Controlled vocabularies of the literature evidence table — knw_literature

The values each controlled column of a table read by knw_literature_read() may take. life_stage is knw_timing_stages() plus access. life_history_form separates stream- and ocean-type Chinook and resident, fluvial and adfluvial bull trout; migratory is for a source that says "migratory" without separating fluvial from adfluvial. US units (cfs, mi2, ft, ft/s) are kept as the source wrote them. Width units say which width a source measured, because bankfull and wetted width are not interchangeable. parameter is the habitat-model parameter a row bears on, one of the model's own names, or blank. kind says what sort of number a row is: a parameter someone chose, a habitat-suitability breakpoint, the largest value observed, a statistic of where fish were found, a preference, expert opinion, a laboratory or hatchery measurement (lab: a lethal limit, CTmax, survival or growth at held temperatures, or a development time in degree-days), a qualitative statement, or none, a search that found nothing. quote_source says how a quote can be checked against its PDF: running text, a table cell (checked by its numbers), or ocr of a scan with no text layer. abstract is the fallback for a work whose PDF cannot be had: the quote is checked against the publisher's abstract, held as the reference item's abstract, and so carries no page. An abstract states less than the paper (often not which body length was measured, or how), so a row resting on one says only what the abstract says. scale is the grain a value was measured at: a redd or microhabitat site, a surveyed reach, a model segment, or a network summary; a site value is not a reach cutoff.

Usage

knw_literature_vocab()

Value

A named list of character vectors, one per controlled column.

Details

metric says which statistic a temperature or air_temperature value is (a daily maximum, mwmt the maximum weekly maximum, 7dadm the 7-day average of daily maxima, mwat the maximum weekly mean, 7dec the 7-day equivalent constant midway between 7DADM and MWAT, a weekly, monthly, August, summer or annual mean, a constant laboratory exposure), and over which window a degree_days value accumulates (growing_season as gsdd defines it after Coleman and Fausch 2007, to_hatch or to_emergence from fertilization, or annual). unstated is for a source that gives a value without saying. Air temperature is its own variable because models use it as a proxy for water temperature, and the two are not interchangeable.

discharge is stream size: a flow statistic used to say how big a channel is, usually its mean annual discharge (MAD), the filter an intrinsic-potential model applies, sometimes a summer flow used the same way. instream_flow is a flow need: the water a life stage needs while it is in the stream, which the stage's window in knw_timing_read() places in the year. The two are not interchangeable, so of the two only instream_flow takes a metric, the statistic the flow is held to (an instantaneous flow, a daily or monthly mean, a monthly median, a 7day_low average). A need written as a fraction of MAD is in percent MAD, which fits no other variable. A need written as a point in a flow distribution is a percentile (the 90th percentile is a high flow) or a percent exceedance (Q95, the flow exceeded 95 % of the time, is a low one); the two run in opposite directions, so the unit says which the source used, and the metric which flows were ranked. A 7day_low row gives its return period (7Q2, 7Q10) in the note. A flow need is no model's stream-size filter, so it carries no parameter or model_id, and the *_mad_* parameters belong to discharge rows alone.

depth and velocity are what a fish meets at a site (a redd, a passage riffle, a rearing position), in the unit the source wrote (cm, ft, cm/s, ft/s as well as m and m/s). A channel's bankfull depth is stream size, and is written in m bankfull.

fish_length is a body length a source ties to survival or recruitment (an age-0 fish's size at the onset of its first winter, say), not a habitat dimension. It reads in mm, and its metric says which length the source measured: fork_length, total_length, or unstated.

groundwater covers upwelling, hyporheic exchange and springs. It takes no unit, so a groundwater row carries no value: no source read so far gives an upwelling measure (a vertical hydraulic gradient, say).

Examples

knw_literature_vocab()$variable
#>  [1] "gradient"           "channel_width"      "stream_order"      
#>  [4] "discharge"          "lake_area"          "wetland_area"      
#>  [7] "bridge_distance"    "temperature"        "substrate"         
#> [10] "depth"              "velocity"           "timing"            
#> [13] "valley_width_index" "drainage_area"      "elevation"         
#> [16] "air_temperature"    "degree_days"        "groundwater"       
#> [19] "instream_flow"      "fish_length"