Get NRS larval fish abundance data

Source: R/utils_larvalfish.R

Load and format larval fish count data from NRS biogeochemistry sampling. Data includes counts and abundance (standardised to 1000 m³) of fish larvae identified to family or species level.

pr_get_LFData()

Value

A dataframe with columns:

  • StationName: NRS station name

  • Latitude, Longitude: Sample location

  • TripCode: Unique voyage identifier

  • SampleTime_UTC, SampleTime_Local: Sampling time

  • Year_Local, Month_Local, Day_Local: Date components

  • SampleDepth_m: Maximum depth of tow

  • Temperature_degC, Salinity_psu: Surface environmental data

  • Volume_m3: Volume of water filtered (m³)

  • Vessel: Research vessel name

  • TowType: Vertical or oblique

  • GearMesh_um: Net mesh size (micrometres)

  • Bathymetry_m: Bottom depth at station

  • Species: Coded species name with WoRMS ID

  • Species2: Formatted species name for display

  • Count: Number of larvae in sample

  • Abundance_1000m3: Larvae per 1000 m³

  • QC_flag: Data quality flag (1-4)

Details

Data Collection

Larval fish samples are collected at NRS stations using:

  • Vertical net tows through the water column

  • Various mesh sizes (typically 100-500 µm)

  • Sample volumes calculated from net dimensions and tow depth

Fish larvae are identified to the lowest possible taxonomic level, typically family but sometimes genus or species for distinctive forms.

Data Format

The function returns data in long format with:

  • One row per species per sample

  • Raw counts and standardised abundance (per 1000 m³)

  • Environmental data (temperature, salinity)

  • Sampling metadata (mesh size, volume filtered, tow type)

Species Names

The Species column contains coded names (e.g., "Acanthuridae_37437900") combining family name and WoRMS taxonomic ID. The Species2 column provides formatted names for display purposes.

Taxonomic Codes

Family names in the data typically end with "idae" (e.g., Acanthuridae for surgeonfishes, Carangidae for trevallies). Codes include:

  • Family name

  • WoRMS AphiaID (taxonomic identifier)

  • Life stage code (3 = larval stage)

Data Availability

Larval fish sampling is conducted opportunistically during NRS voyages. Not all stations or months have larval fish data.

Quality Control

The QC_flag column indicates data quality:

  • 1 = Good data

  • 2 = Probably good data

  • 3 = Probably bad data (use with caution)

  • 4 = Bad data (do not use)

See also

Examples

# Load larval fish data
dat <- pr_get_LFData()

# Check which families are most common
dat %>%
  dplyr::group_by(Species) %>%
  dplyr::summarise(TotalCount = sum(Count, na.rm = TRUE)) %>%
  dplyr::arrange(dplyr::desc(TotalCount))
#> --- planktonr_dat Attributes ---
#>   Type: Fish
#>   Survey: NRS
#> 
#> # A tibble: 240 × 2
#>    Species                                      TotalCount
#>    <chr>                                             <dbl>
#>  1 Myctophidae_Myctophidae_37122000                  82487
#>  2 Clupeidae_Sardinops.sagax_37085002                49015
#>  3 Gonorynchidae_Gonorynchus.greyi_37141001          23047
#>  4 Carangidae_Trachurus.novaezelandiae_37337003      22892
#>  5 Bothidae_Bothidae_37460922                        19145
#>  6 Carangidae_Carangidae_37337000                    17071
#>  7 Labridae_Labridae_37384000                        16646
#>  8 Carangidae_Pseudocaranx.georgianus_37337062       16175
#>  9 Engraulidae_Engraulis.australis_37086001          13735
#> 10 Gonostomatidae_Gonostomatidae_37106912            12542
#> # ℹ 230 more rows

# Abundance at Maria Island
dat %>%
  dplyr::filter(StationName == "Maria Island",
                QC_flag == 1) %>%
  dplyr::group_by(Year_Local, Species2) %>%
  dplyr::summarise(MeanAbundance = mean(Abundance_1000m3, na.rm = TRUE),
                   .groups = "drop")
#> --- planktonr_dat Attributes ---
#>   Type: Fish
#>   Survey: NRS
#> 
#> # A tibble: 1,920 × 3
#>    Year_Local Species2                                      MeanAbundance
#>         <dbl> <chr>                                                 <dbl>
#>  1       2014 Acanthuridae: Acanthuridae (37437900)                     0
#>  2       2014 Acropomatidae: Acropomatidae (37311956)                   0
#>  3       2014 Acropomatidae: Synagrops spp (37311949)                   0
#>  4       2014 Acropomatidae: Verilus anomalus (37311053)                0
#>  5       2014 Ambassidae: Ambassidae (37310900)                         0
#>  6       2014 Ambassidae: Ambassis jacksoniensis (37310012)             0
#>  7       2014 Ambassidae: Ambassis marianus (37310018)                  0
#>  8       2014 Ammodytidae: Ammodytidae (37425000)                       0
#>  9       2014 Ammodytidae: Ammodytoides spp (37425901)                  0
#> 10       2014 Antennariidae: Antennariidae (37210915)                   0
#> # ℹ 1,910 more rows