diff --git a/dwms/.gitignore b/dwms/.gitignore index eec3ab1..dc719c9 100644 --- a/dwms/.gitignore +++ b/dwms/.gitignore @@ -10,3 +10,7 @@ _variables.yml _freeze/ www/ .source_state +*_files/ +/*.pdf +/*.html + diff --git a/dwms/BB/localRef.bib b/dwms/BB/localRef.bib deleted file mode 100644 index e69de29..0000000 diff --git a/dwms/MS.qmd b/dwms/MS.qmd index f53a9a9..54dc3ed 100644 --- a/dwms/MS.qmd +++ b/dwms/MS.qmd @@ -1,146 +1,22 @@ --- msname: MS smname: SM -title: "MANUSCRIPT TITLE" -subtitle: "Supplementary Information" -submitjournal: "JOURNAL" -submitid: -lang: en +isMS: true date: "" -# bibliography: [BB/Ref.bib, BB/localRef.bib] -affilstyle: alphabeta # number -author: - - name: Xxxxx Yyyy - affiliations: - - ref: kleac - # email: 13586740928@163.com - attributes: - corresponding: false - equal-contributor: true - role: - - data-curation: lead - - methodology: lead - - formalanalysis: lead - - writingoriginal: equal - - writingediting: eqaul - - visualisation: supporting - - name: Ming Su - email: mingsu@rcees.ac.cn - orcid: 0000-0001-9821-1268 - url: https://drwater.net/team/ming-su/ - role: - - conceptualization: lead - - methodology: supporting - - formalanalysis: lead - - writingoriginal: equal - - writingediting: equal - - visualisation: lead - - projectadmin: lead - - supervision - affiliations: - - ref: kleac - - ref: ucas - attributes: - corresponding: true - equal-contributor: true - - name: Min Yang - email: yangmin@rcees.ac.cn - affiliations: - - ref: kleac - - ref: ucas - attributes: - corresponding: true -affiliations: - - id: kleac - name: State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences - # address: No. 18 Shuangqing Road - city: Beijing - postal-code: 100085 - country: China - url: https://www.skleac.ac.cn - - id: ucas - name: University of Chinese Academy of Sciences - # address: No. 19A Yuquan Road - city: Beijing - postal-code: 100049 - country: China - url: https://www.ucas.ac.cn -crossref: - fig-title: Fig. # (default is "Figure") - tbl-title: Table # (default is "Table") - eq-title: Eq. # (default is "Equation") - title-delim: ":" # (default is ":") - fig-prefix: Fig. # (default is "Figure") - tbl-prefix: Table # (default is "Table") - eq-prefix: Eq. - ref-hyperlink: true # (default is true) - custom: - - kind: float - key: sfg - reference-prefix: "Supplementary Fig." - space-before-numbering: true - caption-prefix: "Supplementary Fig." - latex-env: sfg - latex-list-of-file-extension: lost - latex-list-of-description: Supplementary Figure - - kind: float - key: stb - reference-prefix: "Supplementary Table" - space-before-numbering: true - caption-prefix: "Supplementary Table" - latex-env: stb - latex-list-of-file-extension: lost - latex-list-of-description: Supplementary Table - - kind: float - key: seq - reference-prefix: "Supplementary Eq." - space-before-numbering: true - caption-prefix: "Supplementary Eq." - latex-env: seq - latex-list-of-file-extension: lost - latex-list-of-description: Supplementary Equation - - kind: float - key: rfg - reference-prefix: "Fig. R" - space-before-numbering: false - caption-prefix: "Fig. R" - latex-env: rfg - latex-list-of-file-extension: lost - latex-list-of-description: Revision Figure - - kind: float - key: rtb - reference-prefix: "Table R" - space-before-numbering: false - caption-prefix: "Table R" - latex-env: rtb - latex-list-of-file-extension: lost - latex-list-of-description: Revision Table - - kind: float - key: req - reference-prefix: "Eq R" - space-before-numbering: false - caption-prefix: "Eq R" - latex-env: req - latex-list-of-file-extension: lost - latex-list-of-description: Revision Equation -prefer-html: true +# bibliography: [../BB/Ref.bib, ../BB/localRef.bib] +# csl: _extensions/drwater/dwms/inst/nature.csl +endfloat: true +doublespacing: true +linenumbers: true format: - # elsevier-html: - # toc: true - # css: _extensions/drwater/dwms/inst/css/style.css - # docx: - # reference-doc: _extensions/drwater/dwms/inst/word/MS.docx - dwms-pdf: - fontsize: 12pt - keep-md: false - keep-tex: true - header-includes: - - \usepackage{endfloat} - - \doublespacing - - \linenumbers + dwms-html: default + dwms-docx: default + dwms-pdf: default # filters: # - latex-environment # - authoraffil +# lightbox: auto +# commands: [clab] --- @@ -162,8 +38,7 @@ dwfun::init() # Abstract {-} - -{{< pagebreak >}} +This is a demo of abstract. {{< pagebreak >}} diff --git a/dwms/RN.qmd b/dwms/RN.qmd new file mode 100644 index 0000000..1e74fc7 --- /dev/null +++ b/dwms/RN.qmd @@ -0,0 +1,61 @@ +--- +subtitle: "Revision Note" +msname: MS +smname: SM +isRN: true +date: "" +# bibliography: [../BB/Ref.bib, ../BB/localRef.bib] +# csl: _extensions/drwater/dwinst/nature.csl +format: + dwms-html: default + dwms-docx: default + dwms-pdf: + number-sections: true +# filters: +# - latex-environment +# - authoraffil +# lightbox: auto +# commands: [clab] +--- + +```{r} +#| include: false +#| cache: false +lang <- "en" +RM <- "F" # global rendermode, L: load pdata; F: fast load pdf +isrendering <- isTRUE(getOption('knitr.in.progress')) +require(tidyverse) +require(patchwork) +require(drwateR) +rmdify::rmd_init() +``` + +# Response to Editor + +> 0. I very much regret to have to tell you that publication in our journal is not recommended. An explanation for this decision is given in the attached review reports (and on https://www.editorialmanager.com/wr/). I hope that the comments contained therein will be of use to you. + +**Response/Action:** + +Thank you. + +::: {#rfg-figr1} + +```{r} +plot(1) +``` + +A figure in RN +::: + + + +# Reviewer #1: + +> 0. COMMENT 1 + +**Response/Action:** + +Thank you very much for your revision. We made changes as shown below. + +`r cref("r1q0101")` + diff --git a/dwms/SM.pdf b/dwms/SM.pdf deleted file mode 100644 index bdbac9f..0000000 Binary files a/dwms/SM.pdf and /dev/null differ diff --git a/dwms/SM.qmd b/dwms/SM.qmd index e944f57..735145b 100644 --- a/dwms/SM.qmd +++ b/dwms/SM.qmd @@ -1,143 +1,22 @@ --- msname: MS smname: SM -title: "MANUSCRIPT TITLE" +isSM: true +# bibliography: [../BB/Ref.bib, ../BB/localRef.bib] +# csl: _extensions/drwater/dwinst/nature.csl subtitle: "Supplementary Information" -submitjournal: "JOURNAL" -submitid: -lang: en date: "" -# bibliography: [BB/Ref.bib, BB/localRef.bib] -affilstyle: alphabeta # number -author: - - name: Xxxxx Yyyy - affiliations: - - ref: kleac - # email: 13586740928@163.com - attributes: - corresponding: false - equal-contributor: true - role: - - data-curation: lead - - methodology: lead - - formalanalysis: lead - - writingoriginal: equal - - writingediting: eqaul - - visualisation: supporting - - name: Ming Su - email: mingsu@rcees.ac.cn - orcid: 0000-0001-9821-1268 - url: https://drwater.net/team/ming-su/ - role: - - conceptualization: lead - - methodology: supporting - - formalanalysis: lead - - writingoriginal: equal - - writingediting: equal - - visualisation: lead - - projectadmin: lead - - supervision - affiliations: - - ref: kleac - - ref: ucas - attributes: - corresponding: true - equal-contributor: true - - name: Min Yang - email: yangmin@rcees.ac.cn - affiliations: - - ref: kleac - - ref: ucas - attributes: - corresponding: true -affiliations: - - id: kleac - name: State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences - # address: No. 18 Shuangqing Road - city: Beijing - postal-code: 100085 - country: China - url: https://www.skleac.ac.cn - - id: ucas - name: University of Chinese Academy of Sciences - # address: No. 19A Yuquan Road - city: Beijing - postal-code: 100049 - country: China - url: https://www.ucas.ac.cn -crossref: - fig-title: Fig. # (default is "Figure") - tbl-title: Table # (default is "Table") - eq-title: Eq. # (default is "Equation") - title-delim: ":" # (default is ":") - fig-prefix: Fig. # (default is "Figure") - tbl-prefix: Table # (default is "Table") - eq-prefix: Eq. - ref-hyperlink: true # (default is true) - custom: - - kind: float - key: sfg - reference-prefix: "Supplementary Fig." - space-before-numbering: true - caption-prefix: "Supplementary Fig." - latex-env: sfg - latex-list-of-file-extension: lost - latex-list-of-description: Supplementary Figure - - kind: float - key: stb - reference-prefix: "Supplementary Table" - space-before-numbering: true - caption-prefix: "Supplementary Table" - latex-env: stb - latex-list-of-file-extension: lost - latex-list-of-description: Supplementary Table - - kind: float - key: seq - reference-prefix: "Supplementary Eq." - space-before-numbering: true - caption-prefix: "Supplementary Eq." - latex-env: seq - latex-list-of-file-extension: lost - latex-list-of-description: Supplementary Equation - - kind: float - key: rfg - reference-prefix: "Fig. R" - space-before-numbering: false - caption-prefix: "Fig. R" - latex-env: rfg - latex-list-of-file-extension: lost - latex-list-of-description: Revision Figure - - kind: float - key: rtb - reference-prefix: "Table R" - space-before-numbering: false - caption-prefix: "Table R" - latex-env: rtb - latex-list-of-file-extension: lost - latex-list-of-description: Revision Table - - kind: float - key: req - reference-prefix: "Eq R" - space-before-numbering: false - caption-prefix: "Eq R" - latex-env: req - latex-list-of-file-extension: lost - latex-list-of-description: Revision Equation -prefer-html: true +latex-clean: false # to keep aux format: - dwms-pdf: - latex-clean: false # to keep aux - keep-md: false - keep-tex: true - header-includes: - - \doublespacing - - \linenumbers - - \let\oldsection\section - - \renewcommand{\section}{\clearpage\oldsection} - - \let\oldsubsection\subsection - - \renewcommand{\subsection}{\clearpage\oldsubsection} + dwms-html: default + dwms-docx: default + dwms-pdf: + toc: false # 手动设置了 # filters: +# - latex-environment # - authoraffil +# lightbox: auto +# commands: [clab] --- \thispagestyle{empty} @@ -155,11 +34,9 @@ require(drwateR) rmdify::rmd_init() ``` + Figures and/or tables are provided below as the supplementary evidences to the main text. -{{< pagebreak >}} - - ```{=latex} \clearpage @@ -171,27 +48,18 @@ Figures and/or tables are provided below as the supplementary evidences to the m ``` -{{< pagebreak >}} - +# [@sfg-demo] ::: {#sfg-demo} ```{r} #| out-width: "40%" - -if (!isRendering) { - data.frame(x = 1:10, y = 1:10) |> - ggplot(aes(x, y)) + - geom_point() + - theme_sci(3, 2.0) - - ggsavep("../figures/demo.pdf", loadit = FALSE) -} - -ggsavep("../figures/demo", loadit = TRUE) +data.frame(x = 1:10, y = 1:10) |> + ggplot(aes(x, y)) + + geom_point() + + dwfun::theme_sci(3, 2.0) ``` Caption of demo figure - ::: diff --git a/dwms/_extensions/drwater/dwms/header.tex b/dwms/_extensions/drwater/dwms/header.tex index bf33a39..814ad48 100644 --- a/dwms/_extensions/drwater/dwms/header.tex +++ b/dwms/_extensions/drwater/dwms/header.tex @@ -12,8 +12,6 @@ \usepackage[normalem]{ulem} \usepackage{setspace} \usepackage{lineno} -\usepackage{caption} -\captionsetup{singlelinecheck=off} \usepackage[UTF8, scheme=plain]{ctex} \usepackage{orcidlink} @@ -100,9 +98,9 @@ %\titlespacing{}{}{}{} % Starred version removes indentation in following paragraph -\titlespacing*{\section}{0em}{2em}{0.1em} -\titlespacing*{\subsection}{0em}{1.25em}{0.1em} -\titlespacing*{\subsubsection}{0em}{0.75em}{0em} +% \titlespacing*{\section}{0em}{2em}{0.1em} +% \titlespacing*{\subsection}{0em}{1.25em}{0.1em} +% \titlespacing*{\subsubsection}{0em}{0.75em}{0em} % ------------------ % Headers/Footers @@ -125,7 +123,7 @@ % Captions % ------------------ \usepackage[labelfont=bf,labelsep=period]{caption} -\captionsetup[figure]{font=footnotesize,justification=raggedright,singlelinecheck=false,format=hang} +\captionsetup[figure]{font=footnotesize,justification=centering,singlelinecheck=false,format=hang} % --------------------------- diff --git a/dwms/_extensions/drwater/dwms/partials/title.tex b/dwms/_extensions/drwater/dwms/partials/title.tex index b86298e..3a5ad9b 100644 --- a/dwms/_extensions/drwater/dwms/partials/title.tex +++ b/dwms/_extensions/drwater/dwms/partials/title.tex @@ -13,3 +13,34 @@ $endif$ $-- This supports Quarto's authors normalization \author{$for(authors)$\footnotesize $it.name.literal$$sep$ \and $endfor$} \date{$date$} +$if(isSM)$ +\let\oldsection\section +\renewcommand{\section}{\clearpage\oldsection} +\let\oldsubsection\subsection +\renewcommand{\subsection}{\clearpage\oldsubsection} +\renewcommand{\thetable}{S\arabic{table}} +\renewcommand{\thefigure}{S\arabic{figure}} +\renewcommand{\theequation}{S\arabic{equation}} +\renewcommand{\figurename}{Figure} +\renewcommand{\tablename}{Table} +\usepackage{titlesec} +\newcommand{\sectionbreak}{\clearpage} +$endif$ +$if(isRN)$ +\renewcommand{\thetable}{R\arabic{table}} +\renewcommand{\thefigure}{R\arabic{figure}} +\renewcommand{\theequation}{R\arabic{equation}} +\renewcommand{\figurename}{Figure} +\renewcommand{\tablename}{Table} +\usepackage{titlesec} +\newcommand{\sectionbreak}{\clearpage} +$endif$ +$if(endfloat)$ +\usepackage{endfloat} +$endif$ +$if(linenumber)$ +\linenumbers +$endif$ +$if(doublespacing)$ +\doublespacing +$endif$ diff --git a/dwms/_quarto.yml b/dwms/_quarto.yml new file mode 100644 index 0000000..29b5bb9 --- /dev/null +++ b/dwms/_quarto.yml @@ -0,0 +1,121 @@ +title: "MANUSCRIPT TITLE" +submitjournal: "JOURNAL" +submitid: +lang: en +date: last-modified +# bibliography: [BB/Ref.bib, BB/localRef.bib] +affilstyle: alphabeta # number +author: + - name: Xxxxx Yyyy + affiliations: + - ref: kleac + # email: 13586740928@163.com + attributes: + corresponding: false + equal-contributor: true + role: + - data-curation: lead + - methodology: lead + - formalanalysis: lead + - writingoriginal: equal + - writingediting: eqaul + - visualisation: supporting + - name: Ming Su + email: mingsu@rcees.ac.cn + orcid: 0000-0001-9821-1268 + url: https://drwater.net/team/ming-su/ + role: + - conceptualization: lead + - methodology: supporting + - formalanalysis: lead + - writingoriginal: equal + - writingediting: equal + - visualisation: lead + - projectadmin: lead + - supervision + affiliations: + - ref: kleac + - ref: ucas + attributes: + corresponding: true + equal-contributor: true + - name: Min Yang + email: yangmin@rcees.ac.cn + affiliations: + - ref: kleac + - ref: ucas + attributes: + corresponding: true +affiliations: + - id: kleac + name: Key Laboratory of Environmental Aguatic Chemistry, State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences + # address: No. 18 Shuangqing Road + city: Beijing + postal-code: 100085 + country: China + url: https://www.skleac.ac.cn + - id: ucas + name: University of Chinese Academy of Sciences + # address: No. 19A Yuquan Road + city: Beijing + postal-code: 100049 + country: China + url: https://www.ucas.ac.cn +crossref: + fig-title: Fig. # (default is "Figure") + tbl-title: Table # (default is "Table") + eq-title: Eq. # (default is "Equation") + title-delim: ":" # (default is ":") + fig-prefix: Fig. # (default is "Figure") + tbl-prefix: Table # (default is "Table") + eq-prefix: Eq. + ref-hyperlink: true # (default is true) + custom: + - kind: float + key: sfg + reference-prefix: "Supplementary Fig." + space-before-numbering: true + caption-prefix: "Supplementary Fig." + latex-env: sfg + latex-list-of-file-extension: lost + latex-list-of-description: Supplementary Figure + - kind: float + key: stb + reference-prefix: "Supplementary Table" + space-before-numbering: true + caption-prefix: "Supplementary Table" + latex-env: stb + latex-list-of-file-extension: lost + latex-list-of-description: Supplementary Table + - kind: float + key: seq + reference-prefix: "Supplementary Eq." + space-before-numbering: true + caption-prefix: "Supplementary Eq." + latex-env: seq + latex-list-of-file-extension: lost + latex-list-of-description: Supplementary Equation + - kind: float + key: rfg + reference-prefix: "Fig. R" + space-before-numbering: false + caption-prefix: "Fig. R" + latex-env: rfg + latex-list-of-file-extension: lost + latex-list-of-description: Revision Figure + - kind: float + key: rtb + reference-prefix: "Table R" + space-before-numbering: false + caption-prefix: "Table R" + latex-env: rtb + latex-list-of-file-extension: lost + latex-list-of-description: Revision Table + - kind: float + key: req + reference-prefix: "Eq R" + space-before-numbering: false + caption-prefix: "Eq R" + latex-env: req + latex-list-of-file-extension: lost + latex-list-of-description: Revision Equation diff --git a/dwms/figure/unnamed-chunk-2-1.pdf b/dwms/figure/unnamed-chunk-2-1.pdf new file mode 100644 index 0000000..a142552 Binary files /dev/null and b/dwms/figure/unnamed-chunk-2-1.pdf differ diff --git a/dwms/figure/unnamed-chunk-2-1.png b/dwms/figure/unnamed-chunk-2-1.png new file mode 100644 index 0000000..a6c22b3 Binary files /dev/null and b/dwms/figure/unnamed-chunk-2-1.png differ diff --git a/dwms/figure/unnamed-chunk-2-1.svg b/dwms/figure/unnamed-chunk-2-1.svg new file mode 100644 index 0000000..ad0936a --- /dev/null +++ b/dwms/figure/unnamed-chunk-2-1.svg @@ -0,0 +1,57 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +