From df07995728401f6c6cb02eb65faa1bbf86f4c446 Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 27 Aug 2026 12:14:26 -0400 Subject: [PATCH 1/6] change defaults for bib file and create link to journals package --- R/create_template.R | 35 +++++++++++++++++------------------ R/create_yaml.R | 24 ++++++------------------ 2 files changed, 23 insertions(+), 36 deletions(-) diff --git a/R/create_template.R b/R/create_template.R index ab842072..0d9493df 100644 --- a/R/create_template.R +++ b/R/create_template.R @@ -89,10 +89,11 @@ #' #' Default: NULL #' -#' @param bib_file File path to bibliography file (`.bib`) used for citing references in -#' the report +#' @param bib_file File path to additional bibliography file (`.bib`) used for citing references in +#' the report. By default, all bibliogrphy files from the journals package and +#' references for all NMFS stock assessment reports are provided. #' -#' Default: "asar_references.bib" +#' Default: NULL #' #' @param new_template TRUE/FALSE; Create a new template? If true, #' will pull the last saved stock assessment report skeleton. @@ -249,7 +250,7 @@ create_template <- function( tables_dir = getwd(), figures_dir = getwd(), spp_image = NULL, - bib_file = "asar_references.bib", + bib_file = NULL, new_template = TRUE, rerender_skeleton = FALSE, custom_sections = NULL, @@ -501,16 +502,18 @@ create_template <- function( } # Add bib file - if (bib_file == "asar_references.bib") { - bib_loc <- system.file("resources", "asar_references.bib", package = "asar") - bib_name <- bib_file + if (is.null(bib_file)) { + if (!rerender_skeleton) { + bib_dir <- file.path(subdir, "bibliography_files") + dir.create(bib_dir, recursive = FALSE) + journals::download_bibs(bib_dir) + bib_file <- list.files(bib_dir, pattern = ".bib", full.names = TRUE) + bib_name <- list.files(bib_dir, pattern = ".bib", full.names = FALSE) + } else { + bib_name <- NULL + } } else { - # check if enter file exists - # if (!file.exists(bib_file)) stop(".bib file not found.") - cli::cli_alert_warning("Bibliography file {bib_file} not in the report directory.") - cli::cli_alert_info("The file will not be read in on render if not in the same path as the skeleton file.") - - bib_loc <- bib_file # dirname(bib_file) + file.copy(bib_file, subdir, overwrite = TRUE) |> suppressWarnings() bib_name <- stringr::str_extract(bib_file, "[^/]+$") # utils::tail(stringr::str_split(bib_file, "/")[[1]], n = 1) } @@ -576,7 +579,7 @@ create_template <- function( } else { #### Copy template files to report folder ---- # Check if there are already files in the folder - if (length(list.files(subdir)) < 2) { + if (length(list.files(subdir)) < 3) { # copy quarto files file.copy(file.path(current_folder, files_to_copy), new_folder, overwrite = FALSE) # copy before-body tex @@ -587,8 +590,6 @@ create_template <- function( create_inheader_tex(species = species, year = year, subdir = supdir) # Copy species image from package file.copy(spp_image, supdir, overwrite = FALSE) |> suppressWarnings() - # Copy bib file - file.copy(bib_loc, subdir, overwrite = TRUE) |> suppressWarnings() # Copy us doc logo file.copy(system.file("resources", "us_doc_logo.png", package = "asar"), supdir, overwrite = FALSE) |> suppressWarnings() # Copy glossary @@ -645,8 +646,6 @@ create_template <- function( create_inheader_tex(species = species, year = year, subdir = supdir) # Copy species image from package file.copy(spp_image, supdir, overwrite = FALSE) |> suppressWarnings() - # Copy bib file - file.copy(bib_loc, subdir, overwrite = TRUE) |> suppressWarnings() # Copy us doc logo file.copy(system.file("resources", "us_doc_logo.png", package = "asar"), supdir, overwrite = FALSE) |> suppressWarnings() # Copy glossary diff --git a/R/create_yaml.R b/R/create_yaml.R index 83678f2c..98609b81 100644 --- a/R/create_yaml.R +++ b/R/create_yaml.R @@ -16,8 +16,6 @@ #' @param author_list A list of strings containing pre-formatted author names #' and affiliations that would be found in the format in a yaml of a quarto #' file when using base R function `cat()`. -#' @param bib_name Name of a bib file being added into the yaml. For example, -#' "asar.bib". #' #' @return Create a string indicating the important formatting pieces for a #' quarto file for a stock assessment report. @@ -64,7 +62,7 @@ create_yaml <- function( spp_image = NULL, year = NULL, bib_name = NULL, - bib_file = "asar_references.bib", + bib_file = NULL, author_list = NULL, title = "[TITLE]", rerender_skeleton = FALSE, @@ -189,20 +187,11 @@ create_yaml <- function( } # close if params to be included in template # add bib file name - if (bib_name != "asar_references.bib") { - # check if input bib file contains a path - if (file.exists(bib_file)) { - cli::cli_alert("Copying bibliography file to report folder...") - file.copy(bib_file, file_dir) - # bib_file_only <- stringr::str_extract(bib_file, "[^/]+$") - bib_format <- paste("- ", bib_name, sep = "") - } else if (!file.exists(file.path(file_dir, bib_file))) { - cli::cli_alert_warning("Bibliography file {bib_file} is not in the report directory. The file will not be read in on render if it is not in the same path as the skeleton file.", - wrap = TRUE - ) - bib_format <- paste("- ", bib_name, sep = "") - } + if (!is.null(bib_name)) { + new_bib_name <- bib_name[grepl(bib_name), new_bibs] + bib_format <- paste("- ", bib_name, sep = "") } + yaml <- paste(yaml, collapse = " \n") } else { # not rerendering skeleton # Creating YAML @@ -326,7 +315,7 @@ create_yaml <- function( bib <- glue::glue( "bibliography: ", "\n" ) - bib_all <- paste0(" ", "- ", bib_file, "\n", collapse = "") + bib_all <- paste0(" ", "- ", paste0("bibliography_files/", bib_name), "\n", collapse = "") bib <- glue::glue("{bib} \n {bib_all}") yaml <- paste(yaml, bib, sep = "") # add citation style @@ -335,7 +324,6 @@ create_yaml <- function( "csl: support_files/cjfas.csl\n" ) # } - # add in else statement once a national .bib file is made # Close yaml yaml <- glue::glue("{yaml}---\n") From be28a958427355d30c81ba1c972b07e25e1563ba Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 27 Aug 2026 14:03:48 -0400 Subject: [PATCH 2/6] add journals dependency --- DESCRIPTION | 1 + 1 file changed, 1 insertion(+) diff --git a/DESCRIPTION b/DESCRIPTION index 1ed9c96b..30215175 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -50,6 +50,7 @@ Suggests: withr Remotes: nmfs-ost/stockplotr + nmfs-ost/journals Config/Needs/website: quarto Config/roxygen2/version: 8.1.0 Config/testthat/edition: 3 From eb8a7cb2c619ba507f5814d9f15fd57d3e63e81a Mon Sep 17 00:00:00 2001 From: Sam Schiano <125507018+Schiano-NOAA@users.noreply.github.com> Date: Thu, 27 Aug 2026 14:24:38 -0400 Subject: [PATCH 3/6] remove old bib file --- inst/resources/asar_references.bib | 2478 ---------------------------- 1 file changed, 2478 deletions(-) delete mode 100644 inst/resources/asar_references.bib diff --git a/inst/resources/asar_references.bib b/inst/resources/asar_references.bib deleted file mode 100644 index 14f43eac..00000000 --- a/inst/resources/asar_references.bib +++ /dev/null @@ -1,2478 +0,0 @@ - -@Manual{asar_2026, - title = {asar: Build NOAA Stock Assessment Report}, - author = {Samantha Schiano and Sophie Breitbart and Steve Saul}, - year = {2026}, - note = {R package version 2.2.0}, - url = {https://github.com/nmfs-ost/asar}, -} - - -@phdthesis{Abrams2014, -author = {Abrams, J.L.}, -pages = {148}, -school = {Humboldt State University}, -title = {{The effect of local fishing pressure on the size and age structure of fishes associated with rocky habitats along California's north coast}}, -year = {2014} -} - -@techreport{Adams2019, -author={Adams, G D and Kapur, K and Thurner, S and Hamel, O S and Stephens, A and Wetzel, C}, -title={{Stock assessment update: status of widow rockfish (\emph{Sebastes entomelas}) along the US West Coast in 2019}}, -year = {2019}, -institution = {{Pacific Fishery Management Council, Portland, OR}}, -series = {} -} - -@online{AFSC2016, -author = {Alaska Fisheries Science Center}, -title = {{Assessment of the Other Rockfish stock complex in the Gulf of Alaska}}, -year = 2016, -url = {https://www.afsc.noaa.gov/REFM/Docs/2016/GOAorock.pdf}, -urldate = {2017-06-18} -} - -@techreport{albin1993, -author={Albin, Douglas P. and Karpov, Konstantin A. and Van Buskirk, Wade H.}, -title = {Effort and catch estimates for {N}orthern and {C}entral {C}alifornia marine recreational fisheries, 1981-1986}, -year = {1993}, -institution = {California Department of Fish and Game, Marine Resources Division}, -series = {Administrative Report}, -number = {93-3} -} - -@article{Alverson1964, -author = {Alverson, D L and Pruter, a T and Ronholt, L L}, -journal = {Institute of Fisheries, University of British Columbia}, -title = {{A Study of Demersal Fishes and Fisheries of the Northeastern Pacific Ocean}}, -year = {1964} -} - -@article{AlversonWelander1952, -author={Averson, D L and Welander, A}, -title={Notes on the scorpaenid fishes of {W}ashington and adjacent areas, with a key for their identification}, -journal = {Copeia}, -volume={3}, -pages={138-143}, -year = {1952} -} - -@Article{Anderson:2022:SRP, - title = {{sdmTMB}: an R package for fast, flexible, and user-friendly generalized linear mixed effects models with spatial and spatiotemporal random fields}, - author = {Sean C. Anderson and Eric J. Ward and and Philina A. English and Lewis A. K. Barnett}, - journal = {bioRxiv}, - year = {2022}, - volume = {2022.03.24.485545}, - doi = {10.1101/2022.03.24.485545}, - url = {https://doi.org/10.1101/2022.03.24.485545}, -} - -@phdthesis{Anderson1983, -author = {Anderson, TW}, -school = {Fresno State University}, -title = {{Identification and development of nearshore juvenile rockfishes (genus \emph{Sebastes}) in central California kelp forests}}, -type = {Masters Thesis}, -year = {1983} -} - -@article{Barnett2015, - title={Quantifying the potential for marine reserves or harvest reductions to buffer temporal mismatches caused by climate change}, - author={Barnett, Lewis AK and Baskett, Marissa L and Botsford, Louis W}, - journal={Canadian Journal of Fisheries and Aquatic Sciences}, - volume={72}, - number={3}, - pages={376--389}, - year={2015}, - publisher={NRC Research Press} -} - -@article{Barth2007, - title={Delayed upwelling alters nearshore coastal ocean ecosystems in the northern California current}, - author={Barth, John A and Menge, Bruce A and Lubchenco, Jane and Chan, Francis and Bane, John M and Kirincich, Anthony R and McManus, Margaret A and Nielsen, Karina J and Pierce, Stephen D and Washburn, Libe}, - journal={Proceedings of the National Academy of Sciences}, - volume={104}, - number={10}, - pages={3719--3724}, - year={2007}, - publisher={National Academy of Sciences} -} - -@article{Beamish1979, -author = {Beamish, RJ}, -journal = {Journal of the Fisheries Board of Canada}, -pages = {1395--1400}, -title = {{New information on the longevity of Pacific ocean perch (\emph{Sebastes alutus})}}, -volume = {36}, -year = {1979} -} - -@article{Bell2023, - doi = {10.1371/journal.pone.0271477}, - author = {Bell, Tom W. AND Cavanaugh, Kyle C. AND Saccomanno, Vienna R. AND Cavanaugh, Katherine C. AND Houskeeper, Henry F. AND Eddy, Norah AND Schuetzenmeister, Falk AND Rindlaub, Nathaniel AND Gleason, Mary}, - journal = {PLOS ONE}, - publisher = {Public Library of Science}, - title = {Kelpwatch: A new visualization and analysis tool to explore kelp canopy dynamics reveals variable response to and recovery from marine heatwaves}, - year = {2023}, - month = {03}, - volume = {18}, - url = {https://doi.org/10.1371/journal.pone.0271477}, - pages = {1-21}, - abstract = {Giant kelp and bull kelp forests are increasingly at risk from marine heatwave events, herbivore outbreaks, and the loss or alterations in the behavior of key herbivore predators. The dynamic floating canopy of these kelps is well-suited to study via satellite imagery, which provides high temporal and spatial resolution data of floating kelp canopy across the western United States and Mexico. However, the size and complexity of the satellite image dataset has made ecological analysis difficult for scientists and managers. To increase accessibility of this rich dataset, we created Kelpwatch, a web-based visualization and analysis tool. This tool allows researchers and managers to quantify kelp forest change in response to disturbances, assess historical trends, and allow for effective and actionable kelp forest management. Here, we demonstrate how Kelpwatch can be used to analyze long-term trends in kelp canopy across regions, quantify spatial variability in the response to and recovery from the 2014 to 2016 marine heatwave events, and provide a local analysis of kelp canopy status around the Monterey Peninsula, California. We found that 18.6% of regional sites displayed a significant trend in kelp canopy area over the past 38 years and that there was a latitudinal response to heatwave events for each kelp species. The recovery from heatwave events was more variable across space, with some local areas like Bahía Tortugas in Baja California Sur showing high recovery while kelp canopies around the Monterey Peninsula continued a slow decline and patchy recovery compared to the rest of the Central California region. Kelpwatch provides near real time spatial data and analysis support and makes complex earth observation data actionable for scientists and managers, which can help identify areas for research, monitoring, and management efforts.}, - number = {3}, - -} - -@techreport{berger_status_2023, - title = {Status of the {P}acific {H}ake (whiting) stock in {U}.{S}. and {C}anadian waters in 2023}, - institution = {Joint Technical Committee of the U.S. and Canada Pacific Hake/Whiting Agreement, National Marine Fisheries Service and Fisheries and Oceans Canada.}, - author = {Berger, A.M. and Grandin C.J. and Johnson K.F. and Edwards A.M.}, - year = {2023}, - pages = {208}, -} - -@article{Beyer2015, -title={Variability in rockfish (\emph{Sebastes spp.}) fecundity: species contrasts, maternal size effects, and spatial differences}, -author={Beyer, Sabrina G and Sogard, Susan M and Harvey, Chris J and Field, John C}, -journal={Environmental biology of fishes}, -volume={98}, -number={1}, -pages={81--100}, -year={2015}, -publisher={Springer} -} - -@article{bizzarro2023, - title={A multi-predator trophic database for the California Current Large Marine Ecosystem}, - author={Bizzarro, Joseph J and Dewitt, Lynn and Wells, Brian K and Curtis, K Alexandra and Santora, Jarrod A and Field, John C}, - journal={Scientific Data}, - volume={10}, - number={1}, - pages={496}, - year={2023}, - publisher={Nature Publishing Group UK London} -} - -@article{Bodkin1986, -author = {Bodkin, JL}, -journal = {Fishery Bulletin}, -pages = {799--808}, -title = {{Fish assemblages in \emph{Macrocystis} and \emph{Nereocystis} kelp forests off central California.}}, -volume = {84}, -year = {1986} -} - -@article{Bograd2009, - title={Phenology of coastal upwelling in the California Current}, - author={Bograd, Steven J and Schroeder, Isaac and Sarkar, Nandita and Qiu, Xuemei and Sydeman, William J and Schwing, Franklin B}, - journal={Geophysical Research Letters}, - volume={36}, - number={1}, - year={2009}, - publisher={Wiley Online Library} -} - -@article{Botsford2002, -author = {Botsford, LW and Lawrence, CA}, -journal = {Progress in Oceanography}, -pages = {283--305}, -title = {{Patterns of co-variability among California Current chinook salmon, coho salmon, Dungeness crab, and physical oceanographic conditions}}, -volume = {53}, -year = {2002} -} - -@article{Bradburn2011, -title = {The 2003 to 2008 {US} {West} {Coast} bottom trawl surveys of groundfish resources off {Washington}, {Oregon}, and {California}: estimates of distribution, abundance, length, and age composition}, -journal = {NOAA Technical Memorandum NMFS NOAA-TM-NMFS-NWFSC-114}, -author = {Bradburn, M.J. and Keller, A.A and Horness, B.H.}, -year = {2011}, -pages = {323 pp.} -} - -@article{Buckley1967, -author = {Buckley, R.M.}, -journal = {Supplemental progress report. Department of Fisheries. State of Washington.}, -title = {{1965 bottomfish sport fishery. Sport fishery investigations 1965}}, -year = {1967} -} - -@article{Buonaccorsi2002, -author = {Buonaccorsi, VP}, -journal = {Canadian Journal of Fisheries and Aquatic Sciences}, -pages = {1374--1384}, -title = {{Population structure of copper rockfish (\emph{Sebastes caurinus}) reflects postglacial colonization and contemporary patterns of larval dispersal}}, -volume = {59}, -year = {2002} -} - -@article{Buonaccorsi2004, -author = {Buonaccorsi, VP and Westerman, M and Stannard, J}, -journal = {Marine Biology}, -pages = {779--788}, -title = {{Molecular genetic structure suggests limited larval dispersal in grass rockfish, \emph{Sebastes rastrelliger}}}, -volume = {145}, -year = {2004} -} - -@article{Burford2008, -author = {Burford, MO and Bernardi, G}, -journal = {Marine Biology}, -pages = {701--717}, -title = {{Incipient speciation within a subgenus of rockfish (\emph\{Sebastosomus}) provides evidence of recent radiations within an ancient species flock}} - -, -volume = {154}, -year = {2008} -} -@article{Burton1998, -author = {Burton, RS}, -journal = {Evolution}, -pages = {734--745}, -title = {{Intraspecific phylogeography across the Point Conception biogeographic boundary}}, -url = {http://www.jstor.org/stable/2411268}, -volume = {52}, -year = {1998} -} - -@article{Cabanes2010, - title={CORA (Coriolis Ocean Database for Re-analyses), a new comprehensive and qualified ocean in-situ dataset from 1990 to 2008 and its use in GLORYS}, - author={Cabanes, C{\'e}cile and de Boyer Mont{\'e}gut, Cl{\'e}ment and Coatanoan, Christine and Ferry, Nicolas and Pertuisot, C{\'e}cile and Von Schuckmann, Karina and de la Villeon, Loic Petit and Carval, Thierry and Pouliquen, Sylvie and Le Traon, Pierre-Yves}, - journal={Quarterly Newsletter--Special Issue with Coriolis}, - year={2010} -} - -, -url = {http://www.nativefishlab.net/library/textpdf/17424.pdf}, -volume = {43}, -year = {1981} -} -@article{CalCOFI2002, -author = {CDFG}, -journal = {California Cooperative Oceanic Fisheries Investigations Reports}, -keywords = {China2015}, -mendeley-tags = {China2015}, -pages = {13--30}, -title = {{Review of Some California Fisheries for 2001: market squid, sea urchin, dungeness crab, lobster, prawn, abalone, groundfish, swordfish and shark, coastal pelagic finfish, ocean salmon, nearshore live-fish, Pacific herring, white seabass, and kelp}}, -volume = {43}, -year = {2002} -} - -@techreport{Caretta2024, -author={Caretta, J V and Oleson, E M, Forney, K A and Bradford, A L and Yano, K and Weller, D W and Lang, A R and Baker, J and Orr, A J and Hanson, B and Moore, J E and Wallen, M and Brownwell R L}, -title={{U.S. Pacific marine mammal stock assessments: 2023}}, -year = {2024}, -institution = {{NOAA technical memorandum NMFS-SWFSC ; 704}}, -series = {} -} - -@article{Carlson1981, -author = {Carlson, HR and Straty, RR}, -journal = {Marine Fisheries Review}, -number = {7}, -pages = {13--19}, -title = {{Habitat and nursery grounds of Pacific rockfish, \emph\{Sebastes} spp., in rocky coastal areas of southeastern Alaska}} - -@article{Checkley2009, -author = {Checkley, DM and Barth, JA}, -journal = {Progress in Oceanography}, -pages = {49--64}, -title = {{Patterns and processes in the California Current System}}, -volume = {83}, -year = {2009} -} - -@article{Cluett, - title={Pan-basin warming now overshadows robust Pacific Decadal Oscillation}, - author={Cluett, A A and Bograd, S J and Jacox, M G and Bozo Buil, M and Hazel, E L}, - journal={}, - volume={}, - number={}, - pages={}, - year={In Review}, - publisher={} -} - -@book{Coleman1986, -title={The 1980 Pacific West Coast bottom trawl survey of groundfish resources: estimates of distribution, abundance, length and age composition}, -author={Coleman, Brady A}, -year={1986}, -publisher={National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest and Alaska Fisheries Center, Resource Assessment and Conservation Engineering Division} -} - -@article{conn2017confronting, - title={Confronting preferential sampling when analysing population distributions: diagnosis and model-based triage}, - author={Conn, Paul B and Thorson, James T and Johnson, Devin S}, - journal={Methods in Ecology and Evolution}, - volume={8}, - number={11}, - pages={1535--1546}, - year={2017}, - publisher={Wiley Online Library} -} - -@article{Cope2004, -author = {Cope, JM}, -journal = {Canadian Journal of Fisheries and Aquatic Sciences}, -pages = {332--342}, -title = {{Population genetics and phylogeography of the blue rockfish (Sebastes mystinus) from Washington to California}}, -volume = {61}, -year = {2004} -} - -@article{Cope2011, -author = {Cope, Jason M and DeVore, John and Dick, E J and Ames, Kelly and Budrick, John and Erickson, Daniel L. and Grebel, Joanna and Hanshew, Gretchen and Jones, Robert and Mattes, Lynn and Niles, Corey and Williams, Sarah}, -journal = {North American Journal of Fisheries Management}, -pages = {589--604}, -title = {{An approach to defining stock complexes for U.S. West Coast groundfishes using vulnerabilities and ecological distributions}}, -volume = {31}, -year = {2011} -} - -@article{Cope2013, -title={Data-moderate stock assessments for brown, China, copper, sharpchin, stripetail, and yellowtail rockfishes and English and rex soles in 2013}, -author={Cope, Jason and Dick, EJ and MacCall, Alec and Monk, Melissa and Soper, Braden and Wetzel, Chantel}, -journal={National Oceanic and Atmospheric Administration, National Marine Fisheries Service}, -year={2013} -} - -@techreport{Cope2015, -address = {Portland, OR}, -author = {Cope, Jason and Dick, E.J. and Maccall, Alec and Monk, Melissa and Soper, Braden and Wetzel, Chantell}, -institution = {Pacific Fisheries Management Council}, -keywords = {China2015}, -mendeley-tags = {China2015}, -pages = {298}, -title = {{Data-moderate stock assessments for brown, China, copper, sharpchin, stripetail, and yellowtail rockfishes and English and rex soles in 2013}}, -year = {2015} -} - -@techreport{Cope2023or, -author={Cope, J M and Whitman, A D and Berger, A M and Rasmuson, L K and Rosemond, R C}, -title={{Status of Black Rockfish (\emph{Sebastes melanops}) in 2023 in state and federal waters off Oregon.}}, -year = {2023}, -institution = {{Pacific Fishery Management Council, Portland, Oregon. 248 p.}}, -series = {} -} - -@techreport{Cope2023wa, -author={Cope, J M and Hillier, L K and Niles, C B and Tsou, T and Hinton, F and Caltabellotta, F P}, -title={{Status of Black Rockfish (\emph{Sebastes melanops}) in 2023 in state and federal waters off Washington state}}, -year = {2023}, -institution = {{Pacific Fishery Management Council, Portland, Oregon. 217 p.}}, -series = {} -} - -@article{Darby, -author = {Darby, Amanda and Tolimieri, Nick and Feddern, Megan L. and Oken, Kiva L.}, -journal = {}, -keywords = {}, -pages = {}, -title = {{Developing environmental indicators of recruitment for yellowtail rockfish (Sebastes Flavidus)}}, -volume = {22}, -year = {In Prep} -} - -@article{Dawson2001, -author = {Dawson, MN}, -journal = {Journal of Biogeography}, -pages = {723--736}, -title = {{Phylogeography in coastal marine animals: a solution from California?}}, -url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2699.2001.00572.x/full}, -volume = {28}, -year = {2001} -} - -@techreport{Demory1987, -author={Demory, R}, -title={{The widow rockfish fishery in Oregon 1963-80}}, -year = {1987}, -institution = {{Widow Rockfish: Proceedings of a -workshop, Tiburon, California, December 11-12. NOAA technical report 48. }}, -series = {} -} - -@techreport{DFO2015, -author = {{Canadian Science Advisory Secretariat}}, -pages = {14}, -title = {{Yellowtail Rockfish (Sebastes flavidus) Stock assessment for the Coast of British Columbia, Canada}}, -institution = {{Science Advisory Report 2015/010}}, -year = {2015} -} - -@phdthesis{Dick2009, -author = {Dick, E.J.}, -school = {University of California Santa Cruz}, -title = {{Modeling the reproductive potential of rockfishes (\emph{Sebastes} spp.)}}, -type = {PhD Dissertation}, -year = {2009} -} - -@techreport{Dick2010, -author = {Dick E. J. and MacCall A. D.}, -booktitle = {NOAA Technical Memorandum NMFS}, -institution = {Department of Commerce}, -number = {NOAA-TM-NM FS-SWFSC-460}, -pages = {208}, -title = {{Estimates of sustainable yield for 50 data-poor stocks in the Pacific coast groundfish fishery management plan}}, -year = {2010} -} - -@article{Dick2010, -author = {Dick, E J and MacCall, Alec D.}, -journal = {NOAA Technical Memorandum NMFS NOAA-TM-NMFS-SWFSC-460}, -title = {{Estimates of sustainable yield for 50 data-poor stocks in the Pacific Coast Groundfish Fishery Management Plan}}, -year = {2010} -} - -@article{Dick2011, -author = {Dick, E. J. and MacCall, Alec D.}, -issn = {01657836}, -journal = {Fisheries Research}, -keywords = {Data-poor stock assessment,Depletion-Corrected Average Catch,Monte Carlo methods,Stochastic stock reduction analysis}, -number = {2}, -pages = {331--341}, -title = {{Depletion-Based Stock Reduction Analysis: A catch-based method for determining sustainable yields for data-poor fish stocks}}, -volume = {110}, -year = {2011} -} - -@article{Dick2017, -title={A meta-analysis of fecundity in rockfishes (genus Sebastes)}, -author={Dick, EJ and Beyer, Sabrina and Mangel, Marc and Ralston, Stephen}, -journal={Fisheries Research}, -volume={187}, -pages={73--85}, -year={2017}, -publisher={Elsevier} -} - -@techreport{Dick2017, -author={Dick, E J and Bizzarro, A and Bosley, K and Cope, J and Field, J and Gilbert-Horvath, L and Grunloh, N and Even-Duran, M and Privitera-Johnson, K and Rodomsy, B H}, -title={{The combined status of blue and deacon rockfishes in U.S. Waters off California and Oregon in 2017}}, -year = {2017}, -institution = {{Pacific Fishery Management Council, Portland, OR}}, -series = {} -} - -@techreport{Dick2023, -author={Dick, E J and Barnes, C and Coates, J and Grunloh, N and Monk, M and Rogers, T}, -title={{The Status of Black Rockfish in U.S. Waters off California in 2023}}, -year = {2023}, -institution = {{Pacific Fishery Management Council, Portland, OR}}, -series = {} -} - -@article{Douglas1998, -author = {Douglas, D.A.}, -journal = {Oregon Deptartment of Fish and Wildlife. 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