NEWS.md

In FSAdata: Data to Support Fish Stock Assessment ('FSA') Package

FSAdata 0.4.1

• Fixed FSAdata-package \alias problem using the "manual approach" (i.e., adding a specific @aliases FSAdata-package line to FSAdata.R) suggested in an e-mail from Kurt Hornik on 19-Aug-2023.
• Changed all http://derekogle.com/ URLs to https://derekogle.com/.
• Updated CITATION file to meet CRAN requirements.

FSAdata 0.4.0

• Changed my (DHO) email in DESCRIPTION.
• Added Code of Conduct
• Updated README.md
• Updated R-CMD-check.yaml GitHub action to v2 (this addresses the issue with the action on Ubuntu-dev).
• Added pkgdown site.
  • Added Suggests for dplyr, fishmethods, FSA, knitr, pkgdown, readxl, and rmarkdown (related to creating website).
  • Added pkgdown.yaml GitHub action.
  • Added "CSV file" links for all datasets' documentation files.
• SpotVA2: Modified documentation to address #8

FSAdata 0.3.9

• Last version maintained by Derek Ogle. Transferring to fishR Core Team for next version.
• Removed Travis-CI.
• Added GitHub Actions for CI/CD (used usethis::use_github_action_check_standard())
• Renamed default repo from master to main (see this).

FSAdata 0.3.8

• Corrected misuse of \concept in Rd files per CRAN request.

FSAdata 0.3.7

• Added Encoding: UTF-8 to DESCRIPTION.
• PygmyWFBC: Modified. Added the 2000 data (thought they were there but they were not).
• RBTroutKenai: Modified. Corrected error (thanks to Robert Black).

FSAdata 0.3.6

• BluegillIL: Modified. Changed names of variables.

FSAdata 0.3.5

• .onAttach(): Modified. Streamlined package startup message.
• Mosquitofish: Fixed small typos in documentation.

FSAdata 0.3.4

• BluegillIL: Added.
• Cabezon: Fixed small typo in documentation.
• RBTroutKenai: Fixed small typo in documentation.
• RuffeSLRH92: Added more specificity to documentation.
• WalleyeErie2: Fixed small typo in documentation.
• WalleyeML: Fixed small typo in documentation.
• YERockfish: Fixed small typo in documentation.

FSAdata 0.3.3

• Started using ROxygen v5.0.0.
• Bonito: Added.
• Mosquitofish: Added.
• RWhitefishAI: Modified. Fixed typo in scientific names and length units. Fixes #3. Thanks to Peter Mous.
• RWhitefishIR: Modified. Fixed typo in scientific names and length units. Fixes #3. Thanks to Peter Mous.
• SnapperHG: Modified. Fixed typo in documentation.
• StripedBass2: Modified. Fixed typo in length units. Fixes #4. Thanks to Peter Mous.
• YPerchTL: Modified. Minor update to documentation.
• YPerchSB1: Modified. Fixed typo in documentation.

FSAdata 0.3.2

• Fixed LaTeX quotes in DESCRIPTION file.
• Removed all \href{}{} and \url{} codes to websites that I don't control. The addresses are now "naked" such that the user will need to copy-and-paste them into a browser to view the web page rather than clicking on a hyper link. Hopefully this will eliminate problems with R CMD CHECK.
• Added notes to all files that were used in IFAR.

FSAdata 0.3.1

• DATE: 21-Oct-15
• Removed Imports for utils due to changes in FSAdata described below.
• Lots of editorial changes to help pages to make it the datalist vignette in FSA work better an to make the documentation more consistent.
• Changed all files in data-raw to CSV files.
• Added and exported the FSAdataTopics object.
• AfricanRivers: Added a topic to help documentation.
• BGHRfish: Added.
• BGHRsample: Added.
• BlackDrum2001: Added.
• Casselman1990: Added a topic to help documentation.
• CCatfishNB: Added.
• CreekChub: Added.
• CreelMN: Added a topic to help documentation.
• CutthroatALf: Modified. Removed href as it seemed inconsistent.
• FSAdata: Modified. Fixed link to FSA package. Removed importFrom for read.table() from utils.
• Ghats: Added a topic to help documentation.
• LakeTroutEggs: Added a topic to help documentation.
• PikeHL: Modified. Removed href as it seemed inconsistent.
• ShadCR: Added.
• SiscowetMI2004: Added.
• StrugeonBG: Added.
• WalleyeWad: Added.
• WalleyeWyrlng: Added.
• WhitefishLS: Added a topic to help documentation.

FSAdata 0.3.0

• Released to CRAN

FSAdata 0.2.2

• DATE: Oct15
• Converted all .txt files to .Rda files. Original .txt files are in the data-raw directory which was added to .Rbuildignore.

FSAdata 0.2.1

• DATE: Sep15
• Updated README.md and DESCRIPTION to reflect the new websites.

FSAdata 0.2.0

• DATE: Aug15
• Added importFrom for utils.
• BluegilLM: Added. Moved from FSA.
• CutthroatALF.R: Modified. Changed to use utils::read.table() rather than read.table().
• WalleyeErie2: Added.
• WalleyeML: Added.

FSAdata 0.1.9

• DATE: Jul15
• Removed several URLs that either did not work consistently or have been moved. Fixed several others.
• Fixed title in DESCRIPTION.
• Fixed CITATION.
• Removed Suggests for FSA.
• Added Travis CI.

FSAdata 0.1.8

• DATE: Apr14
• Updated DESCRIPTION file (following this -- http://r-pkgs.had.co.nz/description.html). Also added LazyData: true.
• Pathfinder: Added.
• YPerchSB: Modified. Corrected bug with data.

FSAdata 0.1.7

• DATE: Aug14
• Modified two examples to use interactive() because of use of FSA package.
• BrookTroutNEWP1: Added. Use as an example to test removal() in the FSA package.
• DarterMahon: Added.
• LobsterPEI: Added. Used as an example to test depletion() in the FSA package.
• ShrimpGuam: Added.
• SnapperHG1: Added.

FSAdata 0.1.6

• DATE: Jul14
• BullTroutRML1: Modified. Updated the source reference.
• BullTroutRML2: Modified. Updated the source reference.
• CutthroatALf: Added.
• RuffeSLRH92: Modified. Changed the species variable to indiv.
• SunfishIn: Modified. Updated example after changes to mrClosed() in FSA.
• WalleyeConsumption: Modified. Updated the source reference.

FSAdata 0.1.5

• DATE: Jun14
• Changed to using github and compiling under R 3.1.0.
• Moved FSA to a "suggests" rather than "depends".
• Made topic sections consistent, added concept fields, and cleaned up titles in the help files so that help.search() worked better.
• Cleaned up help files (consistent spacing and labeling).
• FSAdata.R: Modified. Updated help.search() hints to include the FSA package.
• AlewifeLH: Modified. Changed example to use xtabs(). Cleaned up help file. Added link to reference.
• BluegillWS: Deleted. Moved to FSAWs.
• BluefishAge: Modified. Corrected reference. Cleaned up help file.
• Cabezon: Modified. Changed example to use xtabs(). Cleaned up help file.
• ChinookArg: Removed (moved to FSA).
• CreelMN: Modified. Used a dontrun{} in the examples to remove dependency on FSA. Changed example to use xtabs(). Cleaned up help file.
• Croaker1: Modified. Corrected reference. Changed example to use xtabs(). Cleaned up help file.
• Croaker2: Modified. Corrected reference. Cleaned up help file.
• GreensCreekMine: Added.
• Herman: Modified. Modified a link to the article in the help file. Cleaned up help file.
• JobfishSIO: Modified. Added a link to the article in the help file. Cleaned up help file.
• LakeTroutALTER: Modified. Corrected reference. Cleaned up help file.
• Morwong1: Modified. Changed example to use xtabs(). Cleaned up help file.
• Morwong2: Modified. Changed example to use xtabs(). Cleaned up help file.
• MulletBS: Modified. Changed example to use xtabs(). Cleaned up help file.
• MuskieSLR: Modified. Changed example to use xtabs(). Cleaned up help file.
• PikeHL: Modified. Added a note. Cleaned up help file.
• RuffeSLRH92: Modified. Changed example to use xtabs(). Cleaned up help file.
• RWhitefishAI: Added.
• RWhitefishIR: Added.
• SalmonidsMCCA: Added.
• SardineLK: Modified. Corrected reference. Cleaned up help file.
• SculpinALTER: Modified. Corrected reference. Cleaned up help file.
• SnapperHG1: Added.
• SpottedSucker1: Added.
• SpotVA2: Modified. Corrected reference. Cleaned up help file.
• StripedBass1: Modified. Corrected reference. Changed example to use xtabs(). Cleaned up help file.
• StripedBass2: Modified. Corrected reference. Cleaned up help file.
• StripedBass3: Modified. Corrected reference. Cleaned up help file.
• StripedBass4: Modified. Corrected reference. Changed example to use xtabs(). Cleaned up help file.
• StripedBass5: Modified. Corrected reference. Changed example to use xtabs(). Cleaned up help file.
• StripedBass6: Modified. Corrected reference. Changed example to use xtabs(). Cleaned up help file.
• SunfishIN: Modified. Corrected a data entry error. Added test example. Cleaned up help file.
• WalleyeMN06a: Modified. Added link to reference. Cleaned up help file.
• WalleyeMN06b: Modified. Added link to reference. Cleaned up help file.
• WalleyePL: Added.
• WalleyePL1: Deleted. Combined to form WalleyePL.
• WalleyePL2: Deleted. Combined to form WalleyePL.
• WalleyePL3: Deleted. Combined to form WalleyePL.
• WalleyePL4: Deleted. Combined to form WalleyePL.
• WalleyeWS: Deleted. Moved to FSAWs.
• WhitefishLS: Modified. Corrected reference. Cleaned up help file.
• YPerchTL: Modified. Corrected reference. Cleaned up help file.

FSAdata 0.1.4

• DATE: Apr14
• Changed R dependency to >3.0.0 (because FSA package has that dependency).
• Removed dependency on gdata (no longer needed when RuffeWS was moved to FSA).

• Slight modifications to RD files (capitalized all common names per new AFS "rule", formatted around variables and topics to make easier to edit.)

• BluefishAge: Modified. Removed link to original source (caused problems at check).

• CrappieARMS: Modified.
• Croaker1: Modified. Removed link to original source (caused problems at check).
• Croaker2: Modified. Removed link to original source (caused problems at check).
• Deckeretal1999: Added.
• HumpbackWFCR: Added.
• Menhaden1: Added.
• StripedBass1: Added (from FSA).
• StripedBass2: Modified. Removed link to original source (caused problems at check).
• StripedBass4: Modified. Removed link to original source (caused problems at check).
• StripedBass5: Modified. Removed link to original source (caused problems at check).
• StripedBass6: Modified. Removed link to original source (caused problems at check).
• WalleyeKS: Added.

FSAdata 0.1.3

• DATE: Jun13
• Switched to using roxygen2 to create help files.
• Added a Depends on FSA (note that FSA no longer depends on FSAdata).

• Modified depends to >R2.14.0 to match FSA (which this depens on).

• Moved the following data files to FSA: BluegillJL, BluegillLM, BrookTroutTH, CodNorwegian, CutthroatAL, Ecoli, KS2D_NR, LMBassWs, Mirex, PikeNY, PikeNYPartial1, RSDlit, RuffeWs, SMBassLS, SMBassWB, SpotVA1, StripedBass1, VBGMlit, WalleyeGerowLW, WR79, and WSlit, which eliminated the dependency of FSA on FSAdata.

• .onAttach(): added, was.onLoad()` with a slight modification to avoid possible warnings on RCMD Check.
• .onLoad(): deleted, changed to .onAttach().
• CreelMN: modified examples in help file to reflect dependency on FSA.
• InchLake2: modified by changing "Largemouth Bass (<8)" to "Largemouth Bass" and "Yellow Perch (<5)" to "Yellow Perch". Also removed the sex and mat variables.
• PikeHL: modified by adding URL to the source report.

FSAdata 0.1.2

• DATE: 25Nov12
• Deleted Depends on utils package (wasn't needed).
• Switched to using Project development in RStudio.

• Switched to using semantic versioning for version numbers (which means that the hyphen before the last number in the version is replaced with a period).

• Ecoli: Added (from NCStats).

• Mirex: Added (from NCStats).

FSAdata 0.1-1

• DATE: 20Nov12
• Added a namespace (for 2.14.0 compatability)
• Switched to compiling under R version 2.13.1 (32-bit).

• Changed license specification from "GPL version 2 or newer" to "GPL (>= 2)" to avoid warning on check.

• .onLoad(): Modified. Moved the startup message into packageStartupMessage() in hopes of eliminating the warning when checking the package.

• AnchovetaChile: Modified. Updated to the actual data from the author.
• Cabezon: Added. This is the actual data from the author.
• ChinookArg: Added.
• CreelMN: Added.
• KS2D_NR: Added from NCStats.
• SardineChile: Added. This is the actual data from the author.
• YERockfish: Added. This is the actual data from the author.

FSAdata 0.1-0

• DATE: 19Aug11
• Moved to compiling under 2.13.0 (32 bit)
• Changed dependency to >2.11.1

• Modified description file to show my e-mail address.

• SquareLakePopn: removed. Moved to NCStats package.

• VBGMlit: modified. Changed "to" variable to "t0".

FSAdata 0.0-9

• DATE: 31Jan11

• added examples to each rd file. The examples show the structure and first few rows of each data file. In addition, many provide a simple plot or table of the raw data. The idea was to provide the user with a quick method to see what the data looked like.

• .First.lib(): modified -- Changed to include version number of loaded version.

• BassFL: modified -- corrected misspelling of SantaFe in first few rows.
• BSkateGB: added -- used for stock-recruitment analysis.
• BrookTroutNC: added -- used for stock-recruitment analysis.
• DarterOnt: added -- used for growth modeling.
• FSAdata-package.Rd: modified -- added directions on how to use help.search() to find data frames that can be used for specific concepts/topics.
• KingCrabAK: added -- used for stock-recruitment analysis.
• SimonsonLyons: added -- used for removal estimates.
• SLampreyGL: added -- used for stock-recruit relationships.
• VendaceLP2: added -- used for stock-recruit relationships.
• YPerchCB1: added -- used for catch-curve analysis.
• YPerchCB2: modified -- added a year-class variable and changed the recruit variable to recruits (notice the s).

FSAdata 0.0-8

• DATE: 31Jul10

• moved to compiling under 2.11.1.

• BassFL: added -- used for catch curve analysis.

• BrookTroutOnt: added -- used for Petersen mark-recapture analysis.
• ChinookKR: added -- used for stock-recruitment.
• Hake: added -- used for stock-recruitment.
• HerringBWE: added -- used for stock-recruitment.
• LakeTroutGIS: modified -- changed "recruit" variable to "recruits".
• PSalmonAK: added -- used for stock-recruitment analysis.
• RedDrum: added -- used for von Bertalanffy models (including double von B).
• SockeyeSR: added -- used for stock-recruitment.
• TPrawnsEG: added -- used for stock-recruitment.
• WalleyeMN06a: added -- used for catch curve analysis.
• WalleyeMN06b: added -- used for multiple closed mark-recapture analysis.
• WhiteGrunt1: added -- used for catch curve analysis.
• WhiteGrunt2: added -- used for von Bertalanffy models.

FSAdata 0.0-7

• DATE: 5Jun10
• AHerringChile: added -- used as an example for seasonal von Bertalanffy models.
• AnchovetaChile: added -- used as an example for seasonal von Bertalanffy models.
• WAEConsumption: added -- used as an example for non-linear models.

FSAdata 0.0-6

• DATE: 17Dec09
• moved to compiling under 2.10.1.

• updated FSAdata.rd

• RBTroutKenai: added -- used for Fabens method example.

FSAdata 0.0-5

• DATE: 1Apr09
• added dependency to gdata for example in RuffeWs.
• modified all .Rdata data files to be .txt data files.
• changed to compiling under 2.7.0.

• added CITATION file.

• .First.lib: Added

• BluegillIL1, LMBassIL1: deleted and replaced with InchLake.
• InchLake1: Added -- replaces old BluegillIL1 and LMBassIL1 and includes 2008 data.
• InchLake2: Added -- can be used for length weight and relative weight analyses.
• MuskieWI06MR: Added -- can be used for Petersen mark-recapture analyses.
• RuffeWs: Added -- can be used for standard and relative weight analyses.
• WalleyeGerowLW: Added -- can be used for standard and relative weight analyses. Specifically used to test results of emp() function in FSA against Gerow's Excel Tool.

FSAdata 0.0-4

• DATE: 15May08
• moved to RForge.
• BluegillLM1: Added -- can be used for length-weight analysis.
• BrownTroutVC1: Added -- can be used for M/R by length-class.
• RSDlit: Changed .E variables to .in and changed .m variables to .cm. This better reflects the units of measurement.
• StripedBass2, StripedBass3: Added -- can be used for growth modeling and age-length key.
• StipedBass4, StripedBass5, StripedBass6: Added -- can be used for age comparison (bias and precision) analyses.

FSAdata 0.0-3

• DATE: unknown
• changed to compiling under R 2.6.1.

• redid nearly all RD files for (1) consistency, (2) to make LaTeX work, and (3) added concept and topics sections for search purposes.

• BloaterLH: changed variable Year to year (note lower-case y).

• BluegillWs: Added -- can be used to test the rlp() function in the FSA package.
• BrkTrtTH: Changed name to BrookTroutTH.
• BrookTroutNEWP: Added -- can be used for removal estimates.
• BullTroutRML1: Added -- can be use for length-weight analysis.
• BullTroutRML2: Added -- can be use for size-at-age growth modeling.
• HardingLakeNP: changed name to PikeHL (consistent with other namings).
• JonesStockwell: Added -- can be used for removal estimates.
• LMBassWs: Added -- can be used to test the rlp() function in the FSA package.
• LizardFish: changed name to Lizardfish (note lower-case f).
• Muskie1: changed name to MuskieSLR.
• PacFlounder: changed name to HalibutPAC.
• PikeIL: Added -- can be used for depletion estimates.
• SalmonAPD: Added -- can be used for depletion/removal estimates.
• SardineKL: Added -- can be used for size-at-age growth modeling.
• SockeyeKL: changed variable Year to year (note lower-case y).
• TroutAPD: Added -- can be used for depletion/removal estimates.
• WalleyeWs: Added -- can be used to test the rlp() function in the FSA package.
• WSlit: added information for bridgelip and largescale suckers.

FSAdata 0.0-2

• DATE: unknown
• added BullTroutTC -- can be used for catch curve mortality estimation.
• added FlatheadATL -- can be used for catch curve mortality estimation.
• added SunfishLP -- can be used for catch curve mortality estimation.
• added WalleyePS -- can be used for age bias and precision estimation.

FSAdata documentation built on Aug. 24, 2023, 5:06 p.m.