├── Images
    ├── badheader.png
    ├── goodheader.png
    └── goodheaderlatex.png
├── Output
    ├── Template_LaTeX.pdf
    └── Template_Word.docx
├── Extras
    ├── Reference_Document.docx
    ├── clinical-mass-spectrometry.csl
    ├── scholarly-metadata.lua
    ├── author-info-blocks.lua
    ├── mybibfile.bib
    └── mytemplate.tex
├── README.md
├── Template_LaTeX.Rmd
└── Template_Word.Rmd


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/Extras/clinical-mass-spectrometry.csl:
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 1 | <?xml version="1.0" encoding="utf-8"?>
 2 | <style xmlns="http://purl.org/net/xbiblio/csl" version="1.0" default-locale="en-US">
 3 |   <!-- Elsevier, generated from "elsevier" metadata at https://github.com/citation-style-language/journals -->
 4 |   <info>
 5 |     <title>Clinical Mass Spectrometry</title>
 6 |     <id>http://www.zotero.org/styles/clinical-mass-spectrometry</id>
 7 |     <link href="http://www.zotero.org/styles/clinical-mass-spectrometry" rel="self"/>
 8 |     <link href="http://www.zotero.org/styles/elsevier-with-titles" rel="independent-parent"/>
 9 |     <category citation-format="numeric"/>
10 |     <issn>2376-9998</issn>
11 |     <updated>2016-07-25T11:35:23+00:00</updated>
12 |     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
13 |   </info>
14 | </style>
15 | 


--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
 1 | # Affiliations
 2 | RMarkdown Templates for Managing Academic Affiliations for MS-Word and LaTeX
 3 | 
 4 | ## Background
 5 | The repository provides an RMardown template for MS-Word or PDF output that allows for multiple authors with disparate affiliations. The problem and solution are discussed [here](http://labrtorian.com/2019/08/26/rmarkdown-template-that-manages-academic-affiliations/). The template handles authors, affiliations, emails, cross referencing of figures/tables, references and reference abbrebations.
 6 | 
 7 | The output for MS-Word looks like this:
 8 | 
 9 | ![multiple authors with affiliations](https://raw.githubusercontent.com/drdanholmes/Affiliations/master/Images/goodheader.png "Word Output")
10 | 
11 | ## Requirements
12 | 
13 | + RMarkdown and all the associated knitr goodies
14 | + [bookdown package](https://bookdown.org/)
15 | + [pandoc](https://pandoc.org/)
16 | + [pandoc-citeproc](https://github.com/jgm/pandoc-citeproc)
17 | + [pandoc-crossref](https://github.com/lierdakil/pandoc-crossref)
18 | + [lua language](https://www.lua.org/)
19 | + [lua scholarly metadata filter](https://github.com/pandoc/lua-filters/tree/master/scholarly-metadata)
20 | + [lua author info blocks filter](https://github.com/pandoc/lua-filters/tree/master/author-info-blocks)
21 | + [LaTeX](https://www.latex-project.org/get/) and the [authblk](https://www.ctan.org/pkg/authblk) package if you want PDF output
22 | 
23 | ## Use
24 | 
25 | Download .Rmd templates and folders, put them in a directory, open either the Word or LaTeX template and knit. Files must have the same relative paths as in the repository. All of the necessary filters and files are in the Extras folder.
26 | 
27 | ## Contact
28 | 
29 | dtholmes@mail.ubc.ca
30 | 
31 | 
32 | 
33 | 


--------------------------------------------------------------------------------
/Extras/scholarly-metadata.lua:
--------------------------------------------------------------------------------
  1 | --[[
  2 | ScholarlyMeta – normalize author/affiliation meta variables
  3 | 
  4 | Copyright (c) 2017-2019 Albert Krewinkel, Robert Winkler
  5 | 
  6 | Permission to use, copy, modify, and/or distribute this software for any purpose
  7 | with or without fee is hereby granted, provided that the above copyright notice
  8 | and this permission notice appear in all copies.
  9 | 
 10 | THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
 11 | REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
 12 | FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
 13 | INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
 14 | OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
 15 | TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
 16 | THIS SOFTWARE.
 17 | ]]
 18 | local List = require 'pandoc.List'
 19 | 
 20 | -- Split a string at commas.
 21 | local function comma_separated_values(str)
 22 |   local acc = List:new{}
 23 |   for substr in str:gmatch('([^,]*)') do
 24 |     acc[#acc + 1] = substr:gsub('^%s*', ''):gsub('%s*$', '') -- trim
 25 |   end
 26 |   return acc
 27 | end
 28 | 
 29 | --- Ensure the return value is a list.
 30 | local function ensure_list (val)
 31 |   if type(val) ~= 'table' then
 32 |     -- create singleton list (or empty list if val == nil).
 33 |     return List:new{val}
 34 |   elseif val.t == 'MetaInlines' then
 35 |     -- check if this is really a comma-separated list
 36 |     local csv = comma_separated_values(pandoc.utils.stringify(val))
 37 |     if #csv >= 2 then
 38 |       return csv
 39 |     end
 40 |     return List:new{val}
 41 |   elseif val.t == 'MetaList' then
 42 |     return List:new(val)
 43 |   else
 44 |     -- MetaBlocks or MetaMap, use as a singleton
 45 |     return List:new{val}
 46 |   end
 47 | end
 48 | 
 49 | --- Returns a function which checks whether an object has the given ID.
 50 | local function has_id (id)
 51 |   return function(x) return x.id == id end
 52 | end
 53 | 
 54 | --- Copy all key-value pairs of the first table into the second iff there is no
 55 | -- such key yet in the second table.
 56 | -- @returns the second argument
 57 | function add_missing_entries(a, b)
 58 |   for k, v in pairs(a) do
 59 |     b[k] = b[k] or v
 60 |   end
 61 |   return b
 62 | end
 63 | 
 64 | --- Create an object with a name. The name is either taken directly from the
 65 | -- `name` field, or from the *only* field name (i.e., key) if the object is a
 66 | -- dictionary with just one entry. If neither exists, the name is left unset
 67 | -- (`nil`).
 68 | function to_named_object (obj)
 69 |   local named = {}
 70 |   if type(obj) ~= 'table' then
 71 |     -- if the object isn't a table, just use its value as a name.
 72 |     named.name = pandoc.MetaInlines{pandoc.Str(tostring(obj))}
 73 |     named.id = tostring(obj)
 74 |   elseif obj.t == 'MetaInlines' then
 75 |       -- Treat inlines as the name
 76 |       named.name = obj
 77 |       named.id = pandoc.utils.stringify(obj)
 78 |   elseif obj.name ~= nil then
 79 |     -- object has name attribute → just create a copy of the object
 80 |     add_missing_entries(obj, named)
 81 |     named.id = pandoc.utils.stringify(named.id or named.name)
 82 |   elseif next(obj) and next(obj, next(obj)) == nil then
 83 |     -- the entry's key is taken as the name, the value contains the
 84 |     -- attributes.
 85 |     key, attribs = next(obj)
 86 |     if type(attribs) == "string" or attribs.t == 'MetaInlines' then
 87 |       named.name = attribs
 88 |     else
 89 |       add_missing_entries(attribs, named)
 90 |       named.name = named.name or pandoc.MetaInlines{pandoc.Str(tostring(key))}
 91 |     end
 92 |     named.id = named.id and pandoc.utils.stringify(named.id) or key
 93 |   else
 94 |     -- this is not a named object adhering to the usual conventions.
 95 |     error('not a named object: ' .. tostring(obj))
 96 |   end
 97 |   return named
 98 | end
 99 | 
100 | --- Resolve institute placeholders to full named objects
101 | local function resolve_institutes (institute, known_institutes)
102 |   local unresolved_institutes
103 |   if institute == nil then
104 |     unresolved_institutes = {}
105 |   elseif type(institute) == "string" or type(institute) == "number" then
106 |     unresolved_institutes = {institute}
107 |   else
108 |     unresolved_institutes = institute
109 |   end
110 | 
111 |   local result = List:new{}
112 |   for i, inst in ipairs(unresolved_institutes) do
113 |     result[i] =
114 |       known_institutes[tonumber(inst)] or
115 |       known_institutes:find_if(has_id(pandoc.utils.stringify(inst))) or
116 |       to_named_object(inst)
117 |   end
118 |   return result
119 | end
120 | 
121 | --- Insert a named object into a list; if an object of the same name exists
122 | -- already, add all properties only present in the new object to the existing
123 | -- item.
124 | function merge_on_id (list, namedObj)
125 |   local elem, idx = list:find_if(has_id(namedObj.id))
126 |   local res = elem and add_missing_entries(namedObj, elem) or namedObj
127 |   local obj_idx = idx or (#list + 1)
128 |   -- return res, obj_idx
129 |   list[obj_idx] = res
130 |   return res, #list
131 | end
132 | 
133 | --- Flatten a list of lists.
134 | local function flatten (lists)
135 |   local result = List:new{}
136 |   for _, lst in ipairs(lists) do
137 |     result:extend(lst)
138 |   end
139 |   return result
140 | end
141 | 
142 | --- Canonicalize authors and institutes
143 | local function canonicalize(raw_author, raw_institute)
144 |   local institutes = ensure_list(raw_institute):map(to_named_object)
145 |   local authors = ensure_list(raw_author):map(to_named_object)
146 | 
147 |   for _, author in ipairs(authors) do
148 |     author.institute = resolve_institutes(
149 |       ensure_list(author.institute),
150 |       institutes
151 |     )
152 |   end
153 | 
154 |   -- Merge institutes defined in author objects with those defined in the
155 |   -- top-level list.
156 |   local author_insts = flatten(authors:map(function(x) return x.institute end))
157 |   for _, inst in ipairs(author_insts) do
158 |     merge_on_id(institutes, inst)
159 |   end
160 | 
161 |   -- replace institutes with their indices
162 |   local to_index = function (inst)
163 |     return tostring(select(2, institutes:find_if(has_id(inst.id))))
164 |   end
165 |   for _, author in ipairs(authors) do
166 |     author.institute = pandoc.MetaList(author.institute:map(to_index))
167 |   end
168 | 
169 |   return authors, institutes
170 | end
171 | 
172 | 
173 | return {
174 |   {
175 |     Meta = function(meta)
176 |       meta.author, meta.institute = canonicalize(meta.author, meta.institute)
177 |       return meta
178 |     end
179 |   }
180 | }
181 | 


--------------------------------------------------------------------------------
/Extras/author-info-blocks.lua:
--------------------------------------------------------------------------------
  1 | --[[
  2 | affiliation-blocks – generate title components
  3 | 
  4 | Copyright © 2017–2019 Albert Krewinkel
  5 | 
  6 | Permission to use, copy, modify, and/or distribute this software for any purpose
  7 | with or without fee is hereby granted, provided that the above copyright notice
  8 | and this permission notice appear in all copies.
  9 | 
 10 | THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
 11 | REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
 12 | FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
 13 | INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
 14 | OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
 15 | TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
 16 | THIS SOFTWARE.
 17 | ]]
 18 | local List = require 'pandoc.List'
 19 | local utils = require 'pandoc.utils'
 20 | local stringify = utils.stringify
 21 | 
 22 | local default_marks
 23 | local default_marks = {
 24 |   corresponding_author = FORMAT == 'latex'
 25 |     and {pandoc.RawInline('latex', '*')}
 26 |     or {pandoc.Str '✉'},
 27 |   equal_contributor = FORMAT == 'latex'
 28 |     and {pandoc.RawInline('latex', '$\\dagger{}$')}
 29 |     or {pandoc.Str '*'},
 30 | }
 31 | 
 32 | local function intercalate(lists, elem)
 33 |   local result = List:new{}
 34 |   for i = 1, (#lists - 1) do
 35 |     result:extend(lists[i])
 36 |     result:extend(elem)
 37 |   end
 38 |   if #lists > 0 then
 39 |     result:extend(lists[#lists])
 40 |   end
 41 |   return result
 42 | end
 43 | 
 44 | --- Check whether the given author is a corresponding author
 45 | local function is_corresponding_author(author)
 46 |   return author.correspondence and author.email
 47 | end
 48 | 
 49 | --- Create inlines for a single author (includes all author notes)
 50 | local function author_inline_generator (get_mark)
 51 |   return function (author)
 52 |     local author_marks = List:new{}
 53 |     if author.equal_contributor then
 54 |       author_marks[#author_marks + 1] = get_mark 'equal_contributor'
 55 |     end
 56 |     local idx_str
 57 |     for _, idx in ipairs(author.institute) do
 58 |       if type(idx) ~= 'table' then
 59 |         idx_str = tostring(idx)
 60 |       else
 61 |         idx_str = stringify(idx)
 62 |       end
 63 |       author_marks[#author_marks + 1] = {pandoc.Str(idx_str)}
 64 |     end
 65 |     if is_corresponding_author(author) then
 66 |       author_marks[#author_marks + 1] = get_mark 'corresponding_author'
 67 |     end
 68 |     local res = List.clone(author.name)
 69 |     res[#res + 1] = pandoc.Superscript(intercalate(author_marks, {pandoc.Str ','}))
 70 |     return res
 71 |   end
 72 | end
 73 | 
 74 | local function is_equal_contributor (author)
 75 |   return author.equal_contributor
 76 | end
 77 | 
 78 | --- Create equal contributors note.
 79 | local function create_equal_contributors_block(authors, mark)
 80 |   local has_equal_contribs = List:new(authors):find_if(is_equal_contributor)
 81 |   if not has_equal_contribs then
 82 |     return nil
 83 |   end
 84 |   local contributors = {
 85 |     pandoc.Superscript(mark'equal_contributor'),
 86 |     pandoc.Space(),
 87 |     pandoc.Str 'These authors contributed equally to this work.'
 88 |   }
 89 |   return List:new{pandoc.Para(contributors)}
 90 | end
 91 | 
 92 | --- Generate a block list all affiliations, marked with arabic numbers.
 93 | local function create_affiliations_blocks(affiliations)
 94 |   local affil_lines = List:new(affiliations):map(
 95 |     function (affil, i)
 96 |       local num_inlines = List:new{
 97 |         pandoc.Superscript{pandoc.Str(tostring(i))},
 98 |         pandoc.Space()
 99 |       }
100 |       return num_inlines .. affil.name
101 |     end
102 |                                                 )
103 |   return {pandoc.Para(intercalate(affil_lines, {pandoc.LineBreak()}))}
104 | end
105 | 
106 | --- Generate a block element containing the correspondence information
107 | local function create_correspondence_blocks(authors, mark)
108 |   local corresponding_authors = List:new{}
109 |   for _, author in ipairs(authors) do
110 |     if is_corresponding_author(author) then
111 |       local mailto = 'mailto:' .. pandoc.utils.stringify(author.email)
112 |       local author_with_mail = List:new(
113 |         author.name .. List:new{pandoc.Space(),  pandoc.Str '<'} ..
114 |         author.email .. List:new{pandoc.Str '>'}
115 |       )
116 |       local link = pandoc.Link(author_with_mail, mailto)
117 |       table.insert(corresponding_authors, {link})
118 |     end
119 |   end
120 |   if #corresponding_authors == 0 then
121 |     return nil
122 |   end
123 |   local correspondence = List:new{
124 |     pandoc.Superscript(mark'corresponding_author'),
125 |     pandoc.Space(),
126 |     pandoc.Str'Correspondence:',
127 |     pandoc.Space()
128 |   }
129 |   local sep = List:new{pandoc.Str',',  pandoc.Space()}
130 |   return {
131 |     pandoc.Para(correspondence .. intercalate(corresponding_authors, sep))
132 |   }
133 | end
134 | 
135 | --- Generate a list of inlines containing all authors.
136 | local function create_authors_inlines(authors, mark)
137 |   local inlines_generator = author_inline_generator(mark)
138 |   local inlines = List:new(authors):map(inlines_generator)
139 |   local and_str = List:new{pandoc.Space(), pandoc.Str'and', pandoc.Space()}
140 | 
141 |   local last_author = inlines[#inlines]
142 |   inlines[#inlines] = nil
143 |   local result = intercalate(inlines, {pandoc.Str ',', pandoc.Space()})
144 |   if #authors > 1 then
145 |     result:extend(List:new{pandoc.Str ","} .. and_str)
146 |   end
147 |   result:extend(last_author)
148 |   return result
149 | end
150 | 
151 | return {
152 |   {
153 |     Pandoc = function (doc)
154 |       local meta = doc.meta
155 |       local body = List:new{}
156 | 
157 |       local mark = function (mark_name) return default_marks[mark_name] end
158 | 
159 |       body:extend(create_equal_contributors_block(doc.meta.author, mark) or {})
160 |       body:extend(create_affiliations_blocks(doc.meta.institute) or {})
161 |       body:extend(create_correspondence_blocks(doc.meta.author, mark) or {})
162 |       body:extend(doc.blocks)
163 | 
164 |       -- Overwrite authors with formatted values. We use a single, formatted
165 |       -- string for most formats. LaTeX output, however, looks nicer if we
166 |       -- provide a authors as a list.
167 |       meta.author = FORMAT:match 'latex'
168 |         and pandoc.MetaList(doc.meta.author):map(author_inline_generator(mark))
169 |         or pandoc.MetaInlines(create_authors_inlines(doc.meta.author, mark))
170 |       -- Institute info is now baked into the affiliations block.
171 |       meta.institute = nil
172 | 
173 |       return pandoc.Pandoc(body, meta)
174 |     end
175 |   }
176 | }
177 | 


--------------------------------------------------------------------------------
/Extras/mybibfile.bib:
--------------------------------------------------------------------------------
 1 | @article{EISENHOFER201940,
 2 | 	title = "Steroid metabolomics: machine learning and multidimensional diagnostics for adrenal cortical tumors, hyperplasias, and related disorders",
 3 | 	journal = "Current Opinion in Endocrine and Metabolic Research",
 4 | 	volume = "8",
 5 | 	pages = "40 - 49",
 6 | 	year = "2019",
 7 | 	issn = "2451-9650",
 8 | 	doi = "https://doi.org/10.1016/j.coemr.2019.07.002",
 9 | 	url = "http://www.sciencedirect.com/science/article/pii/S2451965019300341",
10 | 	author = "Graeme Eisenhofer and Claudio Durán and Triantafyllos Chavakis and Carlo Vittorio Cannistraci",
11 | 	keywords = "Steroids, Steroidomics, Machine learning, Mass spectrometry, LC-MS/MS, Adrenal, Primary aldosteronism, Cushing syndrome, Adrenal cortical carcinoma",
12 | 	abstract = "Steroid profiling applications have a long history primarily directed toward diagnosis of endocrine disorders of childhood. Technological advances in mass spectrometry enabling rapid, sensitive, and specific measurements of multiple steroids in biological fluids are now paving the way for numerous other applications, including diagnosis of adrenocortical carcinoma, primary aldosteronism, and different forms of hypercortisolism. Such analytical procedures that target combinations of steroids in a single biological sample have potential for efficient one-shot methods for diagnosis of multiple disorders of steroidogenesis. Moreover, within a specific disorder, such methods can facilitate subtyping for more rapid therapeutic stratification than allowed by current methods that rely on single measurements per sample at sequential time points in a diagnostic process. Combined with advances in computational mathematics, such as machine learning, it is now possible to move from traditional unidimensional approaches for interpreting diagnostic data to methods that can interpret patterns in data. Mass spectrometry–based steroidomics provides an ideal platform for advancing such multidimensional approaches for disease diagnosis and stratification. Bottlenecks that must be overcome to move forward include needs for laboratory harmonization and method certification combined with ingrained reliance on outmoded, but well-accepted, diagnostic methods and general inertia to take advantage of new technologies."
13 | }
14 | 
15 | @article{VICENTE201984,
16 | 	title = "Automation of chromatographic peak review and order to result data transfer in a clinical mass spectrometry laboratory",
17 | 	journal = "Clinica Chimica Acta",
18 | 	volume = "498",
19 | 	pages = "84 - 89",
20 | 	year = "2019",
21 | 	issn = "0009-8981",
22 | 	doi = "https://doi.org/10.1016/j.cca.2019.08.004",
23 | 	url = "http://www.sciencedirect.com/science/article/pii/S0009898119319928",
24 | 	author = "Faye B. Vicente and David C. Lin and Shannon Haymond",
25 | 	keywords = "Mass spectrometry, Informatics, Quality",
26 | 	abstract = "Introduction
27 | 	Mass spectrometry-based assays have increasingly been implemented in clinical laboratories for their multiplexing capacity and high specificity and sensitivity. However, these methods are often associated with labor-intensive and error-prone data-related workflows, due to the volume of data generated that is often manually reviewed and resulted. We aimed to establish a system within our clinical mass spectrometry laboratory to facilitate data ‘flow’ from electronic medical record order to result and to automate processes for chromatogram peak review. The processes and validation are described for a 25-hydroxyvitamin D assay.
28 | 	Methods
29 | 	Automating chromatogram review and order to result data transfer required flat file interfacing, file transfers of standardized data formats, barcode scanning, and software for peak processing and review. Validation of the automated workflow involved (1) correlation of quantified results generated by two chromatogram analysis methods: Waters TargetLynx and Indigo Bioautomation ASCENT, (2) manual verification of quality assurance flags applied in ASCENT, and (3) testing data flow and integrity across all the systems from order to result. Efficiency and quality improvements were assessed through calculation of batch review times and rates for autoverification and manual manipulations.
30 | 	Results
31 | 	The correlation of TargetLynx and ASCENT quantitation methods for 25-hydroxyvitamin D2 in patient samples yielded slope of 0.99 (95% CI: 0.989 to 0.996), intercept of 0.46 (95% CI: 0.363 to 0.565), with r = 0.999. The correlation for the D3 fraction showed Deming regression slope of 0.98 (95% CI: 0.969 to 0.989), intercept of 0.06 (95% CI: −0.115 to 0.313), and r = 0.995. Results from both quantitation approaches were also compared to the assigned value in CDC reference samples. The mean bias relative to the CDC was 4.6% for ASCENT and 2.5% for TargetLynx. The median time for chromatogram review of a full 96-well plate of vitamin D results is reduced from approximately 2 h to 14 min and 80% of batches were reviewed within 30 min. Instead of 100% peak review, technologists review only the peaks that have been flagged by the system based on applied rules. Analysis of full plate batches showed that 2–20% of peaks per batch were flagged for manual review. Manipulations made by technologists during chromatogram review were reduced by 75% when using the automated versus manual system.
32 | 	Conclusions
33 | 	We describe a system to facilitate data ‘flow’ from electronic order to result and to automate chromatogram peak review in a clinical liquid chromatography mass spectrometry assay for 25-hydroxyvitamin D. This eliminated manual result entry, repetitive transcription, and unnecessary review of high quality data while enabling systematic evaluation of data quality indicators. The new processes were accurate, improved the data review and processing times, and helped to reduce manual manipulations during chromatogram review."
34 | }
35 | 
36 | @article{10.1371/journal.pcbi.1003285,
37 | 	author = {Sandve, Geir Kjetil AND Nekrutenko, Anton AND Taylor, James AND Hovig, Eivind},
38 | 	journal = {PLOS Computational Biology},
39 | 	publisher = {Public Library of Science},
40 | 	title = {Ten Simple Rules for Reproducible Computational Research},
41 | 	year = {2013},
42 | 	month = {10},
43 | 	volume = {9},
44 | 	url = {https://doi.org/10.1371/journal.pcbi.1003285},
45 | 	pages = {1-4},
46 | 	abstract = {},
47 | 	number = {10},
48 | 	doi = {10.1371/journal.pcbi.1003285}
49 | }
50 | 
51 | @article{peng2011reproducible,
52 |   title={Reproducible research in computational science},
53 |   author={Peng, Roger D},
54 |   journal={Science},
55 |   volume={334},
56 |   number={6060},
57 |   pages={1226--1227},
58 |   year={2011},
59 |   publisher={American Association for the Advancement of Science}
60 | }
61 | 
62 | @book{xie2018r,
63 | 	title={R markdown: The definitive guide},
64 | 	author={Xie, Yihui and Allaire, Joseph J and Grolemund, Garrett},
65 | 	year={2018},
66 | 	publisher={Chapman and Hall/CRC},
67 | 	url={https://bookdown.org/yihui/bookdown}
68 | }


--------------------------------------------------------------------------------
/Template_LaTeX.Rmd:
--------------------------------------------------------------------------------
  1 | ---
  2 | title: |
  3 |   RMarkdown Template for Managing  
  4 |   Academic Affiliations 
  5 | subtitle: |
  6 |   Also Deals with Cross References and  
  7 |   Reference Abbreviations for PDF Output
  8 | author:
  9 | - name: Duke A Caboom, MD
 10 |   affiliation: University of Tuktoyaktuk, CXVG+62 Tuktoyaktuk, Inuvik, Unorganized, NT Canada
 11 |   email: dtholmes@mail.ubc.ca
 12 |   number: 1
 13 | - name: Justin d'Ottawa, PhD
 14 |   affiliation: University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5, Canada
 15 |   email: justin@uottawa.ca
 16 |   number: 2
 17 | abstract: |
 18 |   **Introduction**: There's a big scientific problem out there. I know how to fix it.
 19 |   
 20 |   **Methods**: My experiments are pure genius.
 21 |   
 22 |   **Results**: Now you have your proof.
 23 |   
 24 |   **Conclusion**: Give me more grant money.
 25 | toc: false
 26 | output: 
 27 |   bookdown::pdf_document2:
 28 |     pandoc_args:
 29 |       - --filter=pandoc-crossref
 30 |       - --csl=Extras/clinical-mass-spectrometry.csl
 31 |       - --citation-abbreviations=Extras/abbreviations.json
 32 |       - --template=Extras/mytemplate.tex
 33 |     keep_tex: true
 34 | bibliography: "Extras/mybibfile.bib"
 35 | ---
 36 | 
 37 | ```{r setup, include=FALSE}
 38 | knitr::opts_chunk$set(echo = TRUE, fig.align = "center", out.width = "5in", out.height = "4in")
 39 | ```
 40 | 
 41 | # Background
 42 | 
 43 | I like writing my academic papers in RMarkdown because it allows reproducible research. The cleanest way to submit a manuscript made in RMarkdown is using the LaTeX code that it generates using the YAML switch `keep_tex = true`. A minimalist YAML header would look like so:
 44 | 
 45 | ```
 46 | ---
 47 | title: The document title
 48 | author: 
 49 |   - Duke A Caboom, MD
 50 |   - Justin d'Ottawa, PhD:
 51 | output: 
 52 |   pdf_document:
 53 |     keep_tex: true
 54 | ---
 55 | ```
 56 | # Introduction 
 57 | 
 58 | However, when you want mutliple authors affiliations you discover that you can't do as you would in LaTeX because [Pandoc]() does not know what to do with the affiliations and you end out a dishearting PDF that looks like the output shown in figure \@ref(fig:sosad) below:
 59 | 
 60 | ```{r sosad, echo=FALSE, fig.cap="This is so sad.", fig.align="center"}
 61 | knitr::include_graphics("Images/badheader.png")
 62 | library(png)
 63 | ```
 64 | 
 65 | The situation worsens if you want MS-Word output.  As those of us in medical fields know, most journals, with some notable exceptions like the [Clinical Mass Spectrometry Journal](https://www.journals.elsevier.com/clinical-mass-spectrometry) and other Elsevier journals like [Clinical Biochemistry](https://www.journals.elsevier.com/clinical-biochemistry) and [Clinica Chimica Acta](https://www.journals.elsevier.com/clinica-chimica-acta), require submission of a document in MS-Word format which goes against all that Data Science and Reprodicible Research stands for. Parenthetically, it is my hope that since [AACC](www.aacc.org) has indicated to make Data Science a strategic priority for Lab Medicine, that they will soon accept submissons to [Clinical Chemistry](http://clinchem.aaccjnls.org/) and [Journal of Applied Laboratory Medicine](http://jalm.aaccjnls.org/) written reproducibly in RMardown or LaTeX. 
 66 | 
 67 | In the mean time, here are the workarounds for getting the affiliations to display correctly along with all the other stuff we want, namely, cross referencing of figures and tables and correct reference formatting and abbreviation of journal names. This allows you to avoid the horror of manually fixing your Word document after it generated from RMarkdown. In any case, let's start with MS-Word. 
 68 | 
 69 | # Dependencies for MS-Word and the Associated YAML
 70 | 
 71 | It goes without saying that you need to install LaTeX. LaTeX markup language is available here: [Mac](http://www.tug.org/mactex/), [Windows](https://miktex.org/download). For Linux, just install from the command line with your package manager. Do a full install with all the glorious bloat of all LaTeX packages. This saves many headaches in the future.
 72 | 
 73 | You will also need to install [Pandoc](https://pandoc.org/) which is the Swiss Army Knife of document conversion. It's going to turn LaTeX code into a .docx file for you. Mac users can do this with Homebrew on the terminal command line:
 74 | 
 75 | ```
 76 | brew install pandoc
 77 | brew install pandoc-citeproc
 78 | brew install pandoc-crossref
 79 | ```
 80 | 
 81 | There are some extra installs required to help Pandoc do its job. Install the prebuilt binaries if you can.
 82 | 
 83 | + [pandoc-citeproc](http://hackage.haskell.org/package/pandoc-citeproc)
 84 | + [pandoc-crossref](https://github.com/lierdakil/pandoc-crossref/releases/tag/v0.3.4.1a)
 85 | 
 86 | Finally, you need to use some scripts written in the Lua scripting language which means you will need the language itself:
 87 | + [lua language](https://www.lua.org/download.html)
 88 | 
 89 | And you will need two Lua scripts:
 90 | 
 91 | These are in Pandoc github repository:
 92 | 
 93 | + [scholarly-metadata.lua](https://github.com/pandoc/lua-filters/tree/master/scholarly-metadata)
 94 | + [author-info-blocks.lua](https://github.com/pandoc/lua-filters/tree/master/author-info-blocks)
 95 | 
 96 | You want the files named [scholarly-metadata.lua](https://raw.githubusercontent.com/pandoc/lua-filters/master/scholarly-metadata/scholarly-metadata.lua) and [author-info-blocks.lua](https://raw.githubusercontent.com/pandoc/lua-filters/master/author-info-blocks/author-info-blocks.lua).
 97 | 
 98 | You will need to choose a .csl file for your journal. This will tell Pandoc how to format the references. You can download the correct .csl file [here](https://www.zotero.org/styles). You will also need a journal abbreviations database. I have made one for you from the [Web of Science list](https://images.webofknowledge.com/images/help/WOS/A_abrvjt.html) and you can download it [here](https://github.com/drdanholmes/Affiliations/blob/master/Extras/abbreviations.json).
 99 | 
100 | You will need to creat a .bibtex database which is just your list of references. This can be exported from various reference managers or built by hand. Name the file `mybibfile.bib`.
101 | 
102 | Now follow the bouncing ball:
103 | 
104 | 1. Go to the directory containing your .Rmd file.
105 | 2. Create a directory in it called "Extras"
106 | 3. Put the two Lua scripts, the Bibtex database, the abbreviations database and the .csl file into the "Extras" folder.
107 | 4. If you want to avoid Pandoc's goofy default .docx formatting, then put [this word document](https://github.com/drdanholmes/Affiliations/blob/master/Extras/Reference_Document.docx) in the same folder.
108 | 
109 | OR
110 | 
111 | Download [the contents of this folder](https://github.com/drdanholmes/Affiliations) from my github folder that has everything set up as I describe above.
112 | 
113 | For two authors, your YAML will need to look like this:
114 | 
115 | ```
116 | title: |
117 |   RMarkdown Template for Managing  
118 |   Academic Affiliations 
119 | subtitle: |
120 |   Also Deals with Cross References and  
121 |   Reference Abbreviations for MS-Word Output
122 | author:
123 |   - Duke A Caboom, MD:
124 |       email: duke.a.caboom@utuktoyaktuk.edu
125 |       institute: [UofT]
126 |       correspondence: true
127 |   - Justin d'Ottawa, PhD:
128 |       email: justin@neverready.ca
129 |       institute: [UofO]
130 |       correspondence: false
131 | institute:
132 |   - UofT: University of Tuktoyaktuk, CXVG+62 Tuktoyaktuk, Inuvik, Unorganized, NT Canada
133 |   - UofO: University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5, Canada
134 | abstract: |
135 |   **Introduction**: There's a big scientific problem out there. I know how to fix it.
136 |   **Methods**: My experiments are pure genius.
137 |   **Results**: Now you have your proof.
138 |   **Conclusion**: Give me more grant money.
139 | journal: "An awesome journal"
140 | date: ""
141 | toc: false
142 | output:
143 |  bookdown::word_document2:
144 |     pandoc_args:
145 |       - --csl=Extras/clinical-biochemistry.csl
146 |       - --citation-abbreviations=Extras/abbreviations.json
147 |       - --filter=pandoc-crossref
148 |       - --lua-filter=Extras/scholarly-metadata.lua
149 |       - --lua-filter=Extras/author-info-blocks.lua
150 |       - --reference-doc=Extras/Reference_Document.docx 
151 | bibliography: "Extras/mybibfile.bib"
152 | keywords: "CRAN, R, RMarkdown, RStudio, YAML"
153 | ```
154 | 
155 | Et voila! Figure \@ref(fig:sohappy) shows that we have something reasonable.
156 | 
157 | ```{r sohappy, echo=FALSE, fig.cap="This is so great", fig.align="center"}
158 | knitr::include_graphics("Images/goodheader.png")
159 | ```
160 | 
161 | # Dependencies for LaTeX and the Associated YAML
162 | 
163 | You don't need the lua scripts for LaTeX although you *can* use them. The issue with LaTeX is that the .tex template that Pandoc uses for generating LaTeX files does not support author affiliations as descibed [in the Pandoc documentation](https://pandoc.org/MANUAL.html). So what you need to do is modify the Pandoc LaTeX template. To get your current working copy of the Pandoc LaTeX template open up a terminal (Mac/Linux) and type:
164 | 
165 | ```
166 | pandoc -D latex > mytemplate.tex
167 | ```
168 | 
169 | This will push the contents to a file. Move the file to the "Extras" folder discussed above. If that seems difficult, you can also download it [here](https://github.com/jgm/pandoc-templates/blob/master/default.latex). Now you have to edit it. Open it up in a text editor and find the section that reads:
170 | 
171 | ```
172 | $if(author)$
173 | \author{$for(author)$$author$$sep$ \and $endfor$}
174 | $endif$
175 | ```
176 | Replace this with this code that will invoke the LaTeX [authblk](https://www.ctan.org/pkg/authblk) package.
177 | 
178 | ```
179 | $if(author)$
180 | 	\usepackage{authblk}
181 | 	$for(author)$
182 | 		$if(author.name)$
183 | 			$if(author.number)$
184 | 				\author[$author.number$]{$author.name$}
185 | 			$else$
186 | 				\author[]{$author.name$}
187 | 			$endif$
188 | 			$if(author.affiliation)$
189 | 				$if(author.email)$
190 | 					\affil{$author.affiliation$ \thanks{$author.email$}}
191 | 				$else$
192 | 					\affil{$author.affiliation$}
193 | 				$endif$
194 | 			$endif$
195 | 			$else$	
196 | 			\author{$author$}
197 | 		$endif$
198 | 	$endfor$
199 | $endif$
200 | ```
201 | 
202 | Then make your YAML header look like this:
203 | 
204 | ```
205 | ---
206 | title: |
207 |   RMarkdown Template for Managing  
208 |   Academic Affiliations 
209 | subtitle: |
210 |   Also Deals with Cross References and  
211 |   Reference Abbreviations for PDF Output
212 | author:
213 | - name: Duke A Caboom, MD
214 |   affiliation: University of Tuktoyaktuk, CXVG+62 Tuktoyaktuk, Inuvik, Unorganized, NT Canada
215 |   email: dtholmes@mail.ubc.ca
216 |   number: 1
217 | - name: Justin d'Ottawa, PhD
218 |   affiliation: University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5, Canada
219 |   email: justin@neverready.ca
220 |   number: 2
221 | abstract: |
222 |   **Introduction**: There's a big scientific problem out there. I know how to fix it.
223 |   
224 |   **Methods**: My experiments are pure genius.
225 |   
226 |   **Results**: Now you have your proof.
227 |   
228 |   **Conclusion**: Give me more grant money.
229 | toc: false
230 | output: 
231 |   bookdown::pdf_document2:
232 |     pandoc_args:
233 |       - --filter=pandoc-crossref
234 |       - --csl=Extras/clinical-biochemistry.csl
235 |       - --citation-abbreviations=Extras/abbreviations.json
236 |       - --template=Extras/mytemplate.tex
237 | bibliography: "Extras/mybibfile.bib"
238 | keep-latex: true
239 | ```
240 | 
241 | And as you can see in \@ref(fig:sohappylatex) you get a correctly list of authors.
242 | 
243 | ```{r sohappylatex, echo=FALSE, fig.cap="This is also great.", fig.align="center"}
244 | knitr::include_graphics("Images/goodheaderlatex.png")
245 | ```
246 | 
247 | ## Cross Reference of a Table
248 | 
249 | Of course, tables can be cross referenced in the same manner as figures. Here is a cross reference to table \@ref(tab:mytable) using the code `\@ref(tab:mytable)` .
250 | 
251 | ```{r mytable, echo = FALSE}
252 | library(broom)
253 | mod <- lm(mpg ~ hp + cyl, data = mtcars)
254 | knitr::kable(tidy(mod), digits = 3, booktabs = TRUE, caption = "A short table")
255 | ```
256 | 
257 | ## This Template also Takes Care of Reference Abbreviation.
258 | 
259 | As usual, you can make a citation with the code `[@bibtexname]`, where `bibtexname` is the articles's abbreviated handle in your bibtex database. Here is a great resource on the bookdown package [@xie2018r] and reproducible research [@peng2011reproducible] and here are references where the journal title is longer [@EISENHOFER201940; @VICENTE201984]. The references in your documnent (and shown below) will have appropriate abbreviations based on the .json abbreviations database I have provided. In this case, I have chosen the .csl file for Clinical Mass Spectrometry--'cause [MSACL](https://www.msacl.org/).
260 | 
261 | 
262 | 
263 | # Other Ways to Skin the YAML Cat
264 | 
265 | I came across some other ways to deal with this that I did not like as much but they are simpler. Here is one using a footnote.
266 | 
267 | ```
268 | title: The document title
269 | author:
270 | - [Duke A Caboom, MD]^(University of Tuktoyaktuk, CXVG+62 Tuktoyaktuk, Inuvik, Unorganized, NT Canada)
271 | - [Justin d'Ottawa, PhD]^(University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5, Canada)
272 | output: pdf_document
273 | ```
274 | 
275 | And you can also misuse the `date` variable:
276 | 
277 | ```
278 | title: The document title
279 | author:
280 | - Duke A Caboom, MD [1]
281 | - Justin d'Ottawa, PhD [2]
282 | date: 1. University of Tuktoyaktuk, CXVG+62 Tuktoyaktuk, Inuvik, Unorganized, NT Canada \newline 2. University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5, Canada
283 | output: pdf_document
284 | ```
285 | 
286 | # Conclusion
287 | 
288 | This concludes my long personal struggle to get a completely reproducible .docx manusript genereated by RMardown and Pandoc.
289 | 
290 | ## Parting Thought
291 | 
292 | **Let us not become weary in doing good, for at the proper time we will reap a harvest if we do not give up.**
293 | 
294 | **Galations 6:9**
295 | 
296 | # References
297 | 


--------------------------------------------------------------------------------
/Template_Word.Rmd:
--------------------------------------------------------------------------------
  1 | ---
  2 | title: |
  3 |   RMarkdown Template for Managing  
  4 |   Academic Affiliations 
  5 | subtitle: |
  6 |   Also Deals with Cross References and  
  7 |   Reference Abbreviations for MS-Word Output
  8 | author:
  9 |   - Duke A Caboom, MD:
 10 |       email: duke.a.caboom@utuktoyaktuk.edu
 11 |       institute: [UofT]
 12 |       correspondence: true
 13 |   - Justin d'Ottawa, PhD:
 14 |       email: justin@uottawa.ca
 15 |       institute: [UofO]
 16 |       correspondence: false
 17 | institute:
 18 |   - UofT: University of Tuktoyaktuk, CXVG+62 Tuktoyaktuk, Inuvik, Unorganized, NT Canada
 19 |   - UofO: University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5, Canada
 20 | abstract: |
 21 |   **Introduction**: There's a big scientific problem out there. I know how to fix it.
 22 |   
 23 |   **Methods**: My experiments are pure genius.
 24 |   
 25 |   **Results**: Now you have your proof.
 26 |   
 27 |   **Conclusion**: Give me more grant money.
 28 | journal: "An awesome journal"
 29 | date: ""
 30 | toc: false
 31 | output:
 32 |  bookdown::word_document2:
 33 |     pandoc_args:
 34 |       - --csl=Extras/clinical-mass-spectrometry.csl
 35 |       - --citation-abbreviations=Extras/abbreviations.json
 36 |       - --filter=pandoc-crossref
 37 |       - --lua-filter=Extras/scholarly-metadata.lua
 38 |       - --lua-filter=Extras/author-info-blocks.lua
 39 |       - --reference-doc=Extras/Reference_Document.docx
 40 |  bookdown::pdf_document2:
 41 |       pandoc_args:
 42 |       - --csl=Extras/clinical-mass-spectrometry.csl
 43 |       - --citation-abbreviations=Extras/abbreviations.json
 44 |       - --filter=pandoc-crossref
 45 |       - --lua-filter=Extras/scholarly-metadata.lua
 46 |       - --lua-filter=Extras/author-info-blocks.lua
 47 | bibliography: "Extras/mybibfile.bib"
 48 | keywords: "CRAN, R, RMarkdown, RStudio, YAML"
 49 | ---
 50 | # Background
 51 | 
 52 | I like writing my academic papers in RMarkdown because it allows reproducible research. The cleanest way to submit a manuscript made in RMarkdown is using the LaTeX code that it generates using the YAML switch `keep_tex = true`. A minimalist YAML header would look like so:
 53 | 
 54 | ```
 55 | ---
 56 | title: The document title
 57 | author: 
 58 |   - Duke A Caboom, MD
 59 |   - Justin d'Ottawa, PhD:
 60 | output: 
 61 |   pdf_document:
 62 |     keep_tex: true
 63 | ---
 64 | ```
 65 | # Introduction 
 66 | 
 67 | However, when you want mutliple authors affiliations you discover that you can't do as you would in LaTeX because [Pandoc]() does not know what to do with the affiliations and you end out a dishearting PDF that looks like the output shown in figure \@ref(fig:sosad) below:
 68 | 
 69 | ```{r sosad, echo=FALSE, fig.cap="This is so sad.", fig.align="center"}
 70 | knitr::include_graphics("Images/badheader.png")
 71 | library(png)
 72 | ```
 73 | 
 74 | The situation worsens if you want MS-Word output.  As those of us in medical fields know, most journals, with some notable exceptions like the [Clinical Mass Spectrometry Journal](https://www.journals.elsevier.com/clinical-mass-spectrometry) and other Elsevier journals like [Clinical Biochemistry](https://www.journals.elsevier.com/clinical-biochemistry) and [Clinica Chimica Acta](https://www.journals.elsevier.com/clinica-chimica-acta), require submission of a document in MS-Word format which goes against all that Data Science and Reprodicible Research stands for. Parenthetically, it is my hope that since [AACC](www.aacc.org) has indicated to make Data Science a strategic priority for Lab Medicine, that they will soon accept submissons to [Clinical Chemistry](http://clinchem.aaccjnls.org/) and [Journal of Applied Laboratory Medicine](http://jalm.aaccjnls.org/) written reproducibly in RMardown or LaTeX. 
 75 | 
 76 | In the mean time, here are the workarounds for getting the affiliations to display correctly along with all the other stuff we want, namely, cross referencing of figures and tables and correct reference formatting and abbreviation of journal names. This allows you to avoid the horror of manually fixing your Word document after it generated from RMarkdown. In any case, let's start with MS-Word. 
 77 | 
 78 | # Dependencies for MS-Word and the Associated YAML
 79 | 
 80 | It goes without saying that you need to install LaTeX. LaTeX markup language is available here: [Mac](http://www.tug.org/mactex/), [Windows](https://miktex.org/download). For Linux, just install from the command line with your package manager. Do a full install with all the glorious bloat of all LaTeX packages. This saves many headaches in the future.
 81 | 
 82 | You will also need to install [Pandoc](https://pandoc.org/) which is the Swiss Army Knife of document conversion. It's going to turn LaTeX code into a .docx file for you. Mac users can do this with Homebrew on the terminal command line:
 83 | 
 84 | ```
 85 | brew install pandoc
 86 | brew install pandoc-citeproc
 87 | brew install pandoc-crossref
 88 | ```
 89 | 
 90 | There are some extra installs required to help Pandoc do its job. Install the prebuilt binaries if you can.
 91 | 
 92 | + [pandoc-citeproc](http://hackage.haskell.org/package/pandoc-citeproc)
 93 | + [pandoc-crossref](https://github.com/lierdakil/pandoc-crossref/releases/tag/v0.3.4.1a)
 94 | 
 95 | Finally, you need to use some scripts written in the Lua scripting language which means you will need the language itself:
 96 | + [lua language](https://www.lua.org/download.html)
 97 | 
 98 | And you will need two Lua scripts:
 99 | 
100 | These are in Pandoc github repository:
101 | 
102 | + [scholarly-metadata.lua](https://github.com/pandoc/lua-filters/tree/master/scholarly-metadata)
103 | + [author-info-blocks.lua](https://github.com/pandoc/lua-filters/tree/master/author-info-blocks)
104 | 
105 | You want the files named [scholarly-metadata.lua](https://raw.githubusercontent.com/pandoc/lua-filters/master/scholarly-metadata/scholarly-metadata.lua) and [author-info-blocks.lua](https://raw.githubusercontent.com/pandoc/lua-filters/master/author-info-blocks/author-info-blocks.lua).
106 | 
107 | You will need to choose a .csl file for your journal. This will tell Pandoc how to format the references. You can download the correct .csl file [here](https://www.zotero.org/styles). You will also need a journal abbreviations database. I have made one for you from the [Web of Science list](https://images.webofknowledge.com/images/help/WOS/A_abrvjt.html) and you can download it [here](https://github.com/drdanholmes/Affiliations/blob/master/Extras/abbreviations.json).
108 | 
109 | You will need to creat a .bibtex database which is just your list of references. This can be exported from various reference managers or built by hand. Name the file `mybibfile.bib`.
110 | 
111 | Now follow the bouncing ball:
112 | 
113 | 1. Go to the directory containing your .Rmd file.
114 | 2. Create a directory in it called "Extras"
115 | 3. Put the two Lua scripts, the Bibtex database, the abbreviations database and the .csl file into the "Extras" folder.
116 | 4. If you want to avoid Pandoc's goofy default .docx formatting, then put [this word document](https://github.com/drdanholmes/Affiliations/blob/master/Extras/Reference_Document.docx) in the same folder.
117 | 
118 | OR
119 | 
120 | Download [the contents of this folder](https://github.com/drdanholmes/Affiliations) from my github folder that has everything set up as I describe above.
121 | 
122 | For two authors, your YAML will need to look like this:
123 | 
124 | ```
125 | title: |
126 |   RMarkdown Template for Managing  
127 |   Academic Affiliations 
128 | subtitle: |
129 |   Also Deals with Cross References and  
130 |   Reference Abbreviations for MS-Word Output
131 | author:
132 |   - Duke A Caboom, MD:
133 |       email: duke.a.caboom@utuktoyaktuk.edu
134 |       institute: [UofT]
135 |       correspondence: true
136 |   - Justin d'Ottawa, PhD:
137 |       email: justin@neverready.ca
138 |       institute: [UofO]
139 |       correspondence: false
140 | institute:
141 |   - UofT: University of Tuktoyaktuk, CXVG+62 Tuktoyaktuk, Inuvik, Unorganized, NT Canada
142 |   - UofO: University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5, Canada
143 | abstract: |
144 |   **Introduction**: There's a big scientific problem out there. I know how to fix it.
145 |   **Methods**: My experiments are pure genius.
146 |   **Results**: Now you have your proof.
147 |   **Conclusion**: Give me more grant money.
148 | journal: "An awesome journal"
149 | date: ""
150 | toc: false
151 | output:
152 |  bookdown::word_document2:
153 |     pandoc_args:
154 |       - --csl=Extras/clinical-biochemistry.csl
155 |       - --citation-abbreviations=Extras/abbreviations.json
156 |       - --filter=pandoc-crossref
157 |       - --lua-filter=Extras/scholarly-metadata.lua
158 |       - --lua-filter=Extras/author-info-blocks.lua
159 |       - --reference-doc=Extras/Reference_Document.docx 
160 | bibliography: "Extras/mybibfile.bib"
161 | keywords: "CRAN, R, RMarkdown, RStudio, YAML"
162 | ```
163 | 
164 | Et voila! Figure \@ref(fig:sohappy) shows that we have something reasonable.
165 | 
166 | ```{r sohappy, echo=FALSE, fig.cap="This is so great", fig.align="center"}
167 | knitr::include_graphics("Images/goodheader.png")
168 | ```
169 | 
170 | # Dependencies for LaTeX and the Associated YAML
171 | 
172 | You don't need the lua scripts for LaTeX although you *can* use them. The issue with LaTeX is that the .tex template that Pandoc uses for generating LaTeX files does not support author affiliations as descibed [in the Pandoc documentation](https://pandoc.org/MANUAL.html). So what you need to do is modify the Pandoc LaTeX template. To get your current working copy of the Pandoc LaTeX template open up a terminal (Mac/Linux) and type:
173 | 
174 | ```
175 | pandoc -D latex > mytemplate.tex
176 | ```
177 | 
178 | This will push the contents to a file. Move the file to the "Extras" folder discussed above. If that seems difficult, you can also download it [here](https://github.com/jgm/pandoc-templates/blob/master/default.latex). Now you have to edit it. Open it up in a text editor and find the section that reads:
179 | 
180 | ```
181 | $if(author)$
182 | \author{$for(author)$$author$$sep$ \and $endfor$}
183 | $endif$
184 | ```
185 | Replace this with this code that will invoke the LaTeX [authblk](https://www.ctan.org/pkg/authblk) package.
186 | 
187 | ```
188 | $if(author)$
189 | 	\usepackage{authblk}
190 | 	$for(author)$
191 | 		$if(author.name)$
192 | 			$if(author.number)$
193 | 				\author[$author.number$]{$author.name$}
194 | 			$else$
195 | 				\author[]{$author.name$}
196 | 			$endif$
197 | 			$if(author.affiliation)$
198 | 				$if(author.email)$
199 | 					\affil{$author.affiliation$ \thanks{$author.email$}}
200 | 				$else$
201 | 					\affil{$author.affiliation$}
202 | 				$endif$
203 | 			$endif$
204 | 			$else$	
205 | 			\author{$author$}
206 | 		$endif$
207 | 	$endfor$
208 | $endif$
209 | ```
210 | 
211 | Then make your YAML header look like this:
212 | 
213 | ```
214 | ---
215 | title: |
216 |   RMarkdown Template for Managing  
217 |   Academic Affiliations 
218 | subtitle: |
219 |   Also Deals with Cross References and  
220 |   Reference Abbreviations for PDF Output
221 | author:
222 | - name: Duke A Caboom, MD
223 |   affiliation: University of Tuktoyaktuk, CXVG+62 Tuktoyaktuk, Inuvik, Unorganized, NT Canada
224 |   email: dtholmes@mail.ubc.ca
225 |   number: 1
226 | - name: Justin d'Ottawa, PhD
227 |   affiliation: University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5, Canada
228 |   email: justin@neverready.ca
229 |   number: 2
230 | abstract: |
231 |   **Introduction**: There's a big scientific problem out there. I know how to fix it.
232 |   
233 |   **Methods**: My experiments are pure genius.
234 |   
235 |   **Results**: Now you have your proof.
236 |   
237 |   **Conclusion**: Give me more grant money.
238 | toc: false
239 | output: 
240 |   bookdown::pdf_document2:
241 |     pandoc_args:
242 |       - --filter=pandoc-crossref
243 |       - --csl=Extras/clinical-biochemistry.csl
244 |       - --citation-abbreviations=Extras/abbreviations.json
245 |       - --template=Extras/mytemplate.tex
246 | bibliography: "Extras/mybibfile.bib"
247 | keep-latex: true
248 | ```
249 | 
250 | And as you can see in \@ref(fig:sohappylatex) you get a correctly list of authors.
251 | 
252 | ```{r sohappylatex, echo=FALSE, fig.cap="This is also great.", fig.align="center"}
253 | knitr::include_graphics("Images/goodheaderlatex.png")
254 | ```
255 | 
256 | ## Cross Reference of a Table
257 | 
258 | Of course, tables can be cross referenced in the same manner as figures. Here is a cross reference to table \@ref(tab:mytable) using the code `\@ref(tab:mytable)` .
259 | 
260 | ```{r mytable, echo = FALSE}
261 | library(broom)
262 | mod <- lm(mpg ~ hp + cyl, data = mtcars)
263 | knitr::kable(tidy(mod), digits = 3, booktabs = TRUE, caption = "A short table")
264 | ```
265 | 
266 | ## This Template also Takes Care of Reference Abbreviation.
267 | 
268 | As usual, you can make a citation with the code `[@bibtexname]`, where `bibtexname` is the articles's abbreviated handle in your bibtex database. Here is a great resource on the bookdown package [@xie2018r] and reproducible research [@peng2011reproducible] and here are references where the journal title is longer [@EISENHOFER201940; @VICENTE201984]. The references in your documnent (and shown below) will have appropriate abbreviations based on the .json abbreviations database I have provided. In this case, I have chosen the .csl file for Clinical Mass Spectrometry--'cause [MSACL](https://www.msacl.org/).
269 | 
270 | 
271 | 
272 | # Other Ways to Skin the YAML Cat
273 | 
274 | I came across some other ways to deal with this that I did not like as much but they are simpler. Here is one using a footnote.
275 | 
276 | ```
277 | title: The document title
278 | author:
279 | - [Duke A Caboom, MD]^(University of Tuktoyaktuk, CXVG+62 Tuktoyaktuk, Inuvik, Unorganized, NT Canada)
280 | - [Justin d'Ottawa, PhD]^(University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5, Canada)
281 | output: pdf_document
282 | ```
283 | 
284 | And you can also misuse the `date` variable:
285 | 
286 | ```
287 | title: The document title
288 | author:
289 | - Duke A Caboom, MD [1]
290 | - Justin d'Ottawa, PhD [2]
291 | date: 1. University of Tuktoyaktuk, CXVG+62 Tuktoyaktuk, Inuvik, Unorganized, NT Canada \newline 2. University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5, Canada
292 | output: pdf_document
293 | ```
294 | 
295 | # Conclusion
296 | 
297 | This concludes my long personal struggle to get a completely reproducible .docx manusript genereated by RMardown and Pandoc.
298 | 
299 | ## Parting Thought
300 | 
301 | **Let us not become weary in doing good, for at the proper time we will reap a harvest if we do not give up.**
302 | 
303 | **Galations 6:9**
304 | 
305 | # References
306 | 


--------------------------------------------------------------------------------
/Extras/mytemplate.tex:
--------------------------------------------------------------------------------
  1 | % Options for packages loaded elsewhere
  2 | \PassOptionsToPackage{unicode$for(hyperrefoptions)$,$hyperrefoptions$$endfor$}{hyperref}
  3 | \PassOptionsToPackage{hyphens}{url}
  4 | $if(colorlinks)$
  5 | \PassOptionsToPackage{dvipsnames,svgnames*,x11names*}{xcolor}
  6 | $endif$
  7 | $if(dir)$
  8 | $if(latex-dir-rtl)$
  9 | \PassOptionsToPackage{RTLdocument}{bidi}
 10 | $endif$
 11 | $endif$
 12 | %
 13 | \documentclass[
 14 | $if(fontsize)$
 15 |   $fontsize$,
 16 | $endif$
 17 | $if(lang)$
 18 |   $babel-lang$,
 19 | $endif$
 20 | $if(papersize)$
 21 |   $papersize$paper,
 22 | $endif$
 23 | $if(beamer)$
 24 |   ignorenonframetext,
 25 | $if(handout)$
 26 |   handout,
 27 | $endif$
 28 | $if(aspectratio)$
 29 |   aspectratio=$aspectratio$,
 30 | $endif$
 31 | $endif$
 32 | $for(classoption)$
 33 |   $classoption$$sep$,
 34 | $endfor$
 35 | ]{$documentclass$}
 36 | $if(beamer)$
 37 | $if(background-image)$
 38 | \usebackgroundtemplate{%
 39 |   \includegraphics[width=\paperwidth]{$background-image$}%
 40 | }
 41 | $endif$
 42 | \usepackage{pgfpages}
 43 | \setbeamertemplate{caption}[numbered]
 44 | \setbeamertemplate{caption label separator}{: }
 45 | \setbeamercolor{caption name}{fg=normal text.fg}
 46 | \beamertemplatenavigationsymbols$if(navigation)$$navigation$$else$empty$endif$
 47 | $for(beameroption)$
 48 | \setbeameroption{$beameroption$}
 49 | $endfor$
 50 | % Prevent slide breaks in the middle of a paragraph
 51 | \widowpenalties 1 10000
 52 | \raggedbottom
 53 | $if(section-titles)$
 54 | \setbeamertemplate{part page}{
 55 |   \centering
 56 |   \begin{beamercolorbox}[sep=16pt,center]{part title}
 57 |     \usebeamerfont{part title}\insertpart\par
 58 |   \end{beamercolorbox}
 59 | }
 60 | \setbeamertemplate{section page}{
 61 |   \centering
 62 |   \begin{beamercolorbox}[sep=12pt,center]{part title}
 63 |     \usebeamerfont{section title}\insertsection\par
 64 |   \end{beamercolorbox}
 65 | }
 66 | \setbeamertemplate{subsection page}{
 67 |   \centering
 68 |   \begin{beamercolorbox}[sep=8pt,center]{part title}
 69 |     \usebeamerfont{subsection title}\insertsubsection\par
 70 |   \end{beamercolorbox}
 71 | }
 72 | \AtBeginPart{
 73 |   \frame{\partpage}
 74 | }
 75 | \AtBeginSection{
 76 |   \ifbibliography
 77 |   \else
 78 |     \frame{\sectionpage}
 79 |   \fi
 80 | }
 81 | \AtBeginSubsection{
 82 |   \frame{\subsectionpage}
 83 | }
 84 | $endif$
 85 | $endif$
 86 | $if(beamerarticle)$
 87 | \usepackage{beamerarticle} % needs to be loaded first
 88 | $endif$
 89 | $if(fontfamily)$
 90 | \usepackage[$for(fontfamilyoptions)$$fontfamilyoptions$$sep$,$endfor$]{$fontfamily$}
 91 | $else$
 92 | \usepackage{lmodern}
 93 | $endif$
 94 | $if(linestretch)$
 95 | \usepackage{setspace}
 96 | $endif$
 97 | \usepackage{amssymb,amsmath}
 98 | \usepackage{ifxetex,ifluatex}
 99 | \ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
100 |   \usepackage[$if(fontenc)$$fontenc$$else$T1$endif$]{fontenc}
101 |   \usepackage[utf8]{inputenc}
102 |   \usepackage{textcomp} % provide euro and other symbols
103 | \else % if luatex or xetex
104 | $if(mathspec)$
105 |   \ifxetex
106 |     \usepackage{mathspec}
107 |   \else
108 |     \usepackage{unicode-math}
109 |   \fi
110 | $else$
111 |   \usepackage{unicode-math}
112 | $endif$
113 |   \defaultfontfeatures{Scale=MatchLowercase}
114 |   \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
115 | $if(mainfont)$
116 |   \setmainfont[$for(mainfontoptions)$$mainfontoptions$$sep$,$endfor$]{$mainfont$}
117 | $endif$
118 | $if(sansfont)$
119 |   \setsansfont[$for(sansfontoptions)$$sansfontoptions$$sep$,$endfor$]{$sansfont$}
120 | $endif$
121 | $if(monofont)$
122 |   \setmonofont[$for(monofontoptions)$$monofontoptions$$sep$,$endfor$]{$monofont$}
123 | $endif$
124 | $for(fontfamilies)$
125 |   \newfontfamily{$fontfamilies.name$}[$for(fontfamilies.options)$$fontfamilies.options$$sep$,$endfor$]{$fontfamilies.font$}
126 | $endfor$
127 | $if(mathfont)$
128 | $if(mathspec)$
129 |   \ifxetex
130 |     \setmathfont(Digits,Latin,Greek)[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
131 |   \else
132 |     \setmathfont[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
133 |   \fi
134 | $else$
135 |   \setmathfont[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
136 | $endif$
137 | $endif$
138 | $if(CJKmainfont)$
139 |   \ifxetex
140 |     \usepackage{xeCJK}
141 |     \setCJKmainfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$}
142 |   \fi
143 | $endif$
144 | $if(luatexjapresetoptions)$
145 |   \ifluatex
146 |     \usepackage[$for(luatexjapresetoptions)$$luatexjapresetoptions$$sep$,$endfor$]{luatexja-preset}
147 |   \fi
148 | $endif$
149 | $if(CJKmainfont)$
150 |   \ifluatex
151 |     \usepackage[$for(luatexjafontspecoptions)$$luatexjafontspecoptions$$sep$,$endfor$]{luatexja-fontspec}
152 |     \setmainjfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$}
153 |   \fi
154 | $endif$
155 | \fi
156 | $if(beamer)$
157 | $if(theme)$
158 | \usetheme[$for(themeoptions)$$themeoptions$$sep$,$endfor$]{$theme$}
159 | $endif$
160 | $if(colortheme)$
161 | \usecolortheme{$colortheme$}
162 | $endif$
163 | $if(fonttheme)$
164 | \usefonttheme{$fonttheme$}
165 | $endif$
166 | $if(mainfont)$
167 | \usefonttheme{serif} % use mainfont rather than sansfont for slide text
168 | $endif$
169 | $if(innertheme)$
170 | \useinnertheme{$innertheme$}
171 | $endif$
172 | $if(outertheme)$
173 | \useoutertheme{$outertheme$}
174 | $endif$
175 | $endif$
176 | % Use upquote if available, for straight quotes in verbatim environments
177 | \IfFileExists{upquote.sty}{\usepackage{upquote}}{}
178 | \IfFileExists{microtype.sty}{% use microtype if available
179 |   \usepackage[$for(microtypeoptions)$$microtypeoptions$$sep$,$endfor$]{microtype}
180 |   \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
181 | }{}
182 | $if(indent)$
183 | $else$
184 | \makeatletter
185 | \@ifundefined{KOMAClassName}{% if non-KOMA class
186 |   \IfFileExists{parskip.sty}{%
187 |     \usepackage{parskip}
188 |   }{% else
189 |     \setlength{\parindent}{0pt}
190 |     \setlength{\parskip}{6pt plus 2pt minus 1pt}}
191 | }{% if KOMA class
192 |   \KOMAoptions{parskip=half}}
193 | \makeatother
194 | $endif$
195 | $if(verbatim-in-note)$
196 | \usepackage{fancyvrb}
197 | $endif$
198 | \usepackage{xcolor}
199 | \IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
200 | \IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
201 | \hypersetup{
202 | $if(title-meta)$
203 |   pdftitle={$title-meta$},
204 | $endif$
205 | $if(author-meta)$
206 |   pdfauthor={$author-meta$},
207 | $endif$
208 | $if(lang)$
209 |   pdflang={$lang$},
210 | $endif$
211 | $if(subject)$
212 |   pdfsubject={$subject$},
213 | $endif$
214 | $if(keywords)$
215 |   pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$},
216 | $endif$
217 | $if(colorlinks)$
218 |   colorlinks=true,
219 |   linkcolor=$if(linkcolor)$$linkcolor$$else$Maroon$endif$,
220 |   filecolor=$if(filecolor)$$filecolor$$else$Maroon$endif$,
221 |   citecolor=$if(citecolor)$$citecolor$$else$Blue$endif$,
222 |   urlcolor=$if(urlcolor)$$urlcolor$$else$Blue$endif$,
223 | $else$
224 |   hidelinks,
225 | $endif$
226 |   pdfcreator={LaTeX via pandoc}}
227 | \urlstyle{same} % disable monospaced font for URLs
228 | $if(verbatim-in-note)$
229 | \VerbatimFootnotes % allow verbatim text in footnotes
230 | $endif$
231 | $if(geometry)$
232 | $if(beamer)$
233 | \geometry{$for(geometry)$$geometry$$sep$,$endfor$}
234 | $else$
235 | \usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
236 | $endif$
237 | $endif$
238 | $if(beamer)$
239 | \newif\ifbibliography
240 | $endif$
241 | $if(listings)$
242 | \usepackage{listings}
243 | \newcommand{\passthrough}[1]{#1}
244 | \lstset{defaultdialect=[5.3]Lua}
245 | \lstset{defaultdialect=[x86masm]Assembler}
246 | $endif$
247 | $if(lhs)$
248 | \lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
249 | $endif$
250 | $if(highlighting-macros)$
251 | $highlighting-macros$
252 | $endif$
253 | $if(tables)$
254 | \usepackage{longtable,booktabs}
255 | $if(beamer)$
256 | \usepackage{caption}
257 | % Make caption package work with longtable
258 | \makeatletter
259 | \def\fnum@table{\tablename~\thetable}
260 | \makeatother
261 | $else$
262 | % Correct order of tables after \paragraph or \subparagraph
263 | \usepackage{etoolbox}
264 | \makeatletter
265 | \patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
266 | \makeatother
267 | % Allow footnotes in longtable head/foot
268 | \IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
269 | \makesavenoteenv{longtable}
270 | $endif$
271 | $endif$
272 | $if(graphics)$
273 | \usepackage{graphicx,grffile}
274 | \makeatletter
275 | \def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
276 | \def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
277 | \makeatother
278 | % Scale images if necessary, so that they will not overflow the page
279 | % margins by default, and it is still possible to overwrite the defaults
280 | % using explicit options in \includegraphics[width, height, ...]{}
281 | \setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
282 | % Set default figure placement to htbp
283 | \makeatletter
284 | \def\fps@figure{htbp}
285 | \makeatother
286 | $endif$
287 | $if(links-as-notes)$
288 | % Make links footnotes instead of hotlinks:
289 | \DeclareRobustCommand{\href}[2]{#2\footnote{\url{#1}}}
290 | $endif$
291 | $if(strikeout)$
292 | \usepackage[normalem]{ulem}
293 | % Avoid problems with \sout in headers with hyperref
294 | \pdfstringdefDisableCommands{\renewcommand{\sout}{}}
295 | $endif$
296 | \setlength{\emergencystretch}{3em} % prevent overfull lines
297 | \providecommand{\tightlist}{%
298 |   \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
299 | $if(numbersections)$
300 | \setcounter{secnumdepth}{$if(secnumdepth)$$secnumdepth$$else$5$endif$}
301 | $else$
302 | \setcounter{secnumdepth}{-\maxdimen} % remove section numbering
303 | $endif$
304 | $if(beamer)$
305 | $else$
306 | $if(block-headings)$
307 | % Make \paragraph and \subparagraph free-standing
308 | \ifx\paragraph\undefined\else
309 |   \let\oldparagraph\paragraph
310 |   \renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
311 | \fi
312 | \ifx\subparagraph\undefined\else
313 |   \let\oldsubparagraph\subparagraph
314 |   \renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
315 | \fi
316 | $endif$
317 | $endif$
318 | $if(pagestyle)$
319 | \pagestyle{$pagestyle$}
320 | $endif$
321 | $for(header-includes)$
322 | $header-includes$
323 | $endfor$
324 | $if(lang)$
325 | \ifxetex
326 |   % Load polyglossia as late as possible: uses bidi with RTL langages (e.g. Hebrew, Arabic)
327 |   \usepackage{polyglossia}
328 |   \setmainlanguage[$polyglossia-lang.options$]{$polyglossia-lang.name$}
329 | $for(polyglossia-otherlangs)$
330 |   \setotherlanguage[$polyglossia-otherlangs.options$]{$polyglossia-otherlangs.name$}
331 | $endfor$
332 | \else
333 |   \usepackage[shorthands=off,$for(babel-otherlangs)$$babel-otherlangs$,$endfor$main=$babel-lang$]{babel}
334 | $if(babel-newcommands)$
335 |   $babel-newcommands$
336 | $endif$
337 | \fi
338 | $endif$
339 | $if(dir)$
340 | \ifxetex
341 |   % Load bidi as late as possible as it modifies e.g. graphicx
342 |   \usepackage{bidi}
343 | \fi
344 | \ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
345 |   \TeXXeTstate=1
346 |   \newcommand{\RL}[1]{\beginR #1\endR}
347 |   \newcommand{\LR}[1]{\beginL #1\endL}
348 |   \newenvironment{RTL}{\beginR}{\endR}
349 |   \newenvironment{LTR}{\beginL}{\endL}
350 | \fi
351 | $endif$
352 | $if(natbib)$
353 | \usepackage[$natbiboptions$]{natbib}
354 | \bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
355 | $endif$
356 | $if(biblatex)$
357 | \usepackage[$if(biblio-style)$style=$biblio-style$,$endif$$for(biblatexoptions)$$biblatexoptions$$sep$,$endfor$]{biblatex}
358 | $for(bibliography)$
359 | \addbibresource{$bibliography$}
360 | $endfor$
361 | $endif$
362 | 
363 | $if(title)$
364 | \title{$title$$if(thanks)$\thanks{$thanks$}$endif$}
365 | $endif$
366 | $if(subtitle)$
367 | $if(beamer)$
368 | $else$
369 | \usepackage{etoolbox}
370 | \makeatletter
371 | \providecommand{\subtitle}[1]{% add subtitle to \maketitle
372 |   \apptocmd{\@title}{\par {\large #1 \par}}{}{}
373 | }
374 | \makeatother
375 | $endif$
376 | \subtitle{$subtitle$}
377 | $endif$
378 | 
379 | %$if(author)$
380 | %\author{$for(author)$$author$$sep$ \and $endfor$}
381 | %$endif$
382 | 
383 | $if(author)$
384 | 	\usepackage{authblk}
385 | 	$for(author)$
386 | 		$if(author.name)$
387 | 			$if(author.number)$
388 | 				\author[$author.number$]{$author.name$}
389 | 			$else$
390 | 				\author[]{$author.name$}
391 | 			$endif$
392 | 			$if(author.affiliation)$
393 | 				$if(author.email)$
394 | 					\affil{$author.affiliation$ \thanks{$author.email$}}
395 | 				$else$
396 | 					\affil{$author.affiliation$}
397 | 				$endif$
398 | 			$endif$
399 | 			$else$	
400 | 			\author{$author$}
401 | 		$endif$
402 | 	$endfor$
403 | $endif$
404 | 
405 | \date{$date$}
406 | $if(beamer)$
407 | $if(institute)$
408 | \institute{$for(institute)$$institute$$sep$ \and $endfor$}
409 | $endif$
410 | $if(titlegraphic)$
411 | \titlegraphic{\includegraphics{$titlegraphic$}}
412 | $endif$
413 | $if(logo)$
414 | \logo{\includegraphics{$logo$}}
415 | $endif$
416 | $endif$
417 | 
418 | \begin{document}
419 | $if(has-frontmatter)$
420 | \frontmatter
421 | $endif$
422 | $if(title)$
423 | $if(beamer)$
424 | \frame{\titlepage}
425 | $else$
426 | \maketitle
427 | $endif$
428 | $if(abstract)$
429 | \begin{abstract}
430 | $abstract$
431 | \end{abstract}
432 | $endif$
433 | $endif$
434 | 
435 | $for(include-before)$
436 | $include-before$
437 | 
438 | $endfor$
439 | $if(toc)$
440 | $if(toc-title)$
441 | \renewcommand*\contentsname{$toc-title$}
442 | $endif$
443 | $if(beamer)$
444 | \begin{frame}
445 | $if(toc-title)$
446 |   \frametitle{$toc-title$}
447 | $endif$
448 |   \tableofcontents[hideallsubsections]
449 | \end{frame}
450 | $else$
451 | {
452 | $if(colorlinks)$
453 | \hypersetup{linkcolor=$if(toccolor)$$toccolor$$else$$endif$}
454 | $endif$
455 | \setcounter{tocdepth}{$toc-depth$}
456 | \tableofcontents
457 | }
458 | $endif$
459 | $endif$
460 | $if(lot)$
461 | \listoftables
462 | $endif$
463 | $if(lof)$
464 | \listoffigures
465 | $endif$
466 | $if(linestretch)$
467 | \setstretch{$linestretch$}
468 | $endif$
469 | $if(has-frontmatter)$
470 | \mainmatter
471 | $endif$
472 | $body$
473 | 
474 | $if(has-frontmatter)$
475 | \backmatter
476 | $endif$
477 | $if(natbib)$
478 | $if(bibliography)$
479 | $if(biblio-title)$
480 | $if(has-chapters)$
481 | \renewcommand\bibname{$biblio-title$}
482 | $else$
483 | \renewcommand\refname{$biblio-title$}
484 | $endif$
485 | $endif$
486 | $if(beamer)$
487 | \begin{frame}[allowframebreaks]{$biblio-title$}
488 |   \bibliographytrue
489 | $endif$
490 |   \bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
491 | $if(beamer)$
492 | \end{frame}
493 | $endif$
494 | 
495 | $endif$
496 | $endif$
497 | $if(biblatex)$
498 | $if(beamer)$
499 | \begin{frame}[allowframebreaks]{$biblio-title$}
500 |   \bibliographytrue
501 |   \printbibliography[heading=none]
502 | \end{frame}
503 | $else$
504 | \printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$
505 | $endif$
506 | 
507 | $endif$
508 | $for(include-after)$
509 | $include-after$
510 | 
511 | $endfor$
512 | \end{document}
513 | 


--------------------------------------------------------------------------------