├── .DS_Store ├── .gitignore ├── QmdReport.Rproj ├── README.md ├── SEDAR.bib ├── _quarto.yml ├── data ├── .DS_Store ├── CRchum.csv ├── HCchum.csv ├── ICSRFchinook.csv ├── ICSRsthd.csv ├── ICUCchinook.csv ├── ICUCsthd.csv ├── LCchinook.csv ├── LCcoho.csv ├── LCsthd.csv ├── OCcoho.csv ├── PSchinook.csv ├── PSsthd.csv ├── UWchinook.csv ├── UWsthd.csv ├── maplocs.rda └── pnwmap.rda ├── docs ├── An-example-report.docx ├── An-example-report.pdf ├── index.html ├── references.html ├── robots.txt ├── search.json ├── site_libs │ ├── bootstrap │ │ ├── bootstrap-icons.css │ │ ├── bootstrap-icons.woff │ │ ├── bootstrap.min.css │ │ └── bootstrap.min.js │ ├── clipboard │ │ └── clipboard.min.js │ ├── quarto-html │ │ ├── anchor.min.js │ │ ├── popper.min.js │ │ ├── quarto-syntax-highlighting.css │ │ ├── quarto.js │ │ ├── tippy.css │ │ └── tippy.umd.min.js │ ├── quarto-nav │ │ ├── headroom.min.js │ │ └── quarto-nav.js │ ├── quarto-search │ │ ├── autocomplete.umd.js │ │ ├── fuse.min.js │ │ └── quarto-search.js │ └── tabwid-1.0.0 │ │ ├── scrool.css │ │ └── tabwid.css ├── sitemap.xml └── text │ ├── ICSRFchinook.html │ ├── ICSRFchinook_files │ └── figure-html │ │ ├── fig-ICSRFchinook-map-1.png │ │ └── fig-ICSRFchinook-status-1.png │ ├── ICSRsthd.html │ ├── ICSRsthd_files │ └── figure-html │ │ ├── fig-ICSRsthd-map-1.png │ │ └── fig-ICSRsthd-status-1.png │ ├── ICUCchinook.html │ ├── ICUCchinook_files │ └── figure-html │ │ ├── fig-ICUCchinook-map-1.png │ │ └── fig-ICUCchinook-status-1.png │ ├── ICUCsthd.html │ ├── ICUCsthd_files │ └── figure-html │ │ ├── fig-ICUCsthd-map-1.png │ │ └── fig-ICUCsthd-status-1.png │ ├── LCchinook.html │ ├── LCchinook_files │ └── figure-html │ │ ├── fig-LCchinook-map-1.png │ │ └── fig-LCchinook-status-1.png │ ├── LCsthd.html │ ├── LCsthd_files │ └── figure-html │ │ ├── fig-LCsthd-map-1.png │ │ └── fig-LCsthd-status-1.png │ ├── UWchinook.html │ ├── UWchinook_files │ └── figure-html │ │ ├── fig-UWchinook-map-1.png │ │ └── fig-UWchinook-status-1.png │ ├── UWsthd.html │ ├── UWsthd_files │ └── figure-html │ │ ├── fig-UWsthd-map-1.png │ │ └── fig-UWsthd-status-1.png │ └── conclusion.html ├── figures_tables ├── Map_Figure.Rmd ├── Raw_Tables.Rmd ├── Status_Figure.Rmd ├── _common.R ├── _template_map_figure.Rmd ├── _template_raw_table.Rmd └── _template_status_figure.Rmd ├── images ├── doc-logo.png └── logo.png ├── index.qmd ├── partials ├── _two-column-longtable.tex ├── before-body-elsevier.tex ├── before-body.tex ├── before-body1.tex ├── inheader.tex └── title1.tex ├── preface.qmd ├── references.bib ├── references.qmd ├── template.docx └── text ├── CRchum.qmd ├── HCchum.qmd ├── HCchum_files └── figure-pdf │ ├── fig-HCchum-map-1.pdf │ └── fig-HCchum-status-1.pdf ├── ICSRFchinook.qmd ├── ICSRsthd.qmd ├── ICUCchinook.qmd ├── ICUCsthd.qmd ├── LCchinook.qmd ├── LCcoho.qmd ├── LCcoho_files └── figure-pdf │ ├── fig-LCcoho-map-1.pdf │ └── fig-LCcoho-status-1.pdf ├── LCsthd.qmd ├── OCcoho.qmd ├── OCcoho_files └── figure-pdf │ ├── fig-OCcoho-map-1.pdf │ └── fig-OCcoho-status-1.pdf ├── UWchinook.qmd ├── UWsthd.qmd ├── _template.qmd ├── conclusion.qmd └── covert_templates.R /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/QuartoReport_SE/4419539f20879fb3949fcc1ffdd0f8df0e8c564b/.DS_Store -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | .Ruserdata 5 | 6 | /.quarto/ 7 | /_site/ 8 | /_book/ 9 | -------------------------------------------------------------------------------- /QmdReport.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: Sweave 13 | LaTeX: pdfLaTeX 14 | 15 | ZoteroLibraries: "SEDAR" 16 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # QmdReport. 2 | 3 | Example of a Quarto Report with dynamically created tables 4 | 5 | Presentation given on this Aug 11 2022: https://youtu.be/Uay6X65Ukvk. The version given in that talk is Release v2.0. 6 | 7 | ## What is this doing? 8 | 9 | * Dynamic tables and figures where the table number, table caption, number of tables is all dynamically created based on the data set 10 | * Table cross-refs that just work across formats 11 | * Figures that look good across formats and it "just works"---with the caveat that I am using {flextable} for Word/html and {kableExtra} for PDF. 12 | * A custom title page for PDF. 13 | * Link to source code, post issue, edit source code right on the HTML for each page. 14 | * Link to download the PDF and Word. This is auto-generated. None of this is manual. 15 | * HTML that looks good across different sized displays (big screen and phone screen) 16 | 17 | ## How about? 18 | 19 | * {gt} is great. Why not use that for tables? It was not playing nice with Quarto+PDF and broke all table numbering in subsequent tables (flextable or kabelExtra or markdown). I reported the bug and I think the {gt} developers have fixed for the next update. 20 | 21 | ## Can't {bookdown} do this? 22 | 23 | Kind of. I love {bookdown} and I have written multiple on-line books with it but 24 | 25 | * there were a lot of hacks and tricks needed for cross-refs and it would tend to break when you needed multiple formats (PDF, HTML and Word). 26 | * Lack of solid cross-ref working across formats is a deal-breaker for government reports. 27 | * The ability to use "@" to find your cross-refs that you can do with Visual mode in RStudio... I can't live without that now. 28 | * Quarto still has some hacks, but many many fewer. A lot of stuff seems to just work. 29 | -------------------------------------------------------------------------------- /SEDAR.bib: -------------------------------------------------------------------------------- 1 | 2 | @techreport{ansley_migration_1981, 3 | address = {Brunswick, Georgia, USA}, 4 | title = {Migration and standing stock of fishes associated with artificial and natural reefs on {Georgia}’s outer continental shelf}, 5 | institution = {GA. Dep. Natur. Resour.}, 6 | author = {Ansley, H. L. H. and Davis, C. D.}, 7 | year = {1981}, 8 | keywords = {SEDAR2}, 9 | pages = {38}, 10 | } 11 | 12 | @techreport{clark_1960_1962, 13 | title = {The 1960 {Salt}-{Water} {Angling} {Survey}}, 14 | institution = {Department of Interior, U.S. Fish and Wildlife Service, Bureau of Sport Fisheries and Wildlife}, 15 | author = {Clark, J. R.}, 16 | year = {1962}, 17 | keywords = {SEDAR2}, 18 | pages = {36}, 19 | } 20 | 21 | @inproceedings{clark_effect_1993, 22 | title = {The effect of recruitment variability on the choice of a target level of spawning biomass per recruit}, 23 | booktitle = {Proceedings of the {International} {Symposium} on {Management} {Strategies} for {Exploited} {Fish} {Populations}}, 24 | publisher = {Alaska Sea Grant College Program AK–SG–93–02}, 25 | author = {Clark, W. G.}, 26 | year = {1993}, 27 | keywords = {SEDAR2}, 28 | pages = {233--246}, 29 | } 30 | 31 | @incollection{collins_age_1996, 32 | address = {Makati City, Philippines}, 33 | title = {Age validation, movements, and growth rates of tagged gag ({Mycteroperca} microlepis), black sea bass ({Centropristis} striata) and red porgy ({Pagrus} pagrus)}, 34 | booktitle = {Biology, fisheries, and culture of tropical groupers and snappers, {Conference} {Proceedings} 48}, 35 | publisher = {ICLARM (International Center for Living Aquatic Resources Management)}, 36 | author = {Collins, M. R. and Sant, S. B. Van and Schmidt, D. J. and Sedberry, G. R.}, 37 | editor = {Arrequin-Sanchez, F. and Munro, J. L. and Balgos, M. C. and Pauly, D.}, 38 | year = {1996}, 39 | keywords = {SEDAR2}, 40 | pages = {161--165}, 41 | } 42 | 43 | @article{deriso_relationship_1982, 44 | title = {Relationship of fishing mortality and growth and the level of maximum sustainable yield}, 45 | volume = {39}, 46 | journal = {Canadian Journal of Fisheries and Aquatic Sciences}, 47 | author = {Deriso, R. B.}, 48 | year = {1982}, 49 | keywords = {SEDAR2}, 50 | pages = {1054--1058}, 51 | } 52 | 53 | @techreport{deuel_1970_1973, 54 | title = {1970 {Salt} {Water} {Angling} {Survey}}, 55 | institution = {Department of Commerce, US National Marine Fisheries Service}, 56 | author = {Deuel, D. G.}, 57 | year = {1973}, 58 | keywords = {SEDAR2}, 59 | pages = {106}, 60 | } 61 | 62 | @techreport{deuel_1965_1968, 63 | title = {The 1965 {Salt}-{Water} {Angling} {Survey}}, 64 | institution = {Department of Interior, U.S. Fish and Wildlife Service}, 65 | author = {Deuel, D. G. and Clark, J. R.}, 66 | year = {1968}, 67 | note = {SEDAR2}, 68 | keywords = {SEDAR2}, 69 | pages = {51}, 70 | } 71 | 72 | @article{fox_exponential_1970, 73 | title = {An exponential surplus-yield model for optimizing exploited .sh populations}, 74 | volume = {99}, 75 | journal = {Transactions of the American Fisheries Society}, 76 | author = {Fox, W. W.}, 77 | year = {1970}, 78 | keywords = {SEDAR2}, 79 | pages = {80--88}, 80 | } 81 | 82 | @incollection{goodyear_spawning_1993, 83 | title = {Spawning stock biomass per recruit in fisheries management: foundation and current use}, 84 | booktitle = {Risk evaluation and biological reference points for fisheries management}, 85 | publisher = {Canadian Special Publications in Fisheries and Aquatic Sciences 120}, 86 | author = {Goodyear, C. P.}, 87 | editor = {Smith, S. J. and Hunt, J. J. and Rivard, D.}, 88 | year = {1993}, 89 | keywords = {SEDAR2}, 90 | pages = {67--81}, 91 | } 92 | 93 | @techreport{last_first_author_0_template_noaa_tech_memo_2000, 94 | title = {0\_Template\_NOAA\_Tech\_Memo}, 95 | institution = {U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-91.}, 96 | author = {Last, First Author and Last, Second Author}, 97 | year = {2000}, 98 | pages = {199p}, 99 | } 100 | 101 | @techreport{baum__nodate, 102 | title = {. 2003. {Collapse} and conservation of shark populations in the northwest {Atlantic}. {Science} 299: 389-392.}, 103 | author = {Baum, Julia K. and Ransom A. Myers}, 104 | keywords = {SEDAR2}, 105 | } 106 | 107 | @techreport{goodyear_red_1995, 108 | title = {Red snapper in {U}.{S}. {Waters} of the {Gulf} of {Mexico}.}, 109 | institution = {NMFS/SEFSC Contribution MIA-95/96-05}, 110 | author = {Goodyear, C. P.}, 111 | year = {1995}, 112 | } 113 | 114 | @techreport{hardy_development_1978, 115 | title = {Development of {Fishes} of the {Mid}-{Atlantic} {Bight}. {Vol}. {III}. {Aphredoderidae} through {Rachycentridae}.}, 116 | institution = {FWS/OBS-78/12. 394 pp}, 117 | author = {Hardy, Jr., J. D.}, 118 | year = {1978}, 119 | } 120 | 121 | @article{mace_relationships_1994, 122 | title = {Relationships between common biological reference points used as threshold and targets of fisheries management strategies}, 123 | volume = {51}, 124 | journal = {Canadian Journal of Fisheries and Aquatic Sciences}, 125 | author = {Mace, P. M.}, 126 | year = {1994}, 127 | pages = {110--122}, 128 | } 129 | 130 | @article{mcgovern_temporal_2002, 131 | title = {Temporal and spatial differences in the life history parameters of black sea bass in the southeastern {United} {States}}, 132 | volume = {22}, 133 | journal = {North American Journal of Fisheries Management}, 134 | author = {McGovern, J. C. and Collins, M. R. and Pashuk, O. and Meister, H. S.}, 135 | year = {2002}, 136 | pages = {1151--1163}, 137 | } 138 | 139 | @book{otter_research_introduction_2000, 140 | address = {Sidney, B.C., Canada}, 141 | title = {An introduction to {AD} {Model} {Builder} version 5.0.1 for use in nonlinear modeling and statistics}, 142 | publisher = {Otter Research}, 143 | author = {Otter Research, Ltd}, 144 | year = {2000}, 145 | } 146 | 147 | @article{pella_generalized_1969, 148 | title = {A generalized stock production model}, 149 | volume = {13}, 150 | journal = {Bulletin of the Inter-American Tropical Tuna Commission}, 151 | author = {Pella, J. J. and Tomlinson, P. K.}, 152 | year = {1969}, 153 | pages = {419--496}, 154 | } 155 | 156 | @article{prager_suite_1994, 157 | title = {A suite of extensions to a nonequilibrium surplus–production model}, 158 | volume = {92}, 159 | journal = {U.S. National Marine Fisheries Service Fishery Bulletin}, 160 | author = {Prager, M. H.}, 161 | year = {1994}, 162 | pages = {374--389}, 163 | } 164 | 165 | @techreport{prager_users_1995, 166 | title = {User’s manual for {ASPIC}: {A} stock-production model incorporating covariates, program version 3.6x}, 167 | institution = {NMFS Southeast Fisheries Science Center, Miami Laboratory Document MIA–2/93–55, 4th ed. Available from M.H.P}, 168 | author = {Prager, M. H.}, 169 | year = {1995}, 170 | } 171 | 172 | @article{punt_is_1990, 173 | title = {Is {B1} = {K} an appropriate assumption when applying an observation error production-model estimator to catch–effort data?}, 174 | volume = {9}, 175 | journal = {South African Journal of Marine Science}, 176 | author = {Punt, A. E.}, 177 | year = {1990}, 178 | pages = {249--259}, 179 | } 180 | 181 | @book{quinn_quantitative_1999, 182 | address = {New York. 542 p}, 183 | title = {Quantitative {Fish} {Dynamics}}, 184 | publisher = {Oxford University Press}, 185 | author = {Quinn, T. J. and Deriso, R. B.}, 186 | year = {1999}, 187 | } 188 | 189 | @techreport{restrepo_technical_1998, 190 | title = {Technical guidance on the use of precautionary approaches to implementing {National} {Standard} 1 of the {Magnuson}-{Stevens} {Fishery} {Conservation} and {Management} {Act}}, 191 | institution = {NOAA Technical Memorandum NMFS-F/SPO-31, 54 p}, 192 | author = {Restrepo, V. R. and co-authors, 10}, 193 | year = {1998}, 194 | } 195 | 196 | @article{rose_compensatory_2001, 197 | title = {Compensatory density dependence in fish populations: importance, controversy, understanding and prognosis}, 198 | volume = {2}, 199 | journal = {Fish and Fisheries}, 200 | author = {Rose, K. A. and Cowan, J. H. and Winemiller, K. O. and Myers, R. A. and Hilborn, R.}, 201 | year = {2001}, 202 | pages = {293--327}, 203 | } 204 | 205 | @article{schaefer_aspects_1954, 206 | title = {Some aspects of the dynamics of populations important to the management of the commercial marine fisheries}, 207 | volume = {1}, 208 | number = {2}, 209 | journal = {Bulletin of the Inter-American Tropical Tuna Commission}, 210 | author = {Schaefer, M. B.}, 211 | year = {1954}, 212 | pages = {27--56}, 213 | } 214 | 215 | @article{schaefer_study_1957, 216 | title = {A study of the dynamics of the fishery for yellowfin tuna in the eastern tropical {Pacific} {Ocean}}, 217 | volume = {2}, 218 | journal = {Bulletin of the Inter-American Tropical Tuna Commission}, 219 | author = {Schaefer, M. B.}, 220 | year = {1957}, 221 | pages = {247--268}, 222 | } 223 | 224 | @article{shepherd_versatile_1982, 225 | title = {A versatile new stock–recruitment relationship for fisheries, and the construction of sustainable yield curves}, 226 | volume = {40}, 227 | journal = {Journal du Conseil pour l’Exploration de la Mer}, 228 | author = {Shepherd, J. G.}, 229 | year = {1982}, 230 | pages = {67--75}, 231 | } 232 | 233 | @article{thompson_management_1992, 234 | title = {Management advice from a simple dynamic pool model}, 235 | volume = {90}, 236 | journal = {Fishery Bulletin}, 237 | author = {Thompson, G. G.}, 238 | year = {1992}, 239 | pages = {552--560}, 240 | } 241 | 242 | @article{thompson_proposal_1993, 243 | title = {A proposal for a threshold stock size and maximum fishing mortality rate}, 244 | volume = {120}, 245 | journal = {Canadian Special Publication of Fisheries and Aquatic Science}, 246 | author = {Thompson, G. G.}, 247 | year = {1993}, 248 | pages = {303--320}, 249 | } 250 | 251 | @article{vaughan_population_1992, 252 | title = {Population characteristics of the red porgy, {Pagrus} pagrus, stock off the {Carolinas}}, 253 | volume = {50}, 254 | number = {1}, 255 | journal = {Bulletin of Marine Science}, 256 | author = {Vaughan, D. S. and Huntsman, G. R. and Iii, C. S. Manooch and Rohde, F. C. and Ulrich, G.}, 257 | year = {1992}, 258 | pages = {1--20}, 259 | } 260 | 261 | @article{vaughan_population_1995, 262 | title = {Population characteristics of the black sea bass {Centropristis} striata from the southeastern {U}. {S}.}, 263 | volume = {56}, 264 | number = {1}, 265 | journal = {Bulletin of Marine Science}, 266 | author = {Vaughan, D. S. and Collins, M. R. and Schmidt, D. J.}, 267 | year = {1995}, 268 | pages = {250--267}, 269 | } 270 | 271 | @techreport{vaughan_population_1996, 272 | title = {Population characteristics of the black sea bass {Centropristis} striata from the {U}.{S}. southern {Atlantic} coast.}, 273 | institution = {Report to South Atlantic Fishery Management Council, Charleston, SC, 59 p.}, 274 | author = {Vaughan, D. S. and Collins, M. R. and Zhao, B. and Meister, H. S.}, 275 | year = {1996}, 276 | } 277 | 278 | @inproceedings{vaughan_evaluation_1998, 279 | address = {Fairbanks, AK}, 280 | title = {Evaluation of multiple survey indices in assessment of black sea bass from the {U}.{S}. south {Atlantic} coast}, 281 | booktitle = {International symposium on fishery stock assessment models for the 21st century: combining multiple information sources}, 282 | publisher = {University of Alaska. Alaska Sea Grant College Program 98-01}, 283 | author = {Vaughan, D. S. and Collins, M. R. and McGovern, J. C. and Meister, H. S.}, 284 | year = {1998}, 285 | pages = {121--136}, 286 | } 287 | 288 | @article{wenner_contributions_1986, 289 | title = {Contributions to the life history of black sea bass, {Centropristis} striata, off the southeastern {United} {States}}, 290 | volume = {84}, 291 | journal = {U.S. National Marine Fisheries Service Fishery Bulletin}, 292 | author = {Wenner, C. A. and Roumillat, W. A. and Waltz, C. W.}, 293 | year = {1986}, 294 | pages = {723--741}, 295 | } 296 | -------------------------------------------------------------------------------- /_quarto.yml: -------------------------------------------------------------------------------- 1 | project: 2 | type: book 3 | output-dir: docs 4 | 5 | book: 6 | title: An example report 7 | subtitle: The subtitle 8 | output-file: "QmdReport" 9 | # cover-image: images/logo.png 10 | # image: images/logo.png 11 | downloads: [pdf, docx] 12 | # sharing: [twitter, facebook] 13 | author: 14 | - name: Jane Doe 15 | affiliations: 16 | - name: University of XXX 17 | department: Department of YYY 18 | - name: Eva Nováková 19 | affiliations: 20 | - name: University of XXX 21 | department: Department of YYY 22 | - name: Matti Meikäläinen 23 | affiliations: 24 | - name: University of XXX 25 | department: Department of YYY 26 | chapters: 27 | - index.qmd 28 | # - text/CRchum.qmd 29 | - text/ICSRFchinook.qmd 30 | - text/ICUCchinook.qmd 31 | - text/LCchinook.qmd 32 | - text/UWchinook.qmd 33 | - text/ICSRsthd.qmd 34 | - text/ICUCsthd.qmd 35 | # - text/LCcoho.qmd 36 | - text/LCsthd.qmd 37 | # - text/OCcoho.qmd 38 | # - text/HCchum.qmd 39 | - text/UWsthd.qmd 40 | - text/conclusion.qmd 41 | - references.qmd 42 | 43 | site-url: https://rverse-tutorials.github.io/QuartoReport_SE/ 44 | repo-url: https://github.com/RVerse-Tutorials/QuartoReport_SE 45 | repo-actions: [edit, source, issue] 46 | search: true 47 | 48 | bibliography: [references.bib, SEDAR.bib] 49 | 50 | execute: 51 | echo: false 52 | code-overflow: wrap 53 | 54 | format: 55 | docx: 56 | toc: true 57 | toc-depth: 2 58 | reference-doc: template.docx 59 | always_allow_html: true 60 | html: 61 | theme: cosmo 62 | toc: true 63 | toc-depth: 3 64 | pdf: 65 | documentclass: scrbook 66 | classoption: ["oneside"] 67 | template-partials: ["partials/before-body.tex"] 68 | toc: true 69 | toc-depth: 2 70 | lof: true 71 | lot: true 72 | include-in-header: 73 | - partials/inheader.tex 74 | 75 | 76 | -------------------------------------------------------------------------------- /data/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/QuartoReport_SE/4419539f20879fb3949fcc1ffdd0f8df0e8c564b/data/.DS_Store -------------------------------------------------------------------------------- /data/ICSRFchinook.csv: -------------------------------------------------------------------------------- 1 | "SERIES","ESU","SPECIES","METHOD","MAJOR_POPULATION_GROUP","NMFS_POPID","POPULATION_NAME","COMMON_POPULATION_NAME","DISPLAY_ORDER","RUN_TIMING","STREAM_NAME","YEAR","NUMBER_OF_SPAWNERS","FRACWILD","CATCH","CONTRIBUTOR","COMPILER","CITATION","LINE_NOTES" 2 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1975","1000","1","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 3 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1976","470","1","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 4 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1977","600","1","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 5 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1978","640","1","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 6 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1979","500","1","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 7 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1980","450","1","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 8 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1981","340","1","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 9 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1982","720","1","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 10 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1983","532","0.805","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 11 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1984","618","0.524","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 12 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1985","673","0.651","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 13 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1986","761","0.59","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 14 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1987","902","0.28","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 15 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1988","609","0.604","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 16 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1989","677","0.436","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 17 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1990","317","0.246","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 18 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1991","571","0.557","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 19 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1992","660","0.832","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 20 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1993","937","0.792","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 21 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1994","592","0.686","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 22 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1995","617","0.567","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 23 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1996","899","0.711","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 24 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1997","992","0.803","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 25 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1998","916","0.334","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 26 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","1999","1795","0.504","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 27 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2000","2558","0.449","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 28 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2001","9545","0.541","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 29 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2002","9347","0.226","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 30 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2003","11724","0.278","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 31 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2004","15609","0.39","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 32 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2005","9924","0.462","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 33 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2006","6485","0.6","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 34 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2007","8354","0.337","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 35 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2008","11925","0.251","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 36 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2009","20685","0.207","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 37 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2010","39764","0.185","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 38 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2011","23580","0.342","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 39 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2012","30363","0.373","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 40 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2013","51239","0.399","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 41 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2014","52989","0.248","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 42 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2015","52285","0.295","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 43 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2016","31993","0.27","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 44 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2017","21248","0.289","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 45 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2018","11705","0.42","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 46 | "ICSRFchinook2021","Salmon, Chinook (Snake River fall-run ESU)","Chinook salmon","Survey","","56","Snake River Lower Mainstem","Chinook","1","fall","Snake River","2019","12790","0.39","","Nez Perce Tribe","Mari Williams","Snake River fall Chinook Natural Origin Spawner Abundance Dataset (1975-2019). Spawner abundance data. Nez Perce Tribe. Personal communication with Bill Young email 3172021 by Mari Williams, NOAAF NWFSC/PSMFC.","" 47 | -------------------------------------------------------------------------------- /data/maplocs.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/QuartoReport_SE/4419539f20879fb3949fcc1ffdd0f8df0e8c564b/data/maplocs.rda -------------------------------------------------------------------------------- /data/pnwmap.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/QuartoReport_SE/4419539f20879fb3949fcc1ffdd0f8df0e8c564b/data/pnwmap.rda -------------------------------------------------------------------------------- /docs/An-example-report.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/QuartoReport_SE/4419539f20879fb3949fcc1ffdd0f8df0e8c564b/docs/An-example-report.docx -------------------------------------------------------------------------------- /docs/An-example-report.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/QuartoReport_SE/4419539f20879fb3949fcc1ffdd0f8df0e8c564b/docs/An-example-report.pdf -------------------------------------------------------------------------------- /docs/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | An example report 14 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 60 | 61 | 62 | 63 | 64 | 65 | 66 |
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An example report

185 |

The subtitle

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Authors
191 |
Affiliation
192 | 193 |
194 | Jane Doe 195 |
196 |
197 |

198 | University of XXX 199 |

200 |
201 |
202 | Eva Nováková 203 |
204 |
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206 | University of XXX 207 |

208 |
209 |
210 | Matti Meikäläinen 211 |
212 |
213 |

214 | University of XXX 215 |

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227 | 228 |
229 |

Citation

230 |

EE Holmes, 2022. Quarto Report Template. Northwest Fisheries Science Center.

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343 | 344 | 345 | 346 | -------------------------------------------------------------------------------- /docs/references.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | An example report - References 11 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 76 | 77 | 78 | 79 | 80 | 81 | 82 |
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References

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209 |
210 | Ansley, H. L. H., and C. D. Davis. 1981. “Migration and Standing 211 | Stock of Fishes Associated with Artificial and Natural Reefs on 212 | Georgia’s Outer Continental Shelf.” Brunswick, 213 | Georgia, USA. 214 |
215 |
216 | Clark, W. G. 1993. “The Effect of Recruitment Variability on the 217 | Choice of a Target Level of Spawning Biomass Per Recruit.” In, 218 | 233246. Alaska Sea Grant College Program 219 | AKSG9302. 220 |
221 |
222 | Collins, M. R., S. B. Van Sant, D. J. Schmidt, and G. R. Sedberry. 1996. 223 | “Age Validation, Movements, and Growth Rates of Tagged Gag 224 | (Mycteroperca Microlepis), Black Sea Bass (Centropristis Striata) and 225 | Red Porgy (Pagrus Pagrus).” In, edited by F. Arrequin-Sanchez, J. 226 | L. Munro, M. C. Balgos, and D. Pauly, 161–65. Makati City, Philippines: 227 | ICLARM (International Center for Living Aquatic Resources Management). 228 |
229 |
230 | Deuel, D. G., and J. R. Clark. 1968. “The 1965 Salt-Water Angling 231 | Survey.” 232 |
233 |
234 | Hardy, J. D., Jr. 1978. “Development of Fishes of the Mid-Atlantic 235 | Bight. Vol. III. Aphredoderidae Through Rachycentridae.” 236 |
237 |
238 | 239 | 240 | 241 |
242 | 339 | 348 |
349 | 350 | 351 | 352 | -------------------------------------------------------------------------------- /docs/robots.txt: -------------------------------------------------------------------------------- 1 | Sitemap: https://rverse-tutorials.github.io/QuartoReport_SE/sitemap.xml 2 | -------------------------------------------------------------------------------- /docs/site_libs/bootstrap/bootstrap-icons.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/QuartoReport_SE/4419539f20879fb3949fcc1ffdd0f8df0e8c564b/docs/site_libs/bootstrap/bootstrap-icons.woff -------------------------------------------------------------------------------- /docs/site_libs/clipboard/clipboard.min.js: -------------------------------------------------------------------------------- 1 | /*! 2 | * clipboard.js v2.0.10 3 | * https://clipboardjs.com/ 4 | * 5 | * Licensed MIT © Zeno Rocha 6 | */ 7 | !function(t,e){"object"==typeof 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-------------------------------------------------------------------------------- 1 | const headroomChanged = new CustomEvent("quarto-hrChanged", { 2 | detail: {}, 3 | bubbles: true, 4 | cancelable: false, 5 | composed: false, 6 | }); 7 | 8 | window.document.addEventListener("DOMContentLoaded", function () { 9 | let init = false; 10 | 11 | function throttle(func, wait) { 12 | var timeout; 13 | return function () { 14 | const context = this; 15 | const args = arguments; 16 | const later = function () { 17 | clearTimeout(timeout); 18 | timeout = null; 19 | func.apply(context, args); 20 | }; 21 | 22 | if (!timeout) { 23 | timeout = setTimeout(later, wait); 24 | } 25 | }; 26 | } 27 | 28 | function headerOffset() { 29 | // Set an offset if there is are fixed top navbar 30 | const headerEl = window.document.querySelector("header.fixed-top"); 31 | if (headerEl) { 32 | return headerEl.clientHeight; 33 | } else { 34 | return 0; 35 | } 36 | } 37 | 38 | function footerOffset() { 39 | const 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false; 140 | window.quartoToggleHeadroom = function () { 141 | if (frozen) { 142 | headroom.unfreeze(); 143 | frozen = false; 144 | } else { 145 | headroom.freeze(); 146 | frozen = true; 147 | } 148 | }; 149 | } 150 | 151 | // Observe size changed for the header 152 | const headerEl = window.document.querySelector("header.fixed-top"); 153 | if (headerEl && window.ResizeObserver) { 154 | const observer = new window.ResizeObserver( 155 | throttle(updateDocumentOffsetWithoutAnimation, 50) 156 | ); 157 | observer.observe(headerEl, { 158 | attributes: true, 159 | childList: true, 160 | characterData: true, 161 | }); 162 | } else { 163 | window.addEventListener( 164 | "resize", 165 | throttle(updateDocumentOffsetWithoutAnimation, 50) 166 | ); 167 | setTimeout(updateDocumentOffsetWithoutAnimation, 500); 168 | } 169 | 170 | // fixup index.html links if we aren't on the filesystem 171 | if (window.location.protocol !== "file:") { 172 | const links = window.document.querySelectorAll("a"); 173 | for (let i = 0; i < links.length; i++) { 174 | links[i].href = links[i].href.replace(/\/index\.html/, "/"); 175 | } 176 | 177 | // Fixup any sharing links that require urls 178 | // Append url to any sharing urls 179 | const sharingLinks = window.document.querySelectorAll( 180 | "a.sidebar-tools-main-item" 181 | ); 182 | for (let i = 0; i < sharingLinks.length; i++) { 183 | const sharingLink = sharingLinks[i]; 184 | const href = sharingLink.getAttribute("href"); 185 | if (href) { 186 | sharingLink.setAttribute( 187 | "href", 188 | href.replace("|url|", window.location.href) 189 | ); 190 | } 191 | } 192 | 193 | // Scroll the active navigation item into view, if necessary 194 | const navSidebar = window.document.querySelector("nav#quarto-sidebar"); 195 | if (navSidebar) { 196 | // Find the active item 197 | const activeItem = navSidebar.querySelector("li.sidebar-item a.active"); 198 | if (activeItem) { 199 | // Wait for the scroll height and height to resolve by observing size changes on 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9  Conclusion

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9.1 First off

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We want to reference the Interior Columbia Upper Columbia Entiat population Table 2.2. It is in Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nam commodo sit amet nibh non molestie. Maecenas hendrerit nisl velit, a condimentum enim lobortis sit amet. Ut vitae nunc sed mauris condimentum fermentum. Mauris pellentesque nec neque id elementum. Suspendisse a quam aliquam, facilisis urna venenatis, malesuada diam. Pellentesque in fringilla orci. Cras sed purus urna. Ut pharetra enim ut ligula egestas mattis. I need to reference the work of Hardy (1978).

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Phasellus non diam posuere, laoreet velit sed, egestas felis. Etiam eget neque in tellus lacinia tincidunt. Pellentesque scelerisque odio velit, nec fringilla nibh iaculis non. Aenean sit amet nulla ipsum. Cras felis lacus, pulvinar ac nisi et, convallis pulvinar turpis. Morbi non nibh lacus. Morbi vitae lorem massa. Sed ut turpis vel felis posuere commodo lacinia ac mi. Donec finibus lectus sit amet elit finibus, vitae rhoncus ligula tincidunt. Phasellus vitae blandit lacus. Integer sed nisl fermentum, pulvinar mauris in, posuere enim. Proin sit amet semper urna. Vivamus aliquet rutrum diam ac luctus.

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Quisque in nibh sit amet nunc mollis porttitor quis et mauris. Sed non condimentum leo, ac condimentum est. Duis ac venenatis nulla, et aliquet elit. Suspendisse potenti. Duis mollis dui at semper luctus. Maecenas euismod finibus condimentum. Fusce vitae gravida massa. Mauris metus est, pretium non semper vel, dictum vel augue.

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Curabitur tempus, leo quis volutpat rhoncus, turpis elit vehicula dolor, id tincidunt augue nunc at enim. In vel enim mattis, varius orci at, tempus ante. Morbi massa elit, pharetra ac libero at, porta tempus quam. Ut fringilla, tortor ac tristique euismod, magna felis vestibulum turpis, quis congue mauris leo nec felis. Aliquam viverra et nibh ut blandit. Praesent sed luctus odio. Pellentesque finibus velit dolor. Morbi ac pulvinar ex, id dapibus eros. Cras interdum arcu viverra auctor tristique. Suspendisse venenatis volutpat ultricies.

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Donec bibendum pharetra arcu vitae porttitor. Morbi ac quam nunc. Ut cursus dolor a mauris aliquet vulputate. Morbi elementum ullamcorper augue, et tincidunt libero facilisis posuere. Nam congue velit non elit sollicitudin aliquet. Donec lobortis nunc ligula, id sollicitudin erat rhoncus cursus. Ut egestas orci libero, eu malesuada ex sollicitudin sed. Sed ornare nunc eget massa scelerisque, nec egestas nulla commodo. Pellentesque efficitur accumsan ullamcorper. Nulla facilisi. Maecenas tristique luctus malesuada. Phasellus id enim maximus, tempus tellus eu, dignissim sapien. Integer et mauris in lectus condimentum pellentesque non a felis.

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342 | 343 | 344 | 345 | -------------------------------------------------------------------------------- /figures_tables/Map_Figure.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Map Figure" 3 | --- 4 | 5 | 6 | ```{r include=FALSE} 7 | out <- knitr::knit_expand(here::here('figures_tables', '_template_map_figure.Rmd')) 8 | ``` 9 | `r paste(knitr::knit(text = out), collapse = '\n')` 10 | -------------------------------------------------------------------------------- /figures_tables/Raw_Tables.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Raw Data Tables" 3 | --- 4 | 5 | 8 | 9 | ```{r include=FALSE} 10 | knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE) 11 | source(here::here("figures_tables", "_common.R")) 12 | ``` 13 | 14 | ```{r} 15 | startYr <- 2000 16 | ``` 17 | 18 | ```{r} 19 | # So that I can later have many cvsfiles 20 | datafil <- here::here("data", paste0(data_id, ".csv")) 21 | tmp <- read.csv(datafil, stringsAsFactors=FALSE) 22 | ntbl <- tmp %>% distinct(COMMON_POPULATION_NAME) %>% nrow() 23 | ``` 24 | 25 | ```{r include=FALSE} 26 | # This is cycling through all the populations in the data 27 | # this is a big hacky because I can't use variables in `label: ` 28 | # So I am having to create popid here so I can use {{popid}} in the label 29 | out <- NULL 30 | for(table.num.to.print in 1:ntbl){ 31 | popname <- unique(tmp$`COMMON_POPULATION_NAME`)[table.num.to.print] 32 | tmp2 <- subset(tmp, `COMMON_POPULATION_NAME`==popname) 33 | popid <- unique(tmp2$NMFS_POPID)[1] 34 | out = c(out, knit_expand(here::here('figures_tables', '_template_raw_table.Rmd'))) 35 | } 36 | ``` 37 | `r paste(knit(text = out), collapse = '\n')` 38 | 39 | -------------------------------------------------------------------------------- /figures_tables/Status_Figure.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Status Figure" 3 | --- 4 | 5 | 6 | ```{r include=FALSE} 7 | out <- knitr::knit_expand(here::here('figures_tables', '_template_status_figure.Rmd')) 8 | ``` 9 | `r paste(knitr::knit(text = out), collapse = '\n')` 10 | -------------------------------------------------------------------------------- /figures_tables/_common.R: -------------------------------------------------------------------------------- 1 | require(knitr) 2 | require(dplyr) 3 | require(flextable) 4 | require(ggplot2) 5 | require(kableExtra) 6 | 7 | ishtml <- knitr::is_html_output() 8 | ispdf <- knitr::is_latex_output() 9 | isword <- !ishtml & !ispdf 10 | if(ishtml) table.engine <- "flextable" 11 | if(isword) table.engine <- "flextable" 12 | if(ispdf) table.engine <- "kbl" 13 | 14 | mapfigure <- function(title, id=NULL){ 15 | require(ggmap) 16 | # bbox_dat <- c(left = -125, bottom = 42, right = -110, top = 50) 17 | # p <- ggmap(get_stamenmap(bbox_dat, zoom = 5, maptype="terrain-background")) 18 | load(here::here("data", "pnwmap.rda")) 19 | p + ggtitle(title) 20 | if(!is.null(id)){ 21 | load(here::here("data", "maplocs.rda")) 22 | if(!all(id %in% maplocs$id)) stop("mapfigure function: some of the id's are not in the maplocs data") 23 | points <- maplocs[maplocs$id %in% id,] 24 | p + 25 | geom_point(data=points, alpha = .7, aes(x=lon, y=lat, size =5), color='red') + 26 | theme(legend.position="none") 27 | } 28 | } 29 | 30 | statusfigure <- function(title, id, x="YEAR", y="NUMBER_OF_SPAWNERS"){ 31 | filename <- here::here("data", paste0(id, ".csv")) 32 | dat <- read.csv(filename, stringsAsFactors = FALSE) 33 | dat$x <- dat[[x]] 34 | dat$y <- log(dat[[y]]) 35 | ggplot(dat, aes(x=x, y=y)) + 36 | xlab("Year") + 37 | ylab("log(Spawners)") + 38 | ggtitle(title) + 39 | geom_line() + 40 | facet_wrap(~COMMON_POPULATION_NAME) 41 | } 42 | 43 | # Table functions 44 | 45 | 46 | 47 | fixcols <- function(x){ 48 | # fix _ and . in colname and make title format 49 | x <- stringr::str_replace_all(x, "_", " ") 50 | x <- stringr::str_replace_all(x, "[,]", " ") 51 | x <- stringr::str_to_title(x) 52 | x[x=="Esu"] <- "ESU" 53 | x[x=="Number Of Spawners"] <- "Spawners" 54 | x 55 | } 56 | 57 | myflextable <- function(x){ 58 | if(inherits(x, "data.frame")){ 59 | x <- flextable(x) 60 | } 61 | if(isword){ 62 | x <- x %>% font(fontname="Times New Roman", part="all") %>% 63 | fontsize(size=12) 64 | } 65 | n <- ncol_keys(x) 66 | x %>% 67 | autofit() %>% 68 | add_footer_row(values = "flextable", colwidths = n) 69 | } 70 | 71 | mykbl <- function(x, caption = NULL){ 72 | n <- ncol(x) 73 | x <- kbl(x, booktabs = TRUE, caption = caption) %>% 74 | kableExtra::footnote(general = "kable") %>% 75 | kableExtra::kable_styling(position = "center") 76 | if(n>8) kable_styling(x, latex_options = c("scale_down")) 77 | x 78 | } 79 | # Misc 80 | 81 | wordnewpage <- 82 | '```{=openxml} 83 | 84 | ```' 85 | 86 | 87 | 88 | -------------------------------------------------------------------------------- /figures_tables/_template_map_figure.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | always_allow_html: true 3 | --- 4 | 5 | ```{r include=FALSE} 6 | table_cap <- paste0("{{data_title}}", ". Map of the general location of the ESU.") 7 | ``` 8 | 9 | ```{r} 10 | #| label: fig-{{data_id}}-map 11 | #| fig-cap: !expr table_cap 12 | mapfigure(data_title, id=data_id) 13 | ``` 14 | -------------------------------------------------------------------------------- /figures_tables/_template_raw_table.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | always_allow_html: true 3 | --- 4 | 5 | ```{r include=FALSE} 6 | knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE) 7 | source(here::here("figures_tables", "_common.R")) 8 | ``` 9 | 10 | ```{r} 11 | tbl <- {{table.num.to.print}} 12 | csvfile <- paste0("{{data_id}}", ".csv") 13 | datafile <- here::here("data", csvfile) 14 | counts <- read.csv(datafile, stringsAsFactors=FALSE) 15 | modtime <- system(paste("git log -1 --format=%cd", datafil), intern=TRUE) 16 | ``` 17 | 18 | 20 | 21 | ```{r} 22 | colnames(counts) <- fixcols(colnames(counts)) 23 | ``` 24 | 25 | 26 | ```{r} 27 | popname <- unique(counts$`Common Population Name`)[tbl] 28 | dat <- subset(counts, `Common Population Name`==popname & Year >= {{startYr}}) 29 | rownames(dat) <- c() 30 | tbl_cap <- paste0("Spawners and fracwild from ", popname, " (NMFS_POPID ", {{popid}}, ") for ", min(dat$Year), " to ", max(dat$Year), ". ") 31 | ``` 32 | 33 | 34 | 35 | ```{r results='asis'} 36 | if(isword) cat("\n", wordnewpage, "\n") 37 | if(ispdf) cat("\n\\newpage\n\n") 38 | cat("### ", popname, "\n\n") 39 | 40 | ``` 41 | 42 | 43 | ```{r} 44 | tablecount <- function(data, cols="Spawners"){ 45 | dat <- data[, c("Year", cols)] 46 | f1 <- paste("** data file:", csvfile, "mod date:", modtime) 47 | f2 <- "* These spawner counts are from river redd surveys." 48 | if(table.engine=="flextable"){ 49 | tab <- dat %>% 50 | myflextable() %>% 51 | autofit() %>% 52 | add_footer(., Year = f2) %>% 53 | merge_at(., i = 1, j = 1:ncol(dat), part = "footer") %>% 54 | add_footer(., Year = f1) %>% 55 | merge_at(., i = 1, j = 1:ncol(dat), part = "footer") %>% 56 | colformat_num(., j=1, big.mark = "", na_str = "NA") 57 | # %>% line_spacing(space = 1.0, part = "all") 58 | } 59 | if(table.engine=="kbl"){ 60 | tab <- 61 | dat %>% 62 | mykbl() %>% 63 | kableExtra::add_footnote(c(f1, f2), notation="none") %>% 64 | kableExtra::kable_styling(latex_options = c( "HOLD_position")) 65 | } 66 | tab 67 | } 68 | ``` 69 | 70 | ```{r} 71 | #| label: tbl-raw{{data_id}}-{{popid}} 72 | #| tbl-cap: !expr tbl_cap 73 | out <- NULL 74 | col <- c("Spawners", "Fracwild") 75 | if(nrow(dat) > 0){ 76 | tab <- tablecount(dat, cols=col) 77 | }else{ 78 | tab <- paste("No data for years greater than or equal to", {{startYr}}) 79 | } 80 | tab 81 | ``` 82 | 83 | ```{r results='asis'} 84 | if(isword) cat("\n", wordnewpage, "\n") 85 | if(ispdf) cat("\n\\newpage\n\n") 86 | ``` 87 | -------------------------------------------------------------------------------- /figures_tables/_template_status_figure.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | always_allow_html: true 3 | --- 4 | 5 | ```{r include=FALSE} 6 | #| label: {{data_id}}-tblcap 7 | table_cap <- paste0("{{data_title}}", ". Log spawner count trends.") 8 | ``` 9 | 10 | ```{r} 11 | #| label: fig-{{data_id}}-status 12 | #| fig-cap: !expr table_cap 13 | statusfigure("{{data_title}}", "{{data_id}}") 14 | ``` 15 | -------------------------------------------------------------------------------- /images/doc-logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/QuartoReport_SE/4419539f20879fb3949fcc1ffdd0f8df0e8c564b/images/doc-logo.png -------------------------------------------------------------------------------- /images/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/QuartoReport_SE/4419539f20879fb3949fcc1ffdd0f8df0e8c564b/images/logo.png -------------------------------------------------------------------------------- /index.qmd: -------------------------------------------------------------------------------- 1 | # Citation {.unnumbered} 2 | 3 | EE Holmes, 2022. Quarto Report Template. Northwest Fisheries Science Center. 4 | 5 | 6 | ```{=openxml} 7 | 8 | ``` 9 | -------------------------------------------------------------------------------- /partials/_two-column-longtable.tex: -------------------------------------------------------------------------------- 1 | \usepackage{float} 2 | \makeatletter 3 | \let\oldlt\longtable 4 | \let\endoldlt\endlongtable 5 | \def\longtable{\@ifnextchar[\longtable@i \longtable@ii} 6 | \def\longtable@i[#1]{\begin{figure}[H] 7 | \onecolumn 8 | \begin{minipage}{0.5\textwidth} 9 | \oldlt[#1] 10 | } 11 | \def\longtable@ii{\begin{figure}[H] 12 | \onecolumn 13 | \begin{minipage}{0.5\textwidth} 14 | \oldlt 15 | } 16 | \def\endlongtable{\endoldlt 17 | \end{minipage} 18 | \twocolumn 19 | \end{figure}} 20 | \makeatother 21 | -------------------------------------------------------------------------------- /partials/before-body-elsevier.tex: -------------------------------------------------------------------------------- 1 | 2 | \begin{frontmatter} 3 | \title{$title$} 4 | $for(by-author)$\author[$for(by-author.affiliations)$$it.number$$endfor$]{$by-author.name.literal$% 5 | $if(by-author.attributes.corresponding)$\corref{cor1}$endif$% 6 | $if(by-author.note.text)$\fnref{fn$by-author.note.number$}$endif$} 7 | $if(by-author.email)$ \ead{$by-author.email$} $endif$ 8 | $endfor$ 9 | $for(by-affiliation)$ 10 | \affiliation[$it.number$]{organization={$it.name$}, addressline={$it.address$}, city={$it.city$}, country={$it.country$}, postcode={$it.postal-code$}} 11 | 12 | $endfor$ 13 | 14 | \cortext[cor1]{Corresponding author} 15 | $for(by-author)$ 16 | $if(by-author.note.text)$\fntext[fn$by-author.note.number$]{$by-author.note.text$}$endif$ 17 | $endfor$ 18 | 19 | $if(abstract)$ 20 | \begin{abstract} 21 | $abstract$ 22 | \end{abstract} 23 | $endif$ 24 | 25 | $if(journal.graphical-abstract)$\begin{graphicalabstract} 26 | $journal.graphical-abstract$ 27 | \end{graphicalabstract} 28 | $endif$ 29 | 30 | $if(journal.highlights)$\begin{highlights} 31 | $for(journal.highlights)$\item $it$$endfor$ 32 | \end{highlights} 33 | $endif$ 34 | 35 | $if(keywords)$ 36 | \begin{keyword} 37 | $for(keywords/allbutlast)$$keywords$ \sep $endfor$ 38 | $for(keywords/last)$$keywords$$endfor$ 39 | \end{keyword} 40 | $endif$ 41 | \end{frontmatter} 42 | -------------------------------------------------------------------------------- /partials/before-body.tex: -------------------------------------------------------------------------------- 1 | 2 | 3 | \begin{frontmatter} 4 | 5 | \raggedleft % Right align the title page 6 | 7 | \rule{1pt}{\textheight} % Vertical line 8 | \hspace{0.05\textwidth} % Whitespace between the vertical line and title page text 9 | \parbox[b]{0.85\textwidth}{ % Paragraph box for holding the title page text, adjust the width to move the title page left or right on the page 10 | 11 | {\large\bfseries\nohyphens{$title$}}\\[2\baselineskip] % Title 12 | $if(subtitle)$ 13 | {\large\textit{$subtitle$}}\\[4\baselineskip] % Subtitle or further description 14 | $endif$ 15 | 16 | $if(by-author/allbutlast)$ 17 | $for(by-author/allbutlast)$ 18 | {\large{$by-author.name.literal$}}$sep$, 19 | $endfor$ 20 | $for(by-author/last)$ 21 | {and \large{$by-author.name.literal$}} 22 | $endfor$ 23 | $else$ 24 | ${by-author/last} 25 | $endif$ 26 | 27 | \vspace{0.5\textheight} % Whitespace between the title block and the publisher 28 | 29 | {\noindent The Publisher~~\plogo}\\[\baselineskip] % Publisher and logo 30 | } 31 | 32 | \end{frontmatter} -------------------------------------------------------------------------------- /partials/before-body1.tex: -------------------------------------------------------------------------------- 1 | 2 | \begin{frontmatter} 3 | \title{This is a test} 4 | \end{frontmatter} 5 | -------------------------------------------------------------------------------- /partials/inheader.tex: -------------------------------------------------------------------------------- 1 | \newcommand*{\plogo}{\fbox{$\mathcal{PL}$}} % Generic dummy publisher logo 2 | \usepackage[utf8]{inputenc} % Required for inputting international characters 3 | \usepackage[T1]{fontenc} % Output font encoding for international characters 4 | \usepackage{hyphenat} 5 | \usepackage{authblk} 6 | 7 | % for nicer tables 8 | \usepackage{booktabs} 9 | \usepackage{longtable} 10 | \usepackage{array} 11 | \usepackage{multirow} 12 | \usepackage{wrapfig} 13 | \usepackage{float} 14 | \usepackage{colortbl} 15 | \usepackage{pdflscape} 16 | \usepackage{tabu} 17 | \usepackage{threeparttable} 18 | \usepackage{threeparttablex} 19 | \usepackage[normalem]{ulem} 20 | \usepackage{makecell} 21 | \usepackage{xcolor} 22 | -------------------------------------------------------------------------------- /partials/title1.tex: -------------------------------------------------------------------------------- 1 | 2 | \begin{frontmatter} 3 | \title{$title$} 4 | \author[1]{Author A\thanks{A.A@university.edu}} 5 | \author[1]{Author B\thanks{B.B@university.edu}} 6 | \author[1]{Author C\thanks{C.C@university.edu}} 7 | \author[2]{Author D\thanks{D.D@university.edu}} 8 | \author[2]{Author E\thanks{E.E@university.edu}} 9 | \affil[1]{Department of Computer Science, \LaTeX\ University} 10 | \affil[2]{Department of Mechanical Engineering, \LaTeX\ University} 11 | % Don't want date printed 12 | \date{} 13 | 14 | 15 | \renewcommand\Authands{ and } 16 | \end{frontmatter} 17 | -------------------------------------------------------------------------------- /preface.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: Preface 3 | --- 4 | 5 | ## Acknowledgements {.unlisted .unnumbered} 6 | 7 | Phasellus non diam posuere, laoreet velit sed, egestas felis. Etiam eget neque in tellus lacinia tincidunt. Pellentesque scelerisque odio velit, nec fringilla nibh iaculis non. Aenean sit amet nulla ipsum. Cras felis lacus, pulvinar ac nisi et, convallis pulvinar turpis. Morbi non nibh lacus. Morbi vitae lorem massa. Sed ut turpis vel felis posuere commodo lacinia ac mi. Donec finibus lectus sit amet elit finibus, vitae rhoncus ligula tincidunt. Phasellus vitae blandit lacus. Integer sed nisl fermentum, pulvinar mauris in, posuere enim. Proin sit amet semper urna. Vivamus aliquet rutrum diam ac luctus. 8 | 9 | 10 | ## Abstract {-} 11 | 12 | Phasellus non diam posuere, laoreet velit sed, egestas felis. Etiam eget neque in tellus lacinia tincidunt. Pellentesque scelerisque odio velit, nec fringilla nibh iaculis non. Aenean sit amet nulla ipsum. Cras felis lacus, pulvinar ac nisi et, convallis pulvinar turpis. Morbi non nibh lacus. Morbi vitae lorem massa. Sed ut turpis vel felis posuere commodo lacinia ac mi. Donec finibus lectus sit amet elit finibus, vitae rhoncus ligula tincidunt. Phasellus vitae blandit lacus. Integer sed nisl fermentum, pulvinar mauris in, posuere enim. Proin sit amet semper urna. Vivamus aliquet rutrum diam ac luctus. 13 | 14 | ```{=openxml} 15 | 16 | ``` 17 | 18 | 19 | -------------------------------------------------------------------------------- /references.bib: -------------------------------------------------------------------------------- 1 | @article{knuth84, 2 | author = {Knuth, Donald E.}, 3 | title = {Literate Programming}, 4 | year = {1984}, 5 | issue_date = {May 1984}, 6 | publisher = {Oxford University Press, Inc.}, 7 | address = {USA}, 8 | volume = {27}, 9 | number = {2}, 10 | issn = {0010-4620}, 11 | url = {https://doi.org/10.1093/comjnl/27.2.97}, 12 | doi = {10.1093/comjnl/27.2.97}, 13 | journal = {Comput. J.}, 14 | month = may, 15 | pages = {97–111}, 16 | numpages = {15} 17 | } 18 | 19 | 20 | 21 | @inproceedings{clark1993, 22 | title = {The effect of recruitment variability on the choice of a target level of spawning biomass per recruit}, 23 | author = {Clark, W. G.}, 24 | year = {1993}, 25 | date = {1993}, 26 | publisher = {Alaska Sea Grant College Program AK{\textendash}SG{\textendash}93{\textendash}02}, 27 | pages = {233{\textendash}246} 28 | } 29 | 30 | @techreport{ansley1981, 31 | title = {Migration and standing stock of fishes associated with artificial and natural reefs on Georgia{\textquoteright}s outer continental shelf}, 32 | author = {Ansley, H. L. H. and Davis, C. D.}, 33 | year = {1981}, 34 | date = {1981}, 35 | pages = {38}, 36 | address = {Brunswick, Georgia, USA} 37 | } 38 | 39 | @inbook{collins1996, 40 | title = {Age validation, movements, and growth rates of tagged gag (Mycteroperca microlepis), black sea bass (Centropristis striata) and red porgy (Pagrus pagrus)}, 41 | author = {Collins, M. R. and Sant, S. B. Van and Schmidt, D. J. and Sedberry, G. R.}, 42 | editor = {Arrequin-Sanchez, F. and Munro, J. L. and Balgos, M. C. and Pauly, D.}, 43 | year = {1996}, 44 | date = {1996}, 45 | publisher = {ICLARM (International Center for Living Aquatic Resources Management)}, 46 | pages = {161--165}, 47 | address = {Makati City, Philippines} 48 | } 49 | 50 | @techreport{deuel1968, 51 | title = {The 1965 Salt-Water Angling Survey}, 52 | author = {Deuel, D. G. and Clark, J. R.}, 53 | year = {1968}, 54 | date = {1968}, 55 | pages = {51} 56 | } 57 | 58 | @techreport{hardy1978, 59 | title = {Development of Fishes of the Mid-Atlantic Bight. Vol. III. Aphredoderidae through Rachycentridae.}, 60 | author = {Hardy, {J. D., Jr.}}, 61 | year = {1978}, 62 | date = {1978} 63 | } 64 | -------------------------------------------------------------------------------- /references.qmd: -------------------------------------------------------------------------------- 1 | # References {.unnumbered} 2 | 3 | ::: {#refs} 4 | ::: 5 | -------------------------------------------------------------------------------- /template.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/QuartoReport_SE/4419539f20879fb3949fcc1ffdd0f8df0e8c564b/template.docx -------------------------------------------------------------------------------- /text/CRchum.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | always_allow_html: true 3 | --- 4 | 5 | ```{r warning=FALSE, echo=FALSE, message=FALSE} 6 | knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE) 7 | source(here::here("figures_tables", "_common.R")) 8 | load(here::here("data", "maplocs.rda")) 9 | ``` 10 | 11 | ```{r} 12 | data_title <- "Columbia River Chum" 13 | data_id <- "CRchum" 14 | ``` 15 | 16 | # Columbia River Chum 17 | 18 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. @clark1993 vitae ante quis dui egestas fringilla ac vitae justo [@ansley1981; @collins1996; @deuel1968] . Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 19 | 20 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 21 | 22 | ## General location 23 | 24 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. 25 | 26 | ```{r eval=FALSE} 27 | # run to see what the map is like 28 | mapfigure(data_title, id=data_id) 29 | ``` 30 | 31 | ```{r child=here::here("figures_tables", "Map_Figure.Rmd")} 32 | ``` 33 | 34 | ## Recent trends 35 | 36 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec vitae ante quis dui egestas fringilla ac vitae justo. Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 37 | 38 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 39 | 40 | ```{r eval=FALSE} 41 | # This figure will be included. 42 | # Click green arrow at right to see 43 | source(here::here("figures_tables", "_common.R")) 44 | statusfigure(data_title, data_id) 45 | ``` 46 | 47 | ```{r child=here::here("figures_tables", "Status_Figure.Rmd")} 48 | ``` 49 | 50 | ## Population raw data 51 | 52 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. @tbl-rawICSRsthd-300 Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 53 | 54 | ```{r child=here::here("figures_tables", "Raw_Tables.Rmd")} 55 | ``` 56 | -------------------------------------------------------------------------------- /text/HCchum.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | always_allow_html: true 3 | --- 4 | 5 | ```{r warning=FALSE, echo=FALSE, message=FALSE} 6 | knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE) 7 | source(here::here("figures_tables", "_common.R")) 8 | load(here::here("data", "maplocs.rda")) 9 | ``` 10 | 11 | ```{r} 12 | data_title <- "Hood Canal Chum" 13 | data_id <- "HCchum" 14 | ``` 15 | 16 | # Hood River Chum 17 | 18 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. @clark1993 vitae ante quis dui egestas fringilla ac vitae justo [@ansley1981; @collins1996; @deuel1968] . Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 19 | 20 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 21 | 22 | ## General location 23 | 24 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. 25 | 26 | ```{r eval=FALSE} 27 | # run to see what the map is like 28 | mapfigure(data_title, id=data_id) 29 | ``` 30 | 31 | ```{r child=here::here("figures_tables", "Map_Figure.Rmd")} 32 | ``` 33 | 34 | ## Recent trends 35 | 36 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec vitae ante quis dui egestas fringilla ac vitae justo. Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 37 | 38 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 39 | 40 | ```{r eval=FALSE} 41 | # This figure will be included. 42 | # Click green arrow at right to see 43 | source(here::here("figures_tables", "_common.R")) 44 | statusfigure(data_title, data_id) 45 | ``` 46 | 47 | ```{r child=here::here("figures_tables", "Status_Figure.Rmd")} 48 | ``` 49 | 50 | ## Population raw data 51 | 52 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. @tbl-rawICSRsthd-300 Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 53 | 54 | ```{r child=here::here("figures_tables", "Raw_Tables.Rmd")} 55 | ``` 56 | -------------------------------------------------------------------------------- /text/HCchum_files/figure-pdf/fig-HCchum-map-1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/QuartoReport_SE/4419539f20879fb3949fcc1ffdd0f8df0e8c564b/text/HCchum_files/figure-pdf/fig-HCchum-map-1.pdf -------------------------------------------------------------------------------- /text/HCchum_files/figure-pdf/fig-HCchum-status-1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/QuartoReport_SE/4419539f20879fb3949fcc1ffdd0f8df0e8c564b/text/HCchum_files/figure-pdf/fig-HCchum-status-1.pdf -------------------------------------------------------------------------------- /text/ICSRFchinook.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | always_allow_html: true 3 | --- 4 | 5 | ```{r warning=FALSE, echo=FALSE, message=FALSE} 6 | knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE) 7 | source(here::here("figures_tables", "_common.R")) 8 | load(here::here("data", "maplocs.rda")) 9 | ``` 10 | 11 | ```{r} 12 | data_title <- "Interior Columbia Snake River Chinook" 13 | data_id <- "ICSRFchinook" 14 | ``` 15 | 16 | # Interior Columbia Snake River Chinook 17 | 18 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. @clark1993 vitae ante quis dui egestas fringilla ac vitae justo [@ansley1981; @collins1996; @deuel1968] . Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 19 | 20 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 21 | 22 | ## General location 23 | 24 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. 25 | 26 | ```{r eval=FALSE} 27 | # run to see what the map is like 28 | mapfigure(data_title, id=data_id) 29 | ``` 30 | 31 | ```{r child=here::here("figures_tables", "Map_Figure.Rmd")} 32 | ``` 33 | 34 | ## Recent trends 35 | 36 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec vitae ante quis dui egestas fringilla ac vitae justo. Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 37 | 38 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 39 | 40 | ```{r eval=FALSE} 41 | # This figure will be included. 42 | # Click green arrow at right to see 43 | source(here::here("figures_tables", "_common.R")) 44 | statusfigure(data_title, data_id) 45 | ``` 46 | 47 | ```{r child=here::here("figures_tables", "Status_Figure.Rmd")} 48 | ``` 49 | 50 | ## Population raw data 51 | 52 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 53 | 54 | ```{r child=here::here("figures_tables", "Raw_Tables.Rmd")} 55 | ``` 56 | -------------------------------------------------------------------------------- /text/ICSRsthd.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | always_allow_html: true 3 | --- 4 | 5 | ```{r warning=FALSE, echo=FALSE, message=FALSE} 6 | knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE) 7 | source(here::here("figures_tables", "_common.R")) 8 | load(here::here("data", "maplocs.rda")) 9 | ``` 10 | 11 | ```{r} 12 | data_title <- "Interior Columbia Snake River Chinook steelhead" 13 | data_id <- "ICSRsthd" 14 | ``` 15 | 16 | # Interior Columbia Snake River Chinook steelhead 17 | 18 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. @clark1993 vitae ante quis dui egestas fringilla ac vitae justo [@ansley1981; @collins1996; @deuel1968] . Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 19 | 20 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 21 | 22 | ## General location 23 | 24 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. 25 | 26 | ```{r eval=FALSE} 27 | # run to see what the map is like 28 | mapfigure(data_title, id=data_id) 29 | ``` 30 | 31 | ```{r child=here::here("figures_tables", "Map_Figure.Rmd")} 32 | ``` 33 | 34 | ## Recent trends 35 | 36 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec vitae ante quis dui egestas fringilla ac vitae justo. Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 37 | 38 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 39 | 40 | ```{r eval=FALSE} 41 | # This figure will be included. 42 | # Click green arrow at right to see 43 | source(here::here("figures_tables", "_common.R")) 44 | statusfigure(data_title, data_id) 45 | ``` 46 | 47 | ```{r child=here::here("figures_tables", "Status_Figure.Rmd")} 48 | ``` 49 | 50 | ## Population raw data 51 | 52 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 53 | 54 | ```{r child=here::here("figures_tables", "Raw_Tables.Rmd")} 55 | ``` -------------------------------------------------------------------------------- /text/ICUCchinook.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | always_allow_html: true 3 | --- 4 | 5 | ```{r warning=FALSE, echo=FALSE, message=FALSE} 6 | knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE) 7 | source(here::here("figures_tables", "_common.R")) 8 | load(here::here("data", "maplocs.rda")) 9 | ``` 10 | 11 | ```{r} 12 | data_title <- "Upper Columbia Chinook" 13 | data_id <- "ICUCchinook" 14 | ``` 15 | 16 | # Upper Columbia Chinook 17 | 18 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. @clark1993 vitae ante quis dui egestas fringilla ac vitae justo [@ansley1981; @collins1996; @deuel1968] . Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 19 | 20 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 21 | 22 | ## General location 23 | 24 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. 25 | 26 | ```{r eval=FALSE} 27 | # run to see what the map is like 28 | mapfigure(data_title, id=data_id) 29 | ``` 30 | 31 | ```{r child=here::here("figures_tables", "Map_Figure.Rmd")} 32 | ``` 33 | 34 | ## Recent trends 35 | 36 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec vitae ante quis dui egestas fringilla ac vitae justo. Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 37 | 38 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 39 | 40 | ```{r eval=FALSE} 41 | # This figure will be included. 42 | # Click green arrow at right to see 43 | source(here::here("figures_tables", "_common.R")) 44 | statusfigure(data_title, data_id) 45 | ``` 46 | 47 | ```{r child=here::here("figures_tables", "Status_Figure.Rmd")} 48 | ``` 49 | 50 | ## Population raw data 51 | 52 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 53 | 54 | ```{r child=here::here("figures_tables", "Raw_Tables.Rmd")} 55 | ``` -------------------------------------------------------------------------------- /text/ICUCsthd.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | always_allow_html: true 3 | --- 4 | 5 | ```{r warning=FALSE, echo=FALSE, message=FALSE} 6 | knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE) 7 | source(here::here("figures_tables", "_common.R")) 8 | load(here::here("data", "maplocs.rda")) 9 | ``` 10 | 11 | ```{r} 12 | data_title <- "Upper Columbia steelhead" 13 | data_id <- "ICUCsthd" 14 | ``` 15 | 16 | # Upper Columbia steelhead 17 | 18 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. @clark1993 vitae ante quis dui egestas fringilla ac vitae justo [@ansley1981; @collins1996; @deuel1968] . Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 19 | 20 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 21 | 22 | ## General location 23 | 24 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. 25 | 26 | ```{r eval=FALSE} 27 | # run to see what the map is like 28 | mapfigure(data_title, id=data_id) 29 | ``` 30 | 31 | ```{r child=here::here("figures_tables", "Map_Figure.Rmd")} 32 | ``` 33 | 34 | ## Recent trends 35 | 36 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec vitae ante quis dui egestas fringilla ac vitae justo. Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 37 | 38 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 39 | 40 | ```{r eval=FALSE} 41 | # This figure will be included. 42 | # Click green arrow at right to see 43 | source(here::here("figures_tables", "_common.R")) 44 | statusfigure(data_title, data_id) 45 | ``` 46 | 47 | ```{r child=here::here("figures_tables", "Status_Figure.Rmd")} 48 | ``` 49 | 50 | ## Population raw data 51 | 52 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 53 | 54 | ```{r child=here::here("figures_tables", "Raw_Tables.Rmd")} 55 | ``` -------------------------------------------------------------------------------- /text/LCchinook.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | always_allow_html: true 3 | --- 4 | 5 | ```{r warning=FALSE, echo=FALSE, message=FALSE} 6 | knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE) 7 | source(here::here("figures_tables", "_common.R")) 8 | load(here::here("data", "maplocs.rda")) 9 | ``` 10 | 11 | ```{r} 12 | data_title <- "Lower Columbia Chinook" 13 | data_id <- "LCchinook" 14 | ``` 15 | 16 | # Lower Columbia Chinook 17 | 18 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. @clark1993 vitae ante quis dui egestas fringilla ac vitae justo [@ansley1981; @collins1996; @deuel1968] . Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 19 | 20 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 21 | 22 | ## General location 23 | 24 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. 25 | 26 | ```{r eval=FALSE} 27 | # run to see what the map is like 28 | mapfigure(data_title, id=data_id) 29 | ``` 30 | 31 | ```{r child=here::here("figures_tables", "Map_Figure.Rmd")} 32 | ``` 33 | 34 | ## Recent trends 35 | 36 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec vitae ante quis dui egestas fringilla ac vitae justo. Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 37 | 38 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 39 | 40 | ```{r eval=FALSE} 41 | # This figure will be included. 42 | # Click green arrow at right to see 43 | source(here::here("figures_tables", "_common.R")) 44 | statusfigure(data_title, data_id) 45 | ``` 46 | 47 | ```{r child=here::here("figures_tables", "Status_Figure.Rmd")} 48 | ``` 49 | 50 | ## Population raw data 51 | 52 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 53 | 54 | ```{r child=here::here("figures_tables", "Raw_Tables.Rmd")} 55 | ``` -------------------------------------------------------------------------------- /text/LCcoho.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | always_allow_html: true 3 | --- 4 | 5 | ```{r warning=FALSE, echo=FALSE, message=FALSE} 6 | knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE) 7 | source(here::here("figures_tables", "_common.R")) 8 | load(here::here("data", "maplocs.rda")) 9 | ``` 10 | 11 | ```{r} 12 | data_title <- "Lower Columbia coho" 13 | data_id <- "LCcoho" 14 | ``` 15 | 16 | # Lower Columbia coho 17 | 18 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. @clark1993 vitae ante quis dui egestas fringilla ac vitae justo [@ansley1981; @collins1996; @deuel1968] . Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 19 | 20 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 21 | 22 | ## General location 23 | 24 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. 25 | 26 | ```{r eval=FALSE} 27 | # run to see what the map is like 28 | mapfigure(data_title, id=data_id) 29 | ``` 30 | 31 | ```{r child=here::here("figures_tables", "Map_Figure.Rmd")} 32 | ``` 33 | 34 | ## Recent trends 35 | 36 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec vitae ante quis dui egestas fringilla ac vitae justo. Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 37 | 38 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 39 | 40 | ```{r eval=FALSE} 41 | # This figure will be included. 42 | # Click green arrow at right to see 43 | source(here::here("figures_tables", "_common.R")) 44 | statusfigure(data_title, data_id) 45 | ``` 46 | 47 | ```{r child=here::here("figures_tables", "Status_Figure.Rmd")} 48 | ``` 49 | 50 | ## Population raw data 51 | 52 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 53 | 54 | ```{r child=here::here("figures_tables", "Raw_Tables.Rmd")} 55 | ``` -------------------------------------------------------------------------------- /text/LCcoho_files/figure-pdf/fig-LCcoho-map-1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/QuartoReport_SE/4419539f20879fb3949fcc1ffdd0f8df0e8c564b/text/LCcoho_files/figure-pdf/fig-LCcoho-map-1.pdf -------------------------------------------------------------------------------- /text/LCcoho_files/figure-pdf/fig-LCcoho-status-1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/QuartoReport_SE/4419539f20879fb3949fcc1ffdd0f8df0e8c564b/text/LCcoho_files/figure-pdf/fig-LCcoho-status-1.pdf -------------------------------------------------------------------------------- /text/LCsthd.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | always_allow_html: true 3 | --- 4 | 5 | ```{r warning=FALSE, echo=FALSE, message=FALSE} 6 | knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE) 7 | source(here::here("figures_tables", "_common.R")) 8 | load(here::here("data", "maplocs.rda")) 9 | ``` 10 | 11 | ```{r} 12 | data_title <- "Lower Columbia steelhead" 13 | data_id <- "LCsthd" 14 | ``` 15 | 16 | # Lower Columbia steelhead 17 | 18 | The is a new line. @clark1993 vitae ante quis dui egestas fringilla ac vitae justo [@ansley1981; @collins1996; @deuel1968] . Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 19 | 20 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 21 | 22 | ## General location 23 | 24 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. 25 | 26 | ```{r eval=FALSE} 27 | # run to see what the map is like 28 | mapfigure(data_title, id=data_id) 29 | ``` 30 | 31 | ```{r child=here::here("figures_tables", "Map_Figure.Rmd")} 32 | ``` 33 | 34 | ## Recent trends 35 | 36 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec vitae ante quis dui egestas fringilla ac vitae justo. Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 37 | 38 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 39 | 40 | ```{r eval=FALSE} 41 | # This figure will be included. 42 | # Click green arrow at right to see 43 | source(here::here("figures_tables", "_common.R")) 44 | statusfigure(data_title, data_id) 45 | ``` 46 | 47 | ```{r child=here::here("figures_tables", "Status_Figure.Rmd")} 48 | ``` 49 | 50 | ## Population raw data 51 | 52 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 53 | 54 | ```{r child=here::here("figures_tables", "Raw_Tables.Rmd")} 55 | ``` 56 | -------------------------------------------------------------------------------- /text/OCcoho.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | always_allow_html: true 3 | --- 4 | 5 | ```{r warning=FALSE, echo=FALSE, message=FALSE} 6 | knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE) 7 | source(here::here("figures_tables", "_common.R")) 8 | load(here::here("data", "maplocs.rda")) 9 | ``` 10 | 11 | ```{r} 12 | data_title <- "Oregon Coast coho" 13 | data_id <- "OCcoho" 14 | ``` 15 | 16 | # Oregon Coast coho 17 | 18 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. @clark1993 vitae ante quis dui egestas fringilla ac vitae justo [@ansley1981; @collins1996; @deuel1968] . Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 19 | 20 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 21 | 22 | ## General location 23 | 24 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. 25 | 26 | ```{r eval=FALSE} 27 | # run to see what the map is like 28 | mapfigure(data_title, id=data_id) 29 | ``` 30 | 31 | ```{r child=here::here("figures_tables", "Map_Figure.Rmd")} 32 | ``` 33 | 34 | ## Recent trends 35 | 36 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec vitae ante quis dui egestas fringilla ac vitae justo. Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 37 | 38 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 39 | 40 | ```{r eval=FALSE} 41 | # This figure will be included. 42 | # Click green arrow at right to see 43 | source(here::here("figures_tables", "_common.R")) 44 | statusfigure(data_title, data_id) 45 | ``` 46 | 47 | ```{r child=here::here("figures_tables", "Status_Figure.Rmd")} 48 | ``` 49 | 50 | ## Population raw data 51 | 52 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 53 | 54 | ```{r child=here::here("figures_tables", "Raw_Tables.Rmd")} 55 | ``` -------------------------------------------------------------------------------- /text/OCcoho_files/figure-pdf/fig-OCcoho-map-1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/QuartoReport_SE/4419539f20879fb3949fcc1ffdd0f8df0e8c564b/text/OCcoho_files/figure-pdf/fig-OCcoho-map-1.pdf -------------------------------------------------------------------------------- /text/OCcoho_files/figure-pdf/fig-OCcoho-status-1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/RVerse-Tutorials/QuartoReport_SE/4419539f20879fb3949fcc1ffdd0f8df0e8c564b/text/OCcoho_files/figure-pdf/fig-OCcoho-status-1.pdf -------------------------------------------------------------------------------- /text/UWchinook.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | always_allow_html: true 3 | --- 4 | 5 | ```{r warning=FALSE, echo=FALSE, message=FALSE} 6 | knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE) 7 | source(here::here("figures_tables", "_common.R")) 8 | load(here::here("data", "maplocs.rda")) 9 | ``` 10 | 11 | ```{r} 12 | data_title <- "Upper Willamette Chinook" 13 | data_id <- "UWchinook" 14 | ``` 15 | 16 | # Upper Willamette Chinook 17 | 18 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. @clark1993 vitae ante quis dui egestas fringilla ac vitae justo [@ansley1981; @collins1996; @deuel1968] . Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 19 | 20 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 21 | 22 | ## General location 23 | 24 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. 25 | 26 | ```{r eval=FALSE} 27 | # run to see what the map is like 28 | mapfigure(data_title, id=data_id) 29 | ``` 30 | 31 | ```{r child=here::here("figures_tables", "Map_Figure.Rmd")} 32 | ``` 33 | 34 | ## Recent trends 35 | 36 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec vitae ante quis dui egestas fringilla ac vitae justo. Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 37 | 38 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 39 | 40 | ```{r eval=FALSE} 41 | # This figure will be included. 42 | # Click green arrow at right to see 43 | source(here::here("figures_tables", "_common.R")) 44 | statusfigure(data_title, data_id) 45 | ``` 46 | 47 | ```{r child=here::here("figures_tables", "Status_Figure.Rmd")} 48 | ``` 49 | 50 | ## Population raw data 51 | 52 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 53 | 54 | ```{r child=here::here("figures_tables", "Raw_Tables.Rmd")} 55 | ``` -------------------------------------------------------------------------------- /text/UWsthd.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | always_allow_html: true 3 | --- 4 | 5 | ```{r warning=FALSE, echo=FALSE, message=FALSE} 6 | knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE) 7 | source(here::here("figures_tables", "_common.R")) 8 | load(here::here("data", "maplocs.rda")) 9 | ``` 10 | 11 | ```{r} 12 | data_title <- "Upper Willamette steelhead" 13 | data_id <- "UWsthd" 14 | ``` 15 | 16 | # Upper Willamette steelhead 17 | 18 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. @clark1993 vitae ante quis dui egestas fringilla ac vitae justo [@ansley1981; @collins1996; @deuel1968] . Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 19 | 20 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 21 | 22 | ## General location 23 | 24 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. 25 | 26 | ```{r eval=FALSE} 27 | # run to see what the map is like 28 | mapfigure(data_title, id=data_id) 29 | ``` 30 | 31 | ```{r child=here::here("figures_tables", "Map_Figure.Rmd")} 32 | ``` 33 | 34 | ## Recent trends 35 | 36 | Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec vitae ante quis dui egestas fringilla ac vitae justo. Pellentesque quis magna vel odio malesuada rutrum a volutpat nisl. Aliquam fermentum, urna eget tristique mattis, augue augue tristique ipsum, eget finibus nunc eros non nisi. Phasellus mattis hendrerit sapien, quis accumsan dui pretium eget. Nunc eleifend laoreet urna a luctus. Nulla vel sapien in nulla gravida tempus sit amet a metus. Vivamus porta condimentum tempus. Maecenas rhoncus elit id ultricies scelerisque. In gravida urna in ligula fringilla euismod. Curabitur efficitur porta libero ac fermentum. Cras fringilla et libero at posuere. Curabitur sodales dapibus elit a convallis. 37 | 38 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 39 | 40 | ```{r eval=FALSE} 41 | # This figure will be included. 42 | # Click green arrow at right to see 43 | source(here::here("figures_tables", "_common.R")) 44 | statusfigure(data_title, data_id) 45 | ``` 46 | 47 | ```{r child=here::here("figures_tables", "Status_Figure.Rmd")} 48 | ``` 49 | 50 | ## Population raw data 51 | 52 | Morbi iaculis eget augue eget facilisis. Etiam non orci dignissim, efficitur purus viverra, pellentesque neque. Aliquam ornare, magna ut dictum mollis, nunc lorem iaculis nibh, eu consequat lectus urna euismod tortor. Etiam ut felis nisl. Nunc quis euismod felis. Vestibulum gravida nisi mi, quis mollis velit ullamcorper non. Aliquam tempus fringilla bibendum. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce viverra nulla elementum libero mollis, quis cursus velit sagittis. 53 | 54 | ```{r child=here::here("figures_tables", "Raw_Tables.Rmd")} 55 | ``` -------------------------------------------------------------------------------- /text/_template.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | always_allow_html: true 3 | --- 4 | 5 | ```{r warning=FALSE, echo=FALSE, message=FALSE} 6 | knitr::opts_chunk$set(echo = FALSE, warning=FALSE, message=FALSE) 7 | source(here::here("figures_tables", "_common.R")) 8 | load(here::here("data", "maplocs.rda")) 9 | ``` 10 | 11 | ```{r} 12 | data_title <- "ESU name" 13 | data_id <- "ESU id" 14 | ``` 15 | 16 | # Put ESU name here 17 | 18 | ::: callout-note 19 | Add your text in this section 20 | ::: 21 | 22 | ## General location 23 | 24 | ::: callout-note 25 | add text here 26 | ::: 27 | 28 | ```{r child=here::here("figures_tables", "Map_Figure.Rmd")} 29 | ``` 30 | 31 | ## Recent trends 32 | 33 | ::: callout-note 34 | add text here 35 | ::: 36 | 37 | ```{r child=here::here("figures_tables", "Status_Figure.Rmd")} 38 | ``` 39 | 40 | ## Population raw data 41 | 42 | ::: callout-note 43 | add text here 44 | ::: 45 | 46 | ```{r child=here::here("figures_tables", "Raw_Tables.Rmd")} 47 | ``` 48 | -------------------------------------------------------------------------------- /text/conclusion.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: Conclusion 3 | --- 4 | 5 | ## First off 6 | 7 | We want to reference the Interior Columbia Upper Columbia Entiat population @tbl-rawICUCchinook-100. It is in Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nam commodo sit amet nibh non molestie. Maecenas hendrerit nisl velit, a condimentum enim lobortis sit amet. Ut vitae nunc sed mauris condimentum fermentum. Mauris pellentesque nec neque id elementum. Suspendisse a quam aliquam, facilisis urna venenatis, malesuada diam. Pellentesque in fringilla orci. Cras sed purus urna. Ut pharetra enim ut ligula egestas mattis. I need to reference the work of @hardy1978. 8 | 9 | Phasellus non diam posuere, laoreet velit sed, egestas felis. Etiam eget neque in tellus lacinia tincidunt. Pellentesque scelerisque odio velit, nec fringilla nibh iaculis non. Aenean sit amet nulla ipsum. Cras felis lacus, pulvinar ac nisi et, convallis pulvinar turpis. Morbi non nibh lacus. Morbi vitae lorem massa. Sed ut turpis vel felis posuere commodo lacinia ac mi. Donec finibus lectus sit amet elit finibus, vitae rhoncus ligula tincidunt. Phasellus vitae blandit lacus. Integer sed nisl fermentum, pulvinar mauris in, posuere enim. Proin sit amet semper urna. Vivamus aliquet rutrum diam ac luctus. 10 | 11 | Quisque in nibh sit amet nunc mollis porttitor quis et mauris. Sed non condimentum leo, ac condimentum est. Duis ac venenatis nulla, et aliquet elit. Suspendisse potenti. Duis mollis dui at semper luctus. Maecenas euismod finibus condimentum. Fusce vitae gravida massa. Mauris metus est, pretium non semper vel, dictum vel augue. 12 | 13 | Curabitur tempus, leo quis volutpat rhoncus, turpis elit vehicula dolor, id tincidunt augue nunc at enim. In vel enim mattis, varius orci at, tempus ante. Morbi massa elit, pharetra ac libero at, porta tempus quam. Ut fringilla, tortor ac tristique euismod, magna felis vestibulum turpis, quis congue mauris leo nec felis. Aliquam viverra et nibh ut blandit. Praesent sed luctus odio. Pellentesque finibus velit dolor. Morbi ac pulvinar ex, id dapibus eros. Cras interdum arcu viverra auctor tristique. Suspendisse venenatis volutpat ultricies. 14 | 15 | Donec bibendum pharetra arcu vitae porttitor. Morbi ac quam nunc. Ut cursus dolor a mauris aliquet vulputate. Morbi elementum ullamcorper augue, et tincidunt libero facilisis posuere. Nam congue velit non elit sollicitudin aliquet. Donec lobortis nunc ligula, id sollicitudin erat rhoncus cursus. Ut egestas orci libero, eu malesuada ex sollicitudin sed. Sed ornare nunc eget massa scelerisque, nec egestas nulla commodo. Pellentesque efficitur accumsan ullamcorper. Nulla facilisi. Maecenas tristique luctus malesuada. Phasellus id enim maximus, tempus tellus eu, dignissim sapien. Integer et mauris in lectus condimentum pellentesque non a felis. 16 | 17 | ```{=openxml} 18 | 19 | ``` 20 | -------------------------------------------------------------------------------- /text/covert_templates.R: -------------------------------------------------------------------------------- 1 | a = readLines("text/CRchum.qmd") 2 | ids <- c("ICSRFchinook", "ICSRsthd", "ICUCchinook", "ICUCsthd", "LCchinook", "LCcoho", "LCsthd", "OCcoho", "UWchinook", "UWsthd") 3 | nams <- c( 4 | "Interior Columbia Snake River Chinook", 5 | "Interior Columbia Snake River Chinook steelhead", 6 | "Upper Columbia Chinook", 7 | "Upper Columbia steelhead", 8 | "Lower Columbia Chinook", 9 | "Lower Columbia coho", 10 | "Lower Columbia steelhead", 11 | "Oregon Coast coho", 12 | "Upper Willamette Chinook", 13 | "Upper Willamette steelhead") 14 | for(i in 1:length(ids)){ # 15 | b <- paste0(a, collapse="\n") 16 | b <- stringr::str_replace_all(b, "CRchum", ids[i]) 17 | b <- stringr::str_replace_all(b, "Columbia River Chum", nams[i]) 18 | cat(b, file=here::here("text", paste0(ids[i], ".qmd"))) 19 | } --------------------------------------------------------------------------------