diff --git a/.gitignore b/.gitignore index eb3b980..ee7466a 100644 --- a/.gitignore +++ b/.gitignore @@ -10,6 +10,7 @@ inst/doc # folders other +!docs # files *.png diff --git a/docs/404.html b/docs/404.html index 52710b4..ce84049 100644 --- a/docs/404.html +++ b/docs/404.html @@ -67,6 +67,9 @@
  • Data Exploration
    • +
  • + Scallop Example +
  • @@ -76,12 +79,7 @@
  • @@ -142,7 +140,7 @@

    Page not found (404)

    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 85b4fb7..76f409d 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -48,6 +48,9 @@
  • Data Exploration
    • +
  • + Scallop Example +
  • -
  • @@ -77,12 +80,7 @@
  • @@ -117,11 +115,11 @@ - - - - -
    + + + + +

    Explore Fishing Data

    @@ -143,8 +141,8 @@

    Data Sources and cleaningLandings data by box at trip level provided by SSB for the communities at sea project

    Example of data

    -
    -

    Explain the fields

    +
    +

    Explain the fields

    Plot Catch by Box

    @@ -167,8 +165,8 @@

    Port level

    - +
    +

    Ports by State @@ -178,8 +176,8 @@

    Ports by State

    Are the fish landed from the boundary boxes distributed equally among ports or are some ports heavily reliant from landings in these boxes

    -
    - +
    +

    Landings by State @@ -188,8 +186,8 @@

    Landings by State

    - +
    +

    Number of Trips @@ -200,12 +198,12 @@

    Number of Trips

    Gear categories

    -
    -

    There are no GEARCODEs in DMIS that have missing GEARCATs. VTR and +

    +

    There are no GEARCODEs in DMIS that have missing GEARCATs. VTR and DMIS GEARCAT descriptions match. The distinct Gear categories from DMIS are :

    -
    - +
    +

    Landings by GEARCAT @@ -215,9 +213,9 @@

    Landings by GEARCAT#> `summarise()` has grouped output by 'Year', 'STATE'. You can override using the #> `.groups` argument.

    -
    -
    - +
    +
    +

    Species categories @@ -242,7 +240,7 @@

    Species categories

    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/articles/ExploreFishingData_files/datatables-css-0.0.0/datatables-crosstalk.css b/docs/articles/ExploreFishingData_files/datatables-css-0.0.0/datatables-crosstalk.css index fb5bae8..bd1159c 100644 --- a/docs/articles/ExploreFishingData_files/datatables-css-0.0.0/datatables-crosstalk.css +++ b/docs/articles/ExploreFishingData_files/datatables-css-0.0.0/datatables-crosstalk.css @@ -21,3 +21,12 @@ See https://github.com/DataTables/DataTablesSrc/issues/160 table.dataTable { display: table; } + + +/* +When DTOutput(fill = TRUE), it receives a .html-fill-item class (via htmltools::bindFillRole()), which effectively amounts to `flex: 1 1 auto`. That's mostly fine, but the case where `fillContainer=TRUE`+`height:auto`+`flex-basis:auto` and the container (e.g., a bslib::card()) doesn't have a defined height is a bit problematic since the table wants to fit the parent but the parent wants to fit the table, which results pretty small table height (maybe because there is a minimum height somewhere?). It seems better in this case to impose a 400px height default for the table, which we can do by setting `flex-basis` to 400px (the table is still allowed to grow/shrink when the container has an opinionated height). +*/ + +.html-fill-container > .html-fill-item.datatables { + flex-basis: 400px; +} diff --git a/docs/articles/atlantiscas.html b/docs/articles/atlantiscas.html index 9caf54c..6c5631d 100644 --- a/docs/articles/atlantiscas.html +++ b/docs/articles/atlantiscas.html @@ -68,6 +68,9 @@
  • Data Exploration
    • +
  • + Scallop Example +
  • @@ -77,12 +80,7 @@
  • @@ -149,7 +147,7 @@

    atlantiscas

    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/articles/dataQAQC.html b/docs/articles/dataQAQC.html index 5a29281..7072f76 100644 --- a/docs/articles/dataQAQC.html +++ b/docs/articles/dataQAQC.html @@ -68,6 +68,9 @@
  • Data Exploration
    • +
  • + Scallop Example +
  • @@ -77,12 +80,7 @@
  • @@ -117,11 +115,11 @@ - - - - -
    + + + + +

    Data Cleaning

    @@ -135,25 +133,55 @@

    Data Cleaning

    -library(atlantiscas)
-library(magrittr)
    +library(atlantiscas)

    The fishing data is a combination of VTR (1996-2007) and DMIS (2008-2021) data.

    -
    -

    Both have different lookup tables and formatting for species names +

    +

    Both have different lookup tables and formatting for species names (SPPNM), port names (PORT), gear categories (GEARCAT)

    +
    +

    Ports +

      -
    • Ports lack latitude and longitude +
    • Port look up tables lack latitude and longitude
        -
      • Use port, county, state to geocode lat and lon using google maps -api
        • +
      • Use port, county, state to geocode lat and lon using open street +maps
    • Ports have duplicate entries with spelling typos
        -
      • eg. harwichport, harwich port
        • +
      • eg. harwichport, harwich port. These were hand fixed
      • +
    +

    All PORTID within the Atlantis domain were identified. Other PORTIDs +were grouped into either Canadian ports (north of the atlantis domain) +or southern ports (south of atlantis domain)

    +

    PORTID was used to match PORTNM,COUNTY,STATE from the CFDBS.PORT +table (VTR.VLPORTSYN contains too many typos). Port names were then used +to find lat and lon values using tidygeocoder usig open +street maps and online service geocode.maps.co. Many port +names and/or counties had to be edited due to spelling errors, incorrect +information, inconsistent formatting, or missing information. For +example:

    +
      +
    • SALISBURY COVE, ME -> SALSBURY COVE, ME (spelling)
      • +
    • (TOWN OF) -> (inconsistent formatting -removed text “(TOWN OF)” +from port name)
      • +
    • PERKINS COVE, CUMBERLAND, ME -> OGUNQUIT, YORK, ME +(incorrect)
      • +
    • OTHER FAIRFIELD, FAIRFIELD, CT -> FAIRFIELD, FAIRFIELD, CT +(missing port info)
      • +
    • COMBS CREEK, ST. MARYS, MD -> NA, ST.MARY’S, MD (not found on +maps)
      • +
    • DUKES, DUKES, MA -> NA, DUKES, MA (no such port)
      • +
    +
    +
    +

    Species +

    +
    • Species have duplicate names with different formats
      • All species with NK or (NK) (Not known) in their name were formatted @@ -161,11 +189,64 @@

        Data Cleaning

      • All species separated by commas (eg DRUM, BLACK) were formatted as BLACK DRUM
      • LOBSTER was replaced by AMERICAN LOBSTER
        • -
      • LOLIGO SQUID was replcaed by LONGFIN SQUID
        • -
      • +
      • LOLIGO SQUID was replaced by LONGFIN SQUID
      • OTHER FISH have 2 codes (526,529)
      • +
    • Several NESPP3 codes are catch alls. For example: +
        +
      • NS SQUIDS +
          +
        • 803: MKTNM = UNCLASSIFIED
          • +
        • split landings 50/50 into atlantis groups ISQ/LSQ)
          • +
        +
        • +
      • SKATES +
          +
        • 365: MKTNM = UNCLASSIFIED, SMALL (WINGS), LARGE (WINGS)
          • +
        • Split into SK,LSK,WSK (proportions?)
          • +
        +
        • +
      • OTHER FISH +
          +
        • 526: MKTNM = HEADS, FOOD, SPAWN
          • +
        • 529: MKTNM = INDUSTRIAL
          • +
        +
        • +
      • NK DOGFISH +
          +
        • 350: MKTNM: ROUND, TAILS, DRESSED, FINS
          • +
        +
        • +
      • NK SHARK +
          +
        • 359: UNCLASSIFIED DRESSED/ROUND, FINS +DRIED/FRESH/FROZEN,GUTTED,CHUNKS
          • +
        +
        • +
      • NK CLAM +
          +
        • 764:
          • +
        +
        • +
      • HAKE MIX RED & WHITE +
          +
        • 155:
          • +
        +
        • +
      • SILVER&OFFSHIREHAKE MIX +
          +
        • 507:
          • +
        +
        • +
      +
      • +
    +
    +
    +

    GEARS +

    +
    • Gear Codes have different Gear Categories assigned depending on VTR or DMIS data
        @@ -174,10 +255,13 @@

        Data Cleaning

    +
    + +
    @@ -190,7 +274,7 @@

    Data Cleaning

    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/articles/dataQAQC_files/datatables-css-0.0.0/datatables-crosstalk.css b/docs/articles/dataQAQC_files/datatables-css-0.0.0/datatables-crosstalk.css index fb5bae8..bd1159c 100644 --- a/docs/articles/dataQAQC_files/datatables-css-0.0.0/datatables-crosstalk.css +++ b/docs/articles/dataQAQC_files/datatables-css-0.0.0/datatables-crosstalk.css @@ -21,3 +21,12 @@ See https://github.com/DataTables/DataTablesSrc/issues/160 table.dataTable { display: table; } + + +/* +When DTOutput(fill = TRUE), it receives a .html-fill-item class (via htmltools::bindFillRole()), which effectively amounts to `flex: 1 1 auto`. That's mostly fine, but the case where `fillContainer=TRUE`+`height:auto`+`flex-basis:auto` and the container (e.g., a bslib::card()) doesn't have a defined height is a bit problematic since the table wants to fit the parent but the parent wants to fit the table, which results pretty small table height (maybe because there is a minimum height somewhere?). It seems better in this case to impose a 400px height default for the table, which we can do by setting `flex-basis` to 400px (the table is still allowed to grow/shrink when the container has an opinionated height). +*/ + +.html-fill-container > .html-fill-item.datatables { + flex-basis: 400px; +} diff --git a/docs/articles/index.html b/docs/articles/index.html index 3011481..2093ead 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -48,6 +48,9 @@
  • Data Exploration
    • +
  • + Scallop Example +
  • -
  • -
  • @@ -77,12 +80,7 @@
  • @@ -194,7 +192,7 @@

    Developers

    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.0.7.

    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 123b3ec..17f28dc 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,10 +1,11 @@ pandoc: '2.18' -pkgdown: 2.0.6 +pkgdown: 2.0.7 pkgdown_sha: ~ articles: atlantiscas: atlantiscas.html dataQAQC: dataQAQC.html ExploreFishingData: ExploreFishingData.html + scallops: scallops.html SSBData: SSBData.html -last_built: 2023-09-23T18:08Z +last_built: 2024-04-17T17:53Z diff --git a/docs/reference/compare_data.html b/docs/reference/compare_data.html index 1a26da7..2227a83 100644 --- a/docs/reference/compare_data.html +++ b/docs/reference/compare_data.html @@ -48,6 +48,9 @@
  • Data Exploration
    • +
  • + Scallop Example +
  • -
  • -
  • -
  • -
  • -