Description Usage Arguments SpawningProb EggCount AgeDist SurvivalProb CreateSPDataframe Note
spopmodel
requires specific inputs to operate. In the
absence of such inputs, functions herein can generate dataframes to
satisfy model requirements. If such data already exists, however, then
it's best to use those data. NOTE: Functions herein default for use with
San Francisco Estuary-based White Sturgeon. So do keep that in mind when
employing these functions.
Uses glm
to predict spawning probability
based on probability of maturity at length i. Spawning probability
is then adjusted for fraction of females spawning annually.
Uses lm
to predict number of eggs given
length i.
Uses age frequency to provide by age (1) estimated
abundance & (2) estimated abundance of females. Uses arguments supplied
to abund
& fracFemale
to achieve this.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | SpawningProb(pMat = NULL, len, age, mature = 0.15)
EggCount(numEggs = NULL, len, age)
AgeDist(ageFreq, abund = 48000, fracFemale = 0.5)
SurvivalProb(
...,
mu = 0.01,
agesMu = 10:15,
estS = 0.8132,
estMu = 0.1364,
methodSB = TRUE
)
CreateSPDataframe(ages, sRate, sRateErr)
|
pMat |
A dataframe with two fields: length & probability of maturity
for each length. Default uses internal |
len |
Numeric vector of lengths supplied as new data to |
age |
Numeric vector of ages, where each age is appropriate for given
length supplied in |
mature |
Fraction of females spawning in a given year. Default 0.15. |
numEggs |
A dataframe with two fields: length & number of eggs.
for each length. Default uses internal |
ageFreq |
A numeric vector of age frequency (like that derived from age-length key or direct ageing). |
abund |
A numeric scalar given estimated overall abundance for species being modeled. Default 48,000 (as estimated by CDFW). |
fracFemale |
A numerice scalar given fraction of females in population. Default 0.5 from Chapman et al. 1996. |
... |
Passed to internal function |
mu |
A numeric vector giving exploitation (harvest rate; between 0 and 1). Default 0.01. |
agesMu |
A numeric vector of ages on which exploitation applies (i.e., age group subject to harvest). Default 10:15. |
estS |
A numeric scalar given estimated survival rate of (typically)
adult fish. Derived using |
estMu |
A numeric scalar given estimated exploitation rate of
harvestable fish. Derived using |
methodSB |
Logical. Default (TRUE) denotes using S. Blackburn method to
calculate |
ages |
A numeric vector of ages (e.g., 0:19). |
sRate |
A numeric vector giving survival rate (between 0 and 1). |
sRateErr |
A numeric vector given standard error of |
SpawningProb
NA
EggCount
NA
AgeDist
NA
SurvivalProb
NA
CreateSPDataframe
NA
Ideally ages
vector supplied from age distribution data (e.g.,
age_dist
). Vector should contain age-0 sequentially through oldest
age. sRate
and sRateErr
need not match ages
in
length, just not longer. If less than, the last value (e.g.,
sRate[length(sRate)]
is repeated to complete the dataframe.
sRate[length(sRate)]
must be S0, that is survival rate considering
only natural mortality.
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