%% -*- coding: utf-8 -*-
%% Timestamp: "2025-09-30 17:40:26 (ywatanabe)"
%% File: "/ssh:sp:/home/ywatanabe/proj/neurovista/paper/00_shared/latex_styles/bibliography.tex"

%% ============================================================================
%% BIBLIOGRAPHY STYLE CONFIGURATION
%% ============================================================================

%% ----------------------------------------------------------------------------
%% OPTION 1: NUMBERED CITATIONS (Order of Appearance) - CURRENTLY ACTIVE
%% ----------------------------------------------------------------------------
%% Description: Citations numbered [1], [2], [3]... in the order they first
%%              appear in the manuscript
%% Sorting: By first citation order (NOT alphabetical)
%% Example: \cite{Tort2010,Canolty2010} → [1, 2] (if these are first citations)
%% Commands: \cite{key} → [1]
%%           \cite{key1,key2} → [1, 2]
%% Best for: Most scientific journals, clear citation tracking
%% Compatible with: natbib package
\bibliographystyle{unsrtnat}

%% ----------------------------------------------------------------------------
%% OPTION 2: NUMBERED CITATIONS (Alphabetical by Author)
%% ----------------------------------------------------------------------------
%% Description: Citations numbered [1], [2], [3]... sorted alphabetically by
%%              first author's last name
%% Sorting: Alphabetical by author (Canolty before Tort)
%% Example: \cite{Tort2010,Canolty2010} → [2, 1] (C before T alphabetically)
%% Commands: \cite{key} → [1]
%% Best for: When you want bibliography sorted alphabetically
%% Compatible with: elsarticle class
% \bibliographystyle{elsarticle-num}

%% Alternative alphabetical styles:
% \bibliographystyle{plain}      % Basic alphabetical, no natbib features
% \bibliographystyle{ieeetr}     % IEEE style, order of appearance
% \bibliographystyle{siam}       % SIAM style, alphabetical

%% ----------------------------------------------------------------------------
%% OPTION 3: AUTHOR-YEAR CITATIONS
%% ----------------------------------------------------------------------------
%% Description: Citations show author name and year (Smith, 2020) or (Smith 2020)
%% Format: (Author, Year) or Author (Year) depending on command
%% Example: \cite{Tort2010} → (Tort et al., 2010)
%%          \citet{Tort2010} → Tort et al. (2010) [textual]
%%          \cite{Tort2010} → (Tort et al., 2010) [parenthetical]
%% Commands:
%%   - \citet{key}  → Author (Year)  [for text: "As shown by Author (2020)..."]
%%   - \cite{key}  → (Author, Year) [for parentheses: "...as shown (Author, 2020)"]
%%   - \cite{key}   → Same as \cite{key}
%% Best for: Review papers, humanities, some social sciences
%% Requires: natbib package (already loaded)
% \bibliographystyle{plainnat}   % Author-year, alphabetical
% \bibliographystyle{abbrvnat}   % Author-year, abbreviated names
% \bibliographystyle{apalike}    % APA-like author-year style

%% ----------------------------------------------------------------------------
%% OPTION 4: JOURNAL-SPECIFIC STYLES
%% ----------------------------------------------------------------------------
%% Elsevier journals:
% \bibliographystyle{elsarticle-num}        % Numbered, alphabetical
% \bibliographystyle{elsarticle-num-names}  % Numbered, alphabetical, full names
% \bibliographystyle{elsarticle-harv}       % Author-year (Harvard style)

%% Nature family:
% \bibliographystyle{naturemag}             % Nature magazine style

%% IEEE:
% \bibliographystyle{IEEEtran}              % IEEE Transactions style

%% APA:
% \bibliographystyle{apalike}               % APA-like style

%% ----------------------------------------------------------------------------
%% OPTION 5: ADDITIONAL CITATION STYLES
%% ----------------------------------------------------------------------------
%% Note: Many of these styles require biblatex instead of natbib.
%% To use biblatex, you need to modify the preamble and use biber instead of bibtex.
%% Basic conversion: Replace natbib package with biblatex, and use \printbibliography
%% instead of \bibliographystyle + \bibliography commands.

%% ----------------------------------------
%% CHEMISTRY
%% ----------------------------------------
%% American Chemical Society (ACS):
%% Installation: Download achemso.bst or use biblatex with style=chem-acs
%% Format: Numbered, order of appearance, (1) Author, A. B. Title. Journal Year, Volume, Pages.
%% BibTeX method:
% \bibliographystyle{achemso}              % ACS style (requires achemso package)
%% Biblatex method (recommended):
% \usepackage[style=chem-acs]{biblatex}

%% ----------------------------------------
%% MEDICAL & HEALTH SCIENCES
%% ----------------------------------------
%% American Medical Association (AMA) 11th edition:
%% Format: Numbered, order of appearance, superscript numbers
%% Installation: Requires biblatex with biblatex-ama style
%% Method:
% \usepackage[style=ama]{biblatex}         % AMA 11th ed (requires biblatex-ama package)

%% Vancouver style (ICMJE):
%% Format: Numbered [1], order of appearance, commonly used in medical journals
%% Note: unsrtnat (currently active) is very similar to Vancouver
% \bibliographystyle{vancouver}            % Vancouver/ICMJE style (if .bst available)
% \bibliographystyle{unsrtnat}             % Similar to Vancouver (currently active)

%% ----------------------------------------
%% SOCIAL SCIENCES
%% ----------------------------------------
%% American Psychological Association (APA) 7th edition:
%% Format: Author-year, (Author, Year), alphabetical by author
%% BibTeX method (APA-like, not full APA 7th):
% \bibliographystyle{apalike}              % APA-like style (simplified)
% \bibliographystyle{apacite}              % APA 6th/7th (requires apacite package)
%% Biblatex method (recommended for full APA 7th compliance):
% \usepackage[style=apa]{biblatex}         % Full APA 7th edition (requires biblatex-apa)

%% American Sociological Association (ASA) 6th/7th edition:
%% Format: Author-year, (Author Year), alphabetical, similar to Chicago author-date
%% Method:
% \bibliographystyle{asaetr}               % ASA-like style (if .bst available)
%% Biblatex method:
% \usepackage[style=authoryear]{biblatex} % Generic author-year (customizable to ASA)

%% American Political Science Association (APSA):
%% Format: Author-year, similar to Chicago author-date
%% Method:
% \usepackage[style=authoryear-comp]{biblatex}  % Compressed author-year for APSA

%% ----------------------------------------
%% HUMANITIES
%% ----------------------------------------
%% Chicago Manual of Style 18th edition (author-date):
%% Format: Author-year, (Author Year), commonly used in social sciences and humanities
% \bibliographystyle{chicago}              % Chicago author-date (if .bst available)
%% Biblatex method (recommended):
% \usepackage[style=chicago-authordate]{biblatex}  % Chicago 18th ed author-date

%% Chicago Manual of Style 18th edition (notes and bibliography):
%% Format: Footnote/endnote citations with full bibliography
%% Method:
% \usepackage[style=chicago-notes]{biblatex}  % Chicago 18th ed notes style

%% Chicago Manual of Style 18th edition (shortened notes and bibliography):
%% Format: Shortened footnote citations after first full citation
%% Method:
% \usepackage[style=chicago-notes]{biblatex}  % Use with ibidtracker option

%% Modern Language Association (MLA) 9th edition:
%% Format: Author-page, (Author Page), works cited list
%% Method:
% \usepackage[style=mla]{biblatex}         % MLA 9th edition (requires biblatex-mla)

%% Modern Humanities Research Association (MHRA) 4th edition:
%% Format: Footnote citations with bibliography
%% Method:
% \usepackage[style=mhra]{biblatex}        % MHRA 4th edition (requires biblatex-mhra)

%% ----------------------------------------
%% HARVARD STYLES
%% ----------------------------------------
%% Cite Them Right 12th edition - Harvard:
%% Format: Author-year, (Author, Year), widely used in UK universities
% \bibliographystyle{agsm}                 % Harvard style (Australian)
% \bibliographystyle{dcu}                  % Harvard style (Dublin City University)
%% Biblatex method:
% \usepackage[style=authoryear]{biblatex} % Generic Harvard-style (author-year)

%% Elsevier - Harvard (with titles):
%% Format: Author-year with article titles included
% \bibliographystyle{elsarticle-harv}      % Elsevier Harvard style (already listed above)

%% ----------------------------------------
%% ENGINEERING & COMPUTER SCIENCE
%% ----------------------------------------
%% IEEE (Institute of Electrical and Electronics Engineers):
%% Format: Numbered [1], order of appearance, widely used in engineering
% \bibliographystyle{IEEEtran}             % IEEE Transactions style (already listed above)

%% ----------------------------------------
%% NATURAL SCIENCES
%% ----------------------------------------
%% Nature:
%% Format: Numbered, superscript, order of appearance
% \bibliographystyle{naturemag}            % Nature magazine style (already listed above)
% \bibliographystyle{naturemag-doi}        % Nature with DOIs

%% ----------------------------------------------------------------------------
%% BIBLATEX SETUP INSTRUCTIONS
%% ----------------------------------------------------------------------------
%% To switch from natbib to biblatex:
%%
%% 1. In packages.tex, replace:
%%    \usepackage[numbers]{natbib}
%%    with:
%%    \usepackage[style=STYLENAME,backend=biber]{biblatex}
%%    \addbibresource{path/to/bibliography.bib}
%%
%% 2. In this file (bibliography.tex), replace:
%%    \bibliographystyle{...}
%%    with:
%%    % No \bibliographystyle needed with biblatex
%%
%% 3. In your main .tex file, replace:
%%    \bibliography{path/to/bibliography}
%%    with:
%%    \printbibliography
%%
%% 4. Change compilation command:
%%    pdflatex → biber → pdflatex → pdflatex
%%    (instead of pdflatex → bibtex → pdflatex → pdflatex)
%%
%% Example biblatex styles:
%%   style=numeric-comp     → Compressed numeric [1-3,5]
%%   style=authoryear       → (Author, Year)
%%   style=authoryear-comp  → (Author1, 2020; Author2, 2021)
%%   style=apa              → APA 7th edition
%%   style=chicago-authordate → Chicago author-date
%%   style=ieee             → IEEE style
%%   style=nature           → Nature style
%%   style=mla              → MLA 9th edition

%% ----------------------------------------------------------------------------
%% CITATION COMMAND REFERENCE (with natbib)
%% ----------------------------------------------------------------------------
%% Basic commands:
%%   \cite{key}              → [1] or (Author, Year) depending on style
%%   \cite{key1,key2}        → [1, 2] or (Author1, Year1; Author2, Year2)
%%
%% Advanced natbib commands (only work with natbib-compatible styles):
%%   \citet{key}             → Author (Year)  [textual citation]
%%   \cite{key}             → (Author, Year) [parenthetical citation]
%%   \citet*{key}            → Full author list (Year)
%%   \cite*{key}            → (Full author list, Year)
%%   \citealt{key}           → Author Year [no parentheses]
%%   \citealp{key}           → Author, Year [no parentheses]
%%   \citeauthor{key}        → Author [name only]
%%   \citeyear{key}          → Year [year only]
%%   \citeyearpar{key}       → (Year) [year in parentheses]
%%
%% Pre/post notes:
%%   \cite[see][p.~10]{key} → (see Author, Year, p. 10)
%%   \cite[p.~10]{key}      → (Author, Year, p. 10)
%%
%% Multiple citations:
%%   \cite{key1,key2,key3}  → (Author1, Year1; Author2, Year2; Author3, Year3)
%%
%% Suppressing parts:
%%   \cite[e.g.,][]{key}    → (e.g., Author, Year)
%%   \cite[][see p.~10]{key}→ (Author, Year, see p. 10)
%%
%% ----------------------------------------------------------------------------
%% TROUBLESHOOTING
%% ----------------------------------------------------------------------------
%% Problem: Citations appear as [?] or undefined
%% Solution: Run compilation 3-4 times to resolve all references
%%
%% Problem: Citation numbers out of order [3, 1] instead of [1, 3]
%% Solution: Use unsrtnat (order of appearance) instead of elsarticle-num
%%
%% Problem: "Undefined control sequence \citet"
%% Solution: \citet only works with natbib-compatible styles (unsrtnat, plainnat)
%%           Use \cite{} with non-natbib styles
%%
%% Problem: Bibliography not appearing
%% Solution: Ensure \bibliography{path/to/bibfile} command exists in main file
%%           Run: pdflatex → bibtex → pdflatex → pdflatex

%%%% EOF