SampFish: Survey a Fish Population
In JVAdams/artiFISHal: A Pelagic Fish Community Simulator

Description Usage Arguments Details Value References See Also Examples

Sample a simulated population of pelagic fish (created with SimFish) with down-looking acoustics (cross-lake, west-to-east) and midwater trawls (west-to-east).

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SampFish(SimPop, NumEvents = 1, AcNum, AcInterval, AcLayer, AcAngle, MtNum,
  MtHt, MtWd, MtLen, MtMinCat = 2, MtMulti = 6, PlotsPdf = FALSE,
  Seed = NULL)

`SimPop`	A list with elements `LakeInfo`, `FishInfo`, `FishParam`, `FishPop`, typically output from `SimFish`.
`NumEvents`	An integer scalar, number of sampling events, i.e., number of times to repeat the survey.
`AcNum`	An integer scalar > 0, number of equally-spaced, cross-lake, acoustic transects (oriented west-to-east).
`AcInterval`	A numeric scalar, length (distance) of acoustic interval (in m).
`AcLayer`	A numeric scalar, depth of acoustic layer (in m).
`AcAngle`	A numeric scalar, full beam angle width of down-looking acoustic transducer (in degrees).
`MtNum`	An integer scalar > 0, target number of midwater trawl tows (oriented west-to-east along acoustic transects at random water depths).
`MtHt`	A numeric scalar, height of rectangular midwater trawl opening (in m).
`MtWd`	A numeric scalar, width of rectangular midwater trawl opening (in m).
`MtLen`	A numeric scalar, length (distance) of midwater trawl haul (in m).
`MtMinCat`	An integer scalar, the minimum catch (number of fish) per midwater trawl tow, default 2. Tows capturing fewer than `MtMinCat` fish will be tossed out.
`MtMulti`	An integer scalar, the initial number of midwater trawl tows is multiplied by this scalar in an attempt to achieve the target number of tows, `MtNum`, even after eliminating those tows that extend beyond the boundaries of the lake or those with fewer than `MtMinCat`, default 6.
`PlotsPdf`	A character scalar, name of pdf file to store the diagnostic plots in. If FALSE, the default, no plots are created.
`Seed`	An integer scalar, starting seed for stochasticity incorporated in placement of acoustic transects and midwater trawl tows. Use `Seed` to ensure the survey is conducted in the same location with each call to `SampFish`. Otherwise, if set to NULL, the default, a random seed is used, resulting in a different tow location with each call to `SampFish`.

All sampling is assumed to be "perfect" with no issues of fish availability, acoustic dead zones, or trawl selectivity. So, the acoustic transects capture echoes from all fish that fall within the triangular prism defined by the randomly selected northing of the transect and the beam angle (AcAngle) of the transducer, which is assumed to be at the surface of the water. And, the midwater trawl tows capture all fish that fall within the rectangular prism defined by the randomly selected water depth of the tow, the trawl gape (MtHt and MtWd), and the tow length (MtLen).

Three diagnostic plots are produced, if PlotsPdf is not FALSE. The first is a top (bird's eye) view of the acoustic transects and midwater trawls in lake, drawn to scale. In this plot, acoustic transects are shown as solid blue lines and midwater trawl tows are shown as red rectangles. Second is a side view of each acoustic transect separately, showing the individual fish targets as blue circles (larger circles indicate larger fish) and midwater trawl tows as red rectangles with the number of fish captured written inside. The acoustic transect number and the number of targets in the transect are printed on the plot. Third is a length frequency histogram for fish captured in each midwater trawl tow. The midwater trawl tow number and the number of fish captured in the tow are printed on the plot.

A list with 3 elements.

SurvParam is a named vector with the survey inputs supplied as arguments to SampFish.
Targets is a data frame with information on fish detected in the virtual acoustics survey. Each row represents a single target, columns describe the specific location of fish in the lake and their target strengths. Three columns are included that would not be available in a real acoustic survey: group (G) and size (len and wt).
MtCatch is a data frame with information on the fish captured in the virtual midwater trawl survey. Each row represents a single fish, columns describe the specific location of the trawl and the group and size of the fish. Seven columns are included that would not be available in a real midwater trawl survey: the specific location of the fish (f.east, f.north, f.d2sh, f.botdep, f.wdep, f.d2bot) and their target strengths (ts).

Yule, DL, JV Adams, DM Warner, TR Hrabik, PM Kocovsky, BC Weidel, LG Rudstam, and PJ Sullivan. 2013. Evaluating analytical approaches for estimating pelagic fish biomass using simulated fish communities. Canadian Journal of Fisheries and Aquatic Sciences 70:1845-1857. http://www.nrcresearchpress.com/doi/abs/10.1139/cjfas-2013-0072#.U1KYxPldXTQ

Yule, DL. 2000. Comparison of horizontal acoustic and purse-seine estimates of salmonid densities and sizes in eleven Wyoming waters North American Journal of Fisheries Management 20:759-775. http://www.tandfonline.com/doi/abs/10.1577/1548-8675(2000)020%3C0759%3ACOHAAP%3E2.3.CO%3B2

SimFish

# parameters for small (a) and large (A) alewife as input to the simulator
fishp <- data.frame(
  G = c("a", "A", "A"),
  Z = c(50, 140, 140), ZE = c(0.25, 0.2, 0.2),
  LWC1 = 0.000014, LWC2 = 2.8638, LWCE = 0.18,
  TSC1 = -64.2, TSC2 = 20.5, TSCE = c(0.02, 0.07, 0.07),
  PropN = c(0.55, 0.25, 0.20),
  E = c(NA, 900, 2800), EE = c(NA, 4.5, 0.3),
  N = NA, NE = NA,
  WD = c(5, 15, 15), WDE = c(0.5, 0.7, 0.7),
  D2B = NA, D2BE = NA
)

# simulate the fish population
res <- SimFish(LakeName="Clear Lake", LkWidth=3000, LkLength=2000,
 BotDepMin=20, BotDepMax=100, FishParam=fishp, TotNFish=50000, Seed=667)

# survey the population
surv <- SampFish(SimPop=res, NumEvents=2, AcNum=5, AcInterval=3000,
 AcLayer=10, AcAngle=7, MtNum=25, MtHt=10, MtWd=10, MtLen=200, Seed=545)

# look at the results
surv$SurvParam
head(surv$Targets)
head(surv$MtCatch)