add everithing

data/config.json

+{
+    "corpusPath"     : "/home/qlobbe/Documents/recherche/vaccin/process_clinical_trials/output/corpus-26-10-2021-publications.csv",
+    "listPath"       : "/home/qlobbe/Documents/recherche/vaccin/process_clinical_trials/output/list-26-10-2021.json",
+    "outputPath"     : "/home/qlobbe/data/phylo/output/",
+    "corpusParser"   : {
+        "tag" : "Csv'",
+        "_csv'_limit" : 6000
+    },
+    "listParser" : "V4",     
+    "phyloName"      : "vaccines-publications_nov-2021",
+    "phyloLevel"     : 2,
+    "phyloProximity" : {
+        "tag" : "WeightedLogJaccard",
+        "_wlj_sensibility" : 0.5
+    },
+    "seaElevation" : {
+        "tag" : "Constante",
+        "_cons_start" : 0.1,
+        "_cons_step"  : 0.1
+    },
+    "findAncestors" : true,
+    "phyloSynchrony" : {
+        "tag" : "ByProximityThreshold",
+        "_bpt_threshold" : 0.6,
+        "_bpt_sensibility" : 0,
+        "_bpt_scope" : "SingleBranch",
+        "_bpt_strategy" : "MergeAllGroups"
+    },
+    "phyloQuality" : {
+        "tag" : "Quality",
+        "_qua_granularity" : 0.5,
+        "_qua_minBranch" : 1
+    },    
+    "timeUnit" : {
+        "tag" : "Week",
+        "_week_period" : 3,
+        "_week_step" : 1,
+        "_week_matchingFrame" : 30
+    },
+    "clique" : {
+        "tag" : "Fis",
+        "_fis_support" : 1,
+        "_fis_size" : 1
+    }, 
+    "exportLabel" : [
+        {
+            "tag" : "BranchLabel",
+            "_branch_labelTagger" : "MostEmergentTfIdf",
+            "_branch_labelSize" : 2
+        },
+        {
+            "tag" : "GroupLabel",
+            "_group_labelTagger" : "MostEmergentInclusive",
+            "_group_labelSize" : 2
+        }
+    ],     
+    "exportSort" : {
+        "tag" : "ByHierarchy"
+    },
+    "exportFilter" : [
+        {
+            "tag" : "ByBranchSize",
+            "_branch_size" : 1
+        }
+    ]
+}

monitoring.aux

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+\providecommand\HyField@AuxAddToFields[1]{}
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+\bibstyle{pnas-new}
+\citation{boutron_nma_2020,nguyen_research_2021}
+\citation{delanoe_mining_2021}
+\citation{callon_mapping_1986}
+\citation{chavalarias_draw_2021}
+\citation{delanoe_mining_2021}
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+\providecommand*\caption@xref[2]{\@setref\relax\@undefined{#1}}
+\newlabel{fig:reconstruction}{{1}{1}{The four operators of the phylomemy reconstruction process: 1. terms indexation, 2. similarity measures, 3. fields detection, 4. inter-temporal matching\relax }{figure.caption.1}{}}
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+\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces Phylomemy of 1794 COVID-19 vaccines trials recorded between February 2020 and October 2021 in the COVID-NMA database. Online and interactive version available at \href  {http://maps.gargantext.org/unpublished_phylo/vaccines_publications_10_2021/}{maps.gargantext.org/publications}\relax }}{2}{figure.caption.2}\protected@file@percent }
+\newlabel{fig:phylomemy-randomized-unrandomized}{{2}{2}{Phylomemy of 1794 COVID-19 vaccines trials recorded between February 2020 and October 2021 in the COVID-NMA database. Online and interactive version available at \href {http://maps.gargantext.org/unpublished_phylo/vaccines_publications_10_2021/}{maps.gargantext.org/publications}\relax }{figure.caption.2}{}}
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+\newlabel{fig:heterologous}{{3}{3}{A focus of \autoref {fig:phylomemy-randomized-unrandomized}. In red are highlighted all the trials evaluating heterologous primary vaccination and heterologous booster. We circle the heterologous trials involving different platforms.\relax }{figure.caption.3}{}}
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+\citation{boutron_nma_2020,nguyen_research_2021}
+\citation{delanoe_mining_2021}
+\bibdata{references}
+\bibcite{boutron_nma_2020}{{1}{}{{}}{{}}}
+\bibcite{nguyen_research_2021}{{2}{}{{}}{{}}}
+\bibcite{delanoe_mining_2021}{{3}{}{{}}{{}}}
+\bibcite{callon_mapping_1986}{{4}{}{{}}{{}}}
+\bibcite{chavalarias_draw_2021}{{5}{}{{}}{{}}}
+\bibcite{lobbe_exploring_2021}{{6}{}{{}}{{}}}
+\bibcite{chumakove_old_2021}{{7}{}{{}}{{}}}
+\bibcite{krause_considerations_2021}{{8}{}{{}}{{}}}
+\providecommand\NAT@force@numbers{}\NAT@force@numbers
+\@writefile{lof}{\contentsline {figure}{\numberline {4}{\ignorespaces Phylomemy of the randomized only COVID-19 vaccines trials. In blue, we highlight all the trials with an associated publication (i.e., preprint or peer-reviewed articles).\relax }}{4}{figure.caption.4}\protected@file@percent }
+\newlabel{fig:phylomemy-randomized-publications}{{4}{4}{Phylomemy of the randomized only COVID-19 vaccines trials. In blue, we highlight all the trials with an associated publication (i.e., preprint or peer-reviewed articles).\relax }{figure.caption.4}{}}
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+\newlabel{LastPage}{{}{4}{}{page.4}{}}
+\xdef\lastpage@lastpage{4}
+\xdef\lastpage@lastpageHy{4}

monitoring.bbl

+\begin{thebibliography}{1}
+
+\bibitem{boutron_nma_2020}
+I Boutron, et~al., {{T}he {C}{O}{V}{I}{D}-{N}{M}{A} {P}roject: {B}uilding an
+  {E}vidence {E}cosystem for the {C}{O}{V}{I}{D}-19 {P}andemic}.
+\newblock {\em\protect\JournalTitle{Ann Intern Med}} \textbf{173}, 1015--1017
+  (2020).
+
+\bibitem{nguyen_research_2021}
+VT Nguyen, et~al., {{R}esearch response to coronavirus disease 2019 needed
+  better coordination and collaboration: a living mapping of registered
+  trials}.
+\newblock {\em\protect\JournalTitle{J Clin Epidemiol}} \textbf{130}, 107--116
+  (2021).
+
+\bibitem{delanoe_mining_2021}
+A Delanoë, D Chavalarias, Mining the digital society - {Gargantext}, a
+  macroscope for collaborative analysis and exploration of textual corpora.
+\newblock (forthcoming 2021).
+
+\bibitem{callon_mapping_1986}
+M Callon, A Rip, J Law, {\em Mapping the dynamics of science and technology:
+  Sociology of science in the real world}.
+\newblock (Springer), (1986).
+
+\bibitem{chavalarias_draw_2021}
+D Chavalarias, Q Lobbe, A Delanoë, Draw me {Science} - multi-level and
+  multi-scale reconstruction of knowledge dynamics with phylomemies.
+\newblock (forthcoming 2021).
+
+\bibitem{lobbe_exploring_2021}
+Q Lobb{\'e}, A Delano{\"e}, D Chavalarias, Exploring, browsing and interacting
+  with multi-level and multi-scale dynamics of knowledge.
+\newblock (forthcoming 2021).
+
+\bibitem{chumakove_old_2021}
+K Chumakov, et~al., Old vaccines for new infections: Exploiting innate immunity
+  to control covid-19 and prevent future pandemics.
+\newblock {\em\protect\JournalTitle{Proceedings of the National Academy of
+  Sciences}} \textbf{118} (2021).
+
+\bibitem{krause_considerations_2021}
+PR Krause, et~al., {{C}onsiderations in boosting {C}{O}{V}{I}{D}-19 vaccine
+  immune responses}.
+\newblock {\em\protect\JournalTitle{Lancet}} \textbf{398}, 1377--1380 (2021).
+
+\end{thebibliography}

monitoring.blg

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+The top-level auxiliary file: monitoring.aux
+The style file: pnas-new.bst
+format.journal is an unknown function---line 563 of file pnas-new.bst
+Database file #1: references.bib
+Warning--empty note in delanoe_mining_2021
+Warning--empty note in chavalarias_draw_2021
+Warning--empty note in lobbe_exploring_2021
+You've used 8 entries,
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+            518 strings with 8277 characters,
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monitoring.out

+\BOOKMARK [0][-]{matmethods@section.1}{Materials}{}% 1

phylomemies/vaccin.json

+{
+    "corpusPath"     : "/home/qlobbe/Documents/recherche/vaccin/process_clinical_trials/output/corpus-fundings-09-2021.csv",
+    "listPath"       : "/home/qlobbe/Documents/recherche/vaccin/process_clinical_trials/output/list-09-2021.csv",
+    "outputPath"     : "/home/qlobbe/data/phylo/output/",
+    "corpusParser"   : {
+        "tag" : "Csv'",
+        "_csv'_limit" : 6000
+    },
+    "listParser" : "V3",     
+    "phyloName"      : "vaccines_fundings_09_2021",
+    "phyloLevel"     : 2,
+    "phyloProximity" : {
+        "tag" : "WeightedLogJaccard",
+        "_wlj_sensibility" : 0.5
+    },
+    "seaElevation" : {
+        "tag" : "Constante",
+        "_cons_start" : 0.1,
+        "_cons_step"  : 0.1
+    },
+    "findAncestors" : true,
+    "phyloSynchrony" : {
+        "tag" : "ByProximityThreshold",
+        "_bpt_threshold" : 0.6,
+        "_bpt_sensibility" : 0,
+        "_bpt_scope" : "SingleBranch",
+        "_bpt_strategy" : "MergeAllGroups"
+    },
+    "phyloQuality" : {
+        "tag" : "Quality",
+        "_qua_granularity" : 0.5,
+        "_qua_minBranch" : 1
+    },    
+    "timeUnit" : {
+        "tag" : "Week",
+        "_week_period" : 3,
+        "_week_step" : 1,
+        "_week_matchingFrame" : 30
+    },
+    "clique" : {
+        "tag" : "Fis",
+        "_fis_support" : 1,
+        "_fis_size" : 1
+    }, 
+    "exportLabel" : [
+        {
+            "tag" : "BranchLabel",
+            "_branch_labelTagger" : "MostEmergentTfIdf",
+            "_branch_labelSize" : 2
+        },
+        {
+            "tag" : "GroupLabel",
+            "_group_labelTagger" : "MostEmergentInclusive",
+            "_group_labelSize" : 2
+        }
+    ],     
+    "exportSort" : {
+        "tag" : "ByHierarchy"
+    },
+    "exportFilter" : [
+        {
+            "tag" : "ByBranchSize",
+            "_branch_size" : 1
+        }
+    ]
+}

pnasbriefreport.sty

+%%% PNAS two column brief-report style file
+%%% For use with pnas-new.cls
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesPackage{pnasbriefreport}[2019/05/28 v1.1 PNAS two column brief report style]
+
+%% Set whether the abstract is set into the first column
+\setboolean{shortarticle}{true} 
+% true = set into first column
+% false = spans page width
+
+%% Set colors
+\definecolor{color2}{RGB}{130,0,0} % color
+
+%% Set up the first page footnote/fact box here
+\RequirePackage{float}
+\floatstyle{plain}
+\newfloat{sigstatement}{b!}{sst}
+
+% \additionalelement{} % Don't use the \additionalelement field (set blank)
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+\additionalelement{%
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+\vskip5pt%
+\@ifundefined{@correspondingauthor}{}{\@correspondingauthor}
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+\apptocmd{\@maketitle}{%
+\tikz[remember picture,overlay]
+  \node[rotate=90,anchor=south east,text=white,fill=black,font=\sffamily\bfseries,inner xsep=2.5em,inner ysep=1em,text depth=1em] at (current page.north east) {BRIEF REPORT};
+}
+
+\endinput
\ No newline at end of file

template/PNAS-template-main.bbl

+\begin{thebibliography}{1}
+
+\bibitem{belkin2002using}
+M Belkin, P Niyogi, Using manifold stucture for partially labeled
+  classification in {\em Advances in neural information processing systems}.
+\newblock pp. 929--936 (2002).
+
+\bibitem{berard1994embedding}
+P B{\'e}rard, G Besson, S Gallot, Embedding riemannian manifolds by their heat
+  kernel.
+\newblock {\em\protect\JournalTitle{Geometric \& Functional Analysis GAFA}}
+  \textbf{4}, 373--398 (1994).
+
+\bibitem{coifman2005geometric}
+RR Coifman, et~al., Geometric diffusions as a tool for harmonic analysis and
+  structure definition of data: Diffusion maps.
+\newblock {\em\protect\JournalTitle{Proceedings of the National Academy of
+  Sciences of the United States of America}} \textbf{102}, 7426--7431 (2005).
+
+\end{thebibliography}

template/latexmkrc

+$dvipdf = 'dvipdfmx %O -o %D %S';
\ No newline at end of file

template/pnas-sample.bib

+@inproceedings{belkin2002using,
+  title={Using manifold stucture for partially labeled classification},
+  author={Belkin, Mikhail and Niyogi, Partha},
+  booktitle={Advances in neural information processing systems},
+  pages={929--936},
+  year={2002}
+}
+
+@article{berard1994embedding,
+  title={Embedding Riemannian manifolds by their heat kernel},
+  author={B{\'e}rard, Pierre and Besson, G{\'e}rard and Gallot, Sylvain},
+  journal={Geometric \& Functional Analysis GAFA},
+  volume={4},
+  number={4},
+  pages={373--398},
+  year={1994},
+  publisher={Springer}
+}
+
+@article{coifman2005geometric,
+  title={Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps},
+  author={Coifman, Ronald R and Lafon, Stephane and Lee, Ann B and Maggioni, Mauro and Nadler, Boaz and Warner, Frederick and Zucker, Steven W},
+  journal={Proceedings of the National Academy of Sciences of the United States of America},
+  volume={102},
+  number={21},
+  pages={7426--7431},
+  year={2005},
+  publisher={National Acad Sciences}
+}