},{"name":"Jonathan Keane"},{"name":"Josh Herr"},{"name":"K. A. S. Mislan"},{"name":"KWHall"},{"name":"Kara Woo"},{"name":"Karen Cranston"},{"name":"Kari L. Jordan"},{"name":"Karthik Ram"},{"name":"Kate Hertweck"},{"name":"Kathe Todd-Brown"},{"name":"Katie Lotterhos"},{"name":"Kayla Peck"},{"name":"Kenan Direk"},{"name":"Kristian Tylén"},{"name":"Kyriakos Chatzidimitriou"},{"name":"Lachlan Deer"},{"name":"Laurent"},{"name":"Leah Wasser"},{"name":"Leszek Tarkowski"},{"name":"Lisa Breckels"},{"name":"M. Foos"},{"name":"Mark Robinson"},{"name":"Markus J. Akenbrand"},{"name":"Mateusz Kuzak"},{"name":"Matthias Grenié"},{"name":"Michael Koontz"},{"name":"Myfanwy Johnston"},{"name":"Nicholas Marino"},{"name":"Nick Carchedi"},{"name":"Olivia Burge"},{"name":"Philip Lijnzaad"},{"name":"Rekyt"},{"name":"Shawn Taylor"},{"name":"Stephanie Labou"},{"name":"Steve Pederson"},{"name":"Tara Webster"},{"name":"Ted Hart"},{"name":"Thomas Sandmann"},{"name":"Tracy Teal"},{"name":"Will Furnass"},{"name":"Will Pearse"},{"name":"Ye Li"},{"name":"ashander"},{"name":"cbahlai"},{"name":"clarashaw"},{"name":"duffymeg"},{"name":"ejh243"},{"name":"fishman"},{"name":"jsta"},{"name":"markrobinsonuzh"},{"name":"mchiapello"},{"name":"mkuzak"},{"name":"plijnzaad"},{"name":"riverpeek"},{"name":"sarahsupp"},{"name":"sfn_brt"},{"name":"stubbsda"},{"name":"suparee"},{"name":"zmml"}]}
+{"contributors":[{"type":"Editor","name":"Francois Michonneau"},{"type":"Editor","name":"Auriel Fournier"}],"creators":[{"name":"Francois Michonneau"},{"name":"Tracy Teal"},{"name":"Adam Obeng"},{"name":"Aleksandra Pawlik"},{"name":"Mateusz Kuzak"},{"name":"Edmund Hart"},{"name":"Kara Woo"},{"name":"Ethan White"},{"name":"Philip Lijnzaad"},{"name":"Hilmar Lapp"},{"name":"Karthik Ram"},{"name":"Ben Marwick"},{"name":"Kari L. Jordan"},{"name":"Matthias Grenié"},{"name":"Auriel Fournier"},{"name":"Harriet Dashnow"},{"name":"Kate Hertweck"},{"name":"Mark Robinson"},{"name":"ashander"},{"name":"Alexey Shiklomanov"},{"name":"K. A. S. Mislan"},{"name":"Steve Pederson"},{"name":"Alex Pletzer"},{"name":"Anne Fouilloux"},{"name":"C. Titus Brown"},{"name":"Christie Bahlai"},{"name":"Francisco Rodriguez-Sanchez"},{"name":"Jaime Ashander"},{"name":"Lisa Breckels"},{"name":"Markus J. Akenbrand"},{"name":"Meghan Duffy"},{"name":"Shawn Taylor"},{"name":"Stephanie Labou"},{"name":"Thomas Sandmann"},{"name":"Zena Lapp"},{"name":"Achaz von Hardenberg"},{"name":"Carolyn Voter"},{"name":"Catherine Hulshof"},{"name":"Clara Shaw"},{"name":"Daina Bouquin"},{"name":"Daniel Stubbs"},{"name":"Darya Vanichkina"},{"name":"Dmytro Fishman"},{"name":"Earle Wilson"},{"name":"Eilis Hannon"},{"name":"Elena Sügis"},{"name":"Eli Strauss"},{"name":"Emilia Gan"},{"name":"Erin Becker"},{"name":"Fred Boehm"},{"name":"Hao Ye"},{"name":"Jarrett Byrnes"},{"name":"Jeffrey W Hollister"},{"name":"Jieming Chen"},{"name":"Jillian Dunic"},{"name":"Jonathan Keane"},{"name":"Joseph Stachelek"},{"name":"Josh Herr"},{"name":"Karen Cranston"},{"name":"Kathe Todd-Brown"},{"name":"Katie Lotterhos"},{"name":"Kayla Peck"},{"name":"Kenan Direk"},{"name":"Kevin Hall"},{"name":"Kristian Tylén"},{"name":"Kyriakos Chatzidimitriou"},{"name":"Lachlan Deer"},{"name":"Laurent Gatto"},{"name":"Leah Wasser"},{"name":"Leszek Tarkowski"},{"name":"M. Foos"},{"name":"Marco Chiapello"},{"name":"Matthias Grenié"},{"name":"Michael Koontz"},{"name":"Myfanwy Johnston"},{"name":"Nicholas Marino"},{"name":"Nick Carchedi"},{"name":"Olivia Burge"},{"name":"Philip Lijnzaad"},{"name":"Ryan Peek"},{"name":"Sarah Supp"},{"name":"Tara Webster"},{"name":"Will Furnass"},{"name":"Will Pearse"},{"name":"Ye Li"},{"name":"sfn_brt"},{"name":"suparee"}]}

AUTHORS

@@ -10,10 +10,15 @@ Ben Marwick <benmarwick@hotmail.com>
 C. Titus Brown <titus@idyll.org>
 Carolyn Voter <cvoter@wisc.edu>
 Catherine Hulshof <catherine.hulshof@gmail.com>
+Christie Bahlai <cbahlai@msu.edu>
+Clara Shaw <claralouise.shaw@gmail.com>
 Daina Bouquin <dbouquin@gmail.com>
+Daniel Stubbs <daniel.stubbs@calculquebec.ca>
 Darya Vanichkina <d.vanichkina@gmail.com>
+Dmytro Fishman <dmytrofishman@gmail.com>
 Earle Wilson <ewilson2011@gmail.com>
 Edmund Hart <edmund.m.hart@gmail.com>
+Eilis Hannon <e.j.hannon@ex.ac.uk>
 Elena Sügis <elena.sugis@gmail.com>
 Eli Strauss <straussed@gmail.com>
 Emilia Gan <efgan@uw.edu>
@@ -31,9 +36,9 @@ Jeffrey W Hollister <jeff.w.hollister@gmail.com>
 Jieming Chen <cjieming@gmail.com>
 Jillian Dunic <jdunic@gmail.com>
 Jonathan Keane <jkeane@gmail.com>
+Joseph Stachelek <jstachelek@utexas.edu>
 Josh Herr <joshua.r.herr@gmail.com>
 K. A. S. Mislan <kallisons@users.noreply.github.com>
-KWHall <KWHall@MSU.edu>
 Kara Woo <woo.kara@gmail.com>
 Karen Cranston <karen.cranston@gmail.com>
 Kari L. Jordan <kariljordan@me.com>
@@ -43,49 +48,41 @@ Kathe Todd-Brown <ktoddbrown@gmail.com>
 Katie Lotterhos <lotterke@wfu.edu>
 Kayla Peck <kmpeck@users.noreply.github.com>
 Kenan Direk <kdirek@users.noreply.github.com>
+Kevin Hall <KWHall@MSU.edu>
 Kristian Tylén <kristian@cc.au.dk>
 Kyriakos Chatzidimitriou <kyrcha@gmail.com>
 Lachlan Deer <lachlan.deer@gmail.com>
-Laurent <lg390@cam.ac.uk>
+Laurent Gatto <lg390@cam.ac.uk>
 Leah Wasser <lwasser@neoninc.org>
 Leszek Tarkowski <leszek@czterybity.pl>
 Lisa Breckels <lms79@cam.ac.uk>
 M. Foos <mfoos@users.noreply.github.com>
-Mark Robinson <markrobinsonuzh@users.noreply.github.com>
+Marco Chiapello <mc983.cam@gmail.com>
+Mark Robinson <mark.robinson@imls.uzh.ch>
 Markus J. Akenbrand <iimog@iimog.org>
 Mateusz Kuzak <mateusz.kuzak@gmail.com>
 Matthias Grenié <matthias.grenie@ens-lyon.fr>
+Matthias Grenié <matthias.grenie@hotmail.com>
+Meghan Duffy <duffy.ma@gmail.com>
 Michael Koontz <mikoontz@gmail.com>
 Myfanwy Johnston <mrowlan1@gmail.com>
 Nicholas Marino <nac.marino@gmail.com>
 Nick Carchedi <ncarchedi@users.noreply.github.com>
 Olivia Burge <olivia.burge@gmail.com>
 Philip Lijnzaad <philip.lijnzaad@gmail.com>
-Rekyt <matthias.grenie@hotmail.com>
+Philip Lijnzaad <plijnzaad@users.noreply.github.com>
+Ryan Peek <rapeek@ucdavis.edu>
+Sarah Supp <sarah@weecology.org>
 Shawn Taylor <sdtaylor@users.noreply.github.com>
 Stephanie Labou <stephlabou@gmail.com>
 Steve Pederson <stephen.pederson.au@gmail.com>
 Tara Webster <taramclancy@users.noreply.github.com>
-Ted Hart <edmund.m.hart@gmail.com>
 Thomas Sandmann <tomsing1@users.noreply.github.com>
 Tracy Teal <tkteal@gmail.com>
 Will Furnass <will@thearete.co.uk>
 Will Pearse <will.pearse@mcgill.ca>
 Ye Li <liye@umich.edu>
+Zena Lapp <zenalapp@umich.edu>
 ashander <ashander@users.noreply.github.com>
-cbahlai <cbahlai@msu.edu>
-clarashaw <claralouise.shaw@gmail.com>
-duffymeg <duffy.ma@gmail.com>
-ejh243 <e.j.hannon@ex.ac.uk>
-fishman <dmytrofishman@gmail.com>
-jsta <jstachelek@utexas.edu>
-markrobinsonuzh <markrobinsonuzh@users.noreply.github.com>
-mchiapello <mc983.cam@gmail.com>
-mkuzak <mateusz.kuzak@gmail.com>
-plijnzaad <plijnzaad@users.noreply.github.com>
-riverpeek <rapeek@ucdavis.edu>
-sarahsupp <sarah@weecology.org>
 sfn_brt <kemya@users.noreply.github.com>
-stubbsda <daniel.stubbs@calculquebec.ca>
 suparee <suparee@uw.edu>
-zmml <zenalapp@umich.edu>

CITATION.Rmd

@@ -25,24 +25,35 @@ generate_citation <- function(authors = "AUTHORS",
 
 }
 
-generate_zenodo_json <- function(authors = "AUTHORS") {
-    aut <- readLines(authors)
-    aut <- aut[-1]
-    aut <- as.person(aut)
+generate_zenodo_json <- function(repo = ".") {
+    tfile <- tempfile()
+    system(paste("git shortlog -n -e -s >", tfile))
+    aut <- read.table(file = tfile, sep = "\t")
+    aut <- as.person(aut[, 2])
     pp <- lapply(aut,  function(x) {
         res <- gsub("^\\s", "", paste(paste(x$given, collapse = " "),
                                       x$family))
         list(name =  res)
     })
+
     res <- list(
-        metadata = list(
+        contributors = list(
+            list(
+                type = "Editor",
+                name = "Francois Michonneau"
+            ),
+            list(
+                type = "Editor",
+                name = "Auriel Fournier"
+            )
+        ),
             creators = pp
         )
-    )
     cat(jsonlite::toJSON(res, auto_unbox = TRUE), file = ".zenodo.json")
 }
 
 system("python3 /usr/local/bin/update-copyright.py")
+generate_zenodo_json()
 ```
 
 

CITATION.html

@@ -327,11 +327,11 @@ <h2>Lessons</h2>
 <p>The <strong><code>ggplot2</code></strong> lesson was initially created by Mateusz Kuzak, Diana Marek, and Hedi Peterson, during a Hackathon in Espoo, Finland on March 16-17, 2015, sponsored by the <a href="http://elixir-europe.org/">ELIXIR project</a>.</p>
 <p>You can cite this Data Carpentry lesson as follow:</p>
 <p>
-Obeng A, Pawlik A, Pletzer A, Shiklomanov A, Fouilloux A, Fournier A, Marwick B, Brown CT, Voter C, Bouquin D, Wilson E, Hart E, Sügis E, Gan E, White E, Michonneau F, Boehm F, Dashnow H, Lapp H, Ashander J, Byrnes J, Hollister JW, Keane J, Herr J, Mislan KAS, KWHall, Woo K, Cranston K, Jordan KL, Ram K, Hertweck K, Todd-Brown K, Lotterhos K, Direk K, Chatzidimitriou K, Deer L, Laurent, Wasser L, Tarkowski L, Breckels L, Foos M, Ankenbrand M, Ankenbrand MJ, Kuzak M, Koontz M, Johnston M, Marino N, Carchedi N, Lijnzaad P, Shawn, Labou S, Pederson S, Webster T, Hart T, Sandmann T, Teal T, Furnass W, Pearse W, Li Y, ashander, cbahlai, clarashaw, duffymeg, ejh243, fishman, jsta, markrobinsonuzh, mchiapello, mkuzak, plijnzaad, riverpeek, sarahsupp, sfn_brt, stubbsda and suparee (2017). “Data Carpentry: R for data analysis and visualization of Ecological Data.” doi: <a href="http://doi.org/10.5281/zenodo.569338">10.5281/zenodo.569338</a>, <a href="http://datacarpentry.org/R-ecology-lesson">http://datacarpentry.org/R-ecology-lesson</a>.
+von Hardenberg A, Obeng A, Pawlik A, Pletzer A, Shiklomanov A, Fouilloux A, Fournier A, Marwick B, Brown CT, Voter C, Hulshof C, Bahlai C, Shaw C, Bouquin D, Stubbs D, Vanichkina D, Fishman D, Wilson E, Hart E, Hannon E, Sügis E, Strauss E, Gan E, Becker E, White E, Rodriguez-Sanchez F, Michonneau F, Boehm F, Ye H, Dashnow H, Lapp H, Ashander J, Byrnes J, Hollister JW, Chen J, Dunic J, Keane J, Stachelek J, Herr J, Mislan KAS, Woo K, Cranston K, Jordan KL, Ram K, Hertweck K, Todd-Brown K, Lotterhos K, Peck K, Direk K, Hall K, Tylén K, Chatzidimitriou K, Deer L, Gatto L, Wasser L, Tarkowski L, Breckels L, Foos M, Chiapello M, Robinson M, Akenbrand MJ, Kuzak M, Grenié M, Grenié M, Duffy M, Koontz M, Johnston M, Marino N, Carchedi N, Burge O, Lijnzaad P, Lijnzaad P, Peek R, Supp S, Taylor S, Labou S, Pederson S, Webster T, Sandmann T, Teal T, Furnass W, Pearse W, Li Y, Lapp Z, ashander, sfn_brt and suparee (2017). “Data Carpentry: R for data analysis and visualization of Ecological Data.” doi: <a href="http://doi.org/10.5281/zenodo.569338">10.5281/zenodo.569338</a>, <a href="http://datacarpentry.org/R-ecology-lesson">http://datacarpentry.org/R-ecology-lesson</a>.
 </p>
 <p>or as a BibTeX entry:</p>
 <pre><code>@Misc{,
-  author = {Adam Obeng and Aleksandra Pawlik and Alex Pletzer and Alexey Shiklomanov and Anne Fouilloux and Auriel Fournier and Ben Marwick and C. Titus Brown and Carolyn Voter and Daina Bouquin and Earle Wilson and Edmund Hart and Elena Sügis and Emilia Gan and Ethan White and Francois Michonneau and Fred Boehm and Harriet Dashnow and Hilmar Lapp and Jaime Ashander and Jarrett Byrnes and Jeffrey W Hollister and Jonathan Keane and Josh Herr and K. A. S. Mislan and {KWHall} and Kara Woo and Karen Cranston and Kari L. Jordan and Karthik Ram and Kate Hertweck and Kathe Todd-Brown and Katie Lotterhos and Kenan Direk and Kyriakos Chatzidimitriou and Lachlan Deer and {Laurent} and Leah Wasser and Leszek Tarkowski and Lisa Breckels and M. Foos and Markus Ankenbrand and Markus J. Ankenbrand and Mateusz Kuzak and Michael Koontz and Myfanwy Johnston and Nicholas Marino and Nick Carchedi and Philip Lijnzaad and {Shawn} and Stephanie Labou and Steve Pederson and Tara Webster and Ted Hart and Thomas Sandmann and Tracy Teal and Will Furnass and Will Pearse and Ye Li and {ashander} and {cbahlai} and {clarashaw} and {duffymeg} and {ejh243} and {fishman} and {jsta} and {markrobinsonuzh} and {mchiapello} and {mkuzak} and {plijnzaad} and {riverpeek} and {sarahsupp} and {sfn_brt} and {stubbsda} and {suparee}},
+  author = {Achaz {von Hardenberg} and Adam Obeng and Aleksandra Pawlik and Alex Pletzer and Alexey Shiklomanov and Anne Fouilloux and Auriel Fournier and Ben Marwick and C. Titus Brown and Carolyn Voter and Catherine Hulshof and Christie Bahlai and Clara Shaw and Daina Bouquin and Daniel Stubbs and Darya Vanichkina and Dmytro Fishman and Earle Wilson and Edmund Hart and Eilis Hannon and Elena Sügis and Eli Strauss and Emilia Gan and Erin Becker and Ethan White and Francisco Rodriguez-Sanchez and Francois Michonneau and Fred Boehm and Hao Ye and Harriet Dashnow and Hilmar Lapp and Jaime Ashander and Jarrett Byrnes and Jeffrey W Hollister and Jieming Chen and Jillian Dunic and Jonathan Keane and Joseph Stachelek and Josh Herr and K. A. S. Mislan and Kara Woo and Karen Cranston and Kari L. Jordan and Karthik Ram and Kate Hertweck and Kathe Todd-Brown and Katie Lotterhos and Kayla Peck and Kenan Direk and Kevin Hall and Kristian Tylén and Kyriakos Chatzidimitriou and Lachlan Deer and Laurent Gatto and Leah Wasser and Leszek Tarkowski and Lisa Breckels and M. Foos and Marco Chiapello and Mark Robinson and Markus J. Akenbrand and Mateusz Kuzak and Matthias Grenié and Matthias Grenié and Meghan Duffy and Michael Koontz and Myfanwy Johnston and Nicholas Marino and Nick Carchedi and Olivia Burge and Philip Lijnzaad and Philip Lijnzaad and Ryan Peek and Sarah Supp and Shawn Taylor and Stephanie Labou and Steve Pederson and Tara Webster and Thomas Sandmann and Tracy Teal and Will Furnass and Will Pearse and Ye Li and Zena Lapp and {ashander} and {sfn_brt} and {suparee}},
   title = {Data Carpentry: R for data analysis and visualization of Ecological Data},
   editor = {Francois Michonneau and Auriel Fournier},
   month = {April},
@@ -375,7 +375,7 @@ <h2>Lessons</h2>
   (function () {
     var script = document.createElement("script");
     script.type = "text/javascript";
-    script.src  = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
+    script.src  = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
     document.getElementsByTagName("head")[0].appendChild(script);
   })();
 </script>