Package 'upriver'

Expand movement parameters

Description

Expands the movement parameters to include a 0th and n+1th reach.

Usage

expand_parameters(parameters)

Arguments

parameters

(list) Movement parameters (names: rates, distances)

Value

(list) Expanded parameters

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Calculate median timing

Description

Calculate median timing given a set of parameters

Usage

median_timing(location, arrival, parameters, arrival_position = 0)

Arguments

location	(numeric) The location at which you want to calculate median timing.
arrival	(data.frame) A data.frame of daily arrivals by proportion. See details.
parameters	(list) See positions for details.
arrival_position	(numeric) Defaults 0. Where to start movement.

Details

#' arrival should be a data.frame describing a set of daily arrivals of fish at arrival_position as a series of daily proportions. It should have a column day and a corresponding column proportion, which should sum to one.

Examples

median_timing(1000,
              data.frame(day=0:40, proportion=dnorm(-20:20, 0, 5)/sum(dnorm(-20:20, 0, 5))),
              list(rates = 50, distances = 1000))

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Calculate an arbitrary timing percentile

Description

Calculate an arbitrary timing percentile given a set of parameters

Usage

percentile_timing(percentile, location, arrival, parameters,
  arrival_position = 0)

Arguments

percentile	(numeric) An arbitrary timing percentile (between 0 and 1)
location	(numeric) The location at which you want to calculate median timing.
arrival	(data.frame) A data.frame of daily arrivals by proportion. See details.
parameters	(list) See positions for details.
arrival_position	(numeric) Defaults 0. Where to start movement.

Details

#' arrival should be a data.frame describing a set of daily arrivals of fish at arrival_position as a series of daily proportions. It should have a column day and a corresponding column proportion, which should sum to one.

Examples

percentile_timing(0.75,
                  1000,
                  data.frame(day=0:40, proportion=dnorm(-20:20, 0, 5)/sum(dnorm(-20:20, 0, 5))),
                  list(rates = 50, distances = 1000))

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Calculate positions after some time.

Description

Calculate positions after ndays has elapsed, given the movement parameters provided in parameters.

Usage

positions(ndays, parameters)

Arguments

ndays	(numeric) The number of days to calculate positions for.
parameters	(list) List with names reaches, rates, distances. See details.

Details

parameters should be a list with three elements, rates, and distances, each of equal size. rates should be a numeric vector of reach-specific daily movement rates, in whatever unit your analysis needs. distances should be a numeric vector of reach-specific reach lengths (end-to-end), in the (ideally) the same or compatible units to the units used in rates

Examples

# Simple upriver movement
positions(10, list(rates = 50, distances = 1000))
# Movement with reach-to-reach variation
positions(10,
          list(rates = c(1, 2, 3, 4, 5),
          distances = c(20, 20, 20, 20, 20)))

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Calculate run timings

Description

Calculates run timing given a set of parameters.

Usage

timings(location, arrival, parameters, arrival_position = 0)

Arguments

location	(numeric) The location at which to calculate to run timing.
arrival	(data.frame) A data.frame of daily arrivals by proportion. See details.
parameters	(list) See positions for details.
arrival_position	(numeric) Defaults 0. Where to start movement.

Details

arrival should be a data.frame describing a set of daily arrivals of fish at arrival_position as a series of daily proportions. It should have a column day and a corresponding column proportion, which should sum to one.

Examples

timings(1000,
        data.frame(day=0:40, proportion = dnorm(-20:20, 0, 5)/sum(dnorm(-20:20, 0, 5))),
        list(rates = 50, distances = 1000))

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