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Get Samples by Season

get_samples_by_season.Rd

View sample by season with status and run (if assigned)

Usage

get_samples_by_season(
  con,
  season,
  dataset = c("raw", "clean", "unprocessed"),
  heterozygote_filter = c(FALSE, TRUE),
  failed_filter = c(FALSE, TRUE)
)

Arguments

con

connection to the database

season

year in format YYYY. You can pass in a min and max season as c(YYYY, YYYY). A season consists of all sampling events from the given year up to September 30th and from the previous year after October 1st.

dataset

either "raw", "clean", or "unprocessed".

heterozygote_filter

defaults to FALSE. If TRUE, only heterozygotes are returned.

failed_filter

defaults to FALSE. If TRUE, only "failed" assays (negative for both OTS28 early and late, or negative for both OTS16 spring and winter)

Details

the parameter dataset can be used to determine what information is included in the tibble. The raw, clean, and unprocessed datasets contain the following variables:

  • stream_name

  • datetime_collected

  • sample_event_number

  • sample_id

  • sherlock_run_assignment

  • field_run_assignment

  • fork_length_mm

  • fin_clip

  • status

  • updated_at

If you select dataset = "raw", the tibble will additionally contain:

  • assay_name

  • raw_fluorescence

  • threshold

  • positive_detection

  • plate_run_id

If you select dataset = "unprocessed", the tibble will additionally contain:

  • assay_name

  • sample_type_name

  • raw_fluorescence

  • background_value

  • time

  • well_location

  • plate_run_id

Examples