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tmcd82070 / CAMP_RST

R code for CAMP rotary screw trap platform
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Preparation for R package campR v1.0.0 #87

Closed jasmyace closed 8 years ago

jasmyace commented 8 years ago

OVERVIEW: At this point, Jared's lifeStage Assignment methodologies have been incorporated into the master branch. We now need to get the R code, as a whole, primed for deployment with the Platform.

RESOLUTION: Set up a list of things to do, so as to maintain timelines and expectations.

DETAILS: In order to ensure a smooth transition for the next release, the following needs to occur.

  1. ✔️ Update the R version utilized by the Platform. The lifeStage development work requires several new packages, and it makes sense to ensure all packages (and base R) are up-to-date.

    The new version of R utilized by the Platform is version 3.3.0 (2016-06-21) "Bug in Your Hair." Packages and their versions utilized in the development of the R Package campR version 1.0.0 "Doug Giggly" include the following:

    Package Version
    assertthat 0.1
    base 3.3.0
    campR 1.0.0
    cluster 2.0.4
    compiler 3.3.0
    datasets 3.3.0
    DBI 0.3.1
    dplyr 0.4.3
    ellipse 0.3-8
    graphics 3.3.0
    grDevices 3.3.0
    grid 3.3.0
    lattice 0.20-33
    lme4 1.1-12
    magrittr 1.5
    MASS 7.3-45
    Matrix 1.2-6
    MatrixModels 0.4-1
    mclust 5.2
    methods 3.3.0
    mgcv 1.8-12
    minqa 1.2.4
    mvtnorm 1.0-5
    nlme 3.1-128
    nloptr 1.0.4
    nnet 7.3-12
    openssl 0.9.4
    parallel 3.3.0
    pbkrtest 0.4-6
    plyr 1.8.3
    quantmod 0.4-5
    quantreg 5.24
    R6 2.1.2
    Rcpp 0.12.5
    RcppEigen 0.3.2.8.1
    RCurl 1.95-4.8
    RDCOMClient 0.93-0.2
    reshape2 1.4.1
    RODBC 1.3-13
    rpart 4.1-10
    SparseM 1.7
    splines 3.3.0
    stats 3.3.0
    stats4 3.3.0
    tidyr 0.4.1
    tools 3.3.0
    utils 3.3.0

  2. :heavy_check_mark: Complete the Big Looper on all reports. This includes reports with dependencies on updated queries and helper functions. a. Estimates production by life stage and run. b. Estimates production for ALL runs. c. View all catch records. d. Export non-Chinook catch records. e. Sum Chinook by date. f. Summarize releases. g. Plot fork length through season. h. Plot histograms of fork length (lifeStage = FALSE). i. Plot histograms of fork length (lifeStage = TRUE). j. Plot the weekly effort over time. k. Estimates production by life stage and run -- Auto lifestage -- 1-3 groups -- Allow Weight. l. Estimates production by life stage and run -- Auto lifestage -- 1-3 groups -- Don't Allow Weight. m. Estimates production by life stage and run -- Auto lifestage -- 2 groups -- Allow Weight. n. Estimates production by life stage and run -- Auto lifestage -- 2 groups -- Don't Allow Weight. o. Estimates production by life stage and run -- Auto lifestage -- 3 groups -- Allow Weight. p. Estimates production by life stage and run -- Auto lifestage -- 3 groups -- Don't Allow Weight. q. Estimate production by fork length (Fall).

  3. :heavy_check_mark: Upload reports to the FTP site, into folder Big Looper 2.0 R Package campR Release 1.0.0 Output in folder For Doug. This is ideally done either early in the morning or on the weekend, when the FTP site generally lacks use. A total of 10 zip files housing 25,703 files should be present. a. American River--American River at Watt Avenue -- 34,744 KB -- 1,046 files b. Feather River--Sunset Pumps -- 46,457 KB -- 1,678 files c. Feather River--Steep Riffle -- 51,270 KB -- 2,311 files d. Feather River--Live Oak -- 15,033 KB -- 668 files e. Feather River--Herringer Riffle -- 79,461 KB -- 3,098 files f. Feather River--Gateway Riffle -- 15,060 KB -- 672 files g. Feather River--Eye riffle -- 56,302 KB -- 2,695 files h. Sacramento River--RBDD RST -- 301,878 KB -- 6,890 files i. Mokelumne River--Golf RST Main Site -- 37,015 KB -- 1,551 files j. Stanislaus River--Caswell State Park -- 134,564 KB -- 5,094 files

  4. :heavy_check_mark: Upload all passage results for people to see / analyze. All passage estimates are contained in this Excel spreadsheet. allEstsCompare.xlsx

  5. :heavy_check_mark: Clean out the R-Interface folder of any old programs, files, etc. no longer needed.

    Note that I received an error about a thumbs.db file on a few folders; so, I could not delete a few folders from the Outputs folder. Maybe they will delete when they're off our file server?

  6. :heavy_check_mark: Clean out the Outputs folder of any old testing output.

  7. :heavy_check_mark: Version Control in the Platform. See Issue #55. a. Place a zip file containing the release name in folder R-Interface, so the appropriate field ends up populated within the Platform and check it's working correctly.

    image

  8. :heavy_check_mark: Test, directly via the Platform, that all reports work as intended. All of the following zip files should have a run_R.out text file, particular to that Platform report run. a. Estimates production by life stage and run. EstProdLSandRun.zip b. Estimates production for ALL runs.

    day. ALLRuns.day.zip week. ALLRuns.week.zip month. ALLRuns.month.zip year. ALLRuns.year.zip c. View all catch records. allCatch.zip d. Export non-Chinook catch records. nonChinook.zip e. Sum Chinook by date. ChinookByDate.zip f. Summarize releases.

    fall. SummarizeReleases.Fall.zip late fall. SummarizeReleases.LateFall.zip spring. SummarizeReleases.Spring.zip winter. SummarizeReleases.Winter.zip g. Plot fork length through season.

    fall.forkLength.Fall.zip late fall. forkLength.LateFall.zip spring.forkLength.Spring.zip winter. forkLength.Winter.zip h. Plot histograms of fork length. lifeStage = TRUE

    a. fall. lengthFreqHisto.Fall.lsY.zip b. late fall. lengthFreqHisto.LateFall.lsY.zip c. winter.lengthFreqHisto.Winter.lsY.zip d. spring. lengthFreqHisto.Spring.lsY.zip lifeStage = FALSE

    a. fall. lengthFreqHisto.Fall.lsN.zip b. late fall.lengthFreqHisto.LateFall.lsN.zip c. winter. lengthFreqHisto.Winter.lsN.zip d. spring.lengthFreqHisto.Spring.lsN.zip i. Plot the weekly effort over time. weeklyEffort.zip j. Auto lifestage -- 1-3 Groups -- Allow Weight lsRun.Anal.13.Allow.zip k. Auto lifestage -- 1-3 Groups -- Don't Allow Weight lsRun.Anal.13.DontAllow.zip l. Auto lifestage -- 2 Groups -- Allow Weight lsRun.Anal.2.Allow.zip m. Auto lifestage -- 2 Groups -- Don't Allow Weight lsRun.Anal.2.DontAllow.zip n. Auto lifestage -- 3 Groups -- Allow Weight lsRun.Anal.3.Allow.zip o. Auto lifestage -- 3 Groups -- Don't Allow Weight lsRun.Anal.3.DontAllow.zip p. Estimate Production by Forklength

    day. EstProdFL.Fall.day.zip week. EstProdFL.Fall.week.zip month. EstProdFL.Fall.month.zip year. EstProdFL.Fall.year.zip

  9. :heavy_check_mark: Run devtools::check() on campR to ensure that the R package to be released is as clean as possible, as defined by CRAN, the organization that defines such things.

    R CMD check results 0 errors | 0 warnings | 1 note (One note is expected, since we assign global variables in the process of running functions.)

  10. :heavy_check_mark: Sync all current code from the R-Interface folder to the jPackageRds branch of GitHub.

  11. :heavy_check_mark: Move a zipped copy of the updated Platform folder, containing everything, to folder ftp://ftp.dfg.ca.gov/For BOR/ on the FTP site. Ensure that a copy of the campR 1.0.0 source and binary are also included, as well as the campR package documentation. The documentation is in the same folder as the Platform documentation.

  12. :heavy_check_mark: Compile release notes for current release, and formally release the release.

At this point, the updated R code is ready for release, and the next stage in the checking process.

jasmyace commented 8 years ago

Package campR 1.0.0 has been released.