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Update vignettes #67

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9de4ed2
Added Anchovy Bay data set
Dec 6, 2021
4cb0461
Added R Ecosystem
Dec 6, 2021
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2 changes: 2 additions & 0 deletions DESCRIPTION
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Expand Up @@ -30,3 +30,5 @@ VignetteBuilder: knitr
RoxygenNote: 7.1.1
URL: https://github.com/NOAA-EDAB/Rpath
BugReports: https://github.com/NOAA-EDAB/Rpath/issues
Depends:
R (>= 2.10)
40 changes: 40 additions & 0 deletions R/Data.R
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#' Rpath parameter set for the fictitious Anchovy Bay
#'
#' This is a parameter set for the example fictitious ecosystem of Anchovy Bay.
#' Anchovy Bay is used as an introduction to Ecopath with Ecosim.
#'
#' @format An Rpath.params object
#' @family rpathParameters
#'
#' \describe{
#'\item{model}{Main model parameters including Biomass, PB, QB, EE, etc.}
#'\item{diet}{Diet composition matrix with predators as columns and prey as rows}
#'\item{stanzas}{List object containing necessary parameters for multistanza groups.
#' Note that Anchovy Bay does not have any multistanza groups.}
#'\item{pedigree}{Matrix of certainty surrounding parameter values. Defaulted to 1
#' for this fictitious system.}
#'
#' }
#'
#'
"AB.params"

#' Rpath parameter set for the fictitious R Ecosystem
#'
#' This is a parameter set for the example fictitious ecosystem of R Ecosystem.
#' R Ecosystem is used as an introduction to Rpath.
#'
#' @format An Rpath.params object
#' @family rpathParameters
#'
#' \describe{
#'\item{model}{Main model parameters including Biomass, PB, QB, EE, etc.}
#'\item{diet}{Diet composition matrix with predators as columns and prey as rows}
#'\item{stanzas}{List object containing necessary parameters for multistanza groups}
#'\item{pedigree}{Matrix of certainty surrounding parameter values. Defaulted to 1
#' for this fictitious system.}
#'
#' }
#'
#'
"REco.params"
60 changes: 60 additions & 0 deletions data_raw/Ancovy_Bay.R
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#Anchovy Bay
#SML

#Required packages
library(data.table); library(Rpath); library(here)

#Anchovy Bay----
groups <- c('whales', 'seals', 'cod', 'whiting', 'mackerel', 'anchovy', 'shrimp',
'benthos', 'zooplankton', 'phytoplankton', 'detritus', 'sealers',
'trawlers', 'seiners', 'bait boats', 'shrimpers')

types <- c(rep(0, 9), 1, 2, rep(3, 5))

AB.params <- create.rpath.params(groups, types)

#Biomass, Production, consumption
biomass <- c(0.08, 0.0609, 3, 1.8, 1.2, 7, 0.8, NA, 14.8, 9, 10, rep(NA, 5))

pb <- c(0.05, 0.164, 0.340, 0.581, 0.723, 1.140, 3, 3, 35, 240, rep(NA, 6))

qb <- c(9, 15, 2.58, 3.3, 4.4, 9.13, rep(NA, 10))

AB.params$model[, Biomass := biomass]
AB.params$model[, PB := pb]
AB.params$model[, QB := qb]

AB.params$model[Group == 'shrimp', ProdCons := 0.25]
AB.params$model[Group == 'benthos', ProdCons := 0.25]
AB.params$model[Group == 'zooplankton', ProdCons := 0.25]

#Add EE's for unknown biomasses
AB.params$model[Group == 'benthos', EE := 0.6]
#Biomass accumulation and unassimilated production
AB.params$model[, BioAcc := c(rep(0, 11), rep(NA, 5))]
AB.params$model[, Unassim := c(rep(0.2, 9), rep(0, 2), rep(NA, 5))]

#Detrital fate
AB.params$model[, detritus := c(rep(1, 10), rep(0, 6))]

#Landings/Discards
AB.params$model[Group == 'seals', sealers := .0045]
AB.params$model[Group == 'cod', trawlers := 0.45]
AB.params$model[Group == 'whiting', trawlers := 0.2]
AB.params$model[Group == 'mackerel', seiners := 0.4]
AB.params$model[Group == 'anchovy', seiners := 1.2]
AB.params$model[Group == 'anchovy', "bait boats" := 0.2]
AB.params$model[Group == 'shrimp', shrimpers := 0.05]

#Diet
AB.params$diet[, whales := c(rep(NA, 2), 0.1, 0.1, 0.2, 0.5, NA, 0.1, rep(NA, 4))]
AB.params$diet[, seals := c(NA, NA, 0.04, 0.05, NA, NA, 0.01, 0.9, rep(NA, 4))]
AB.params$diet[, cod := c(NA, NA, NA, 0.05, NA, 0.1, 0.01, 0.84, rep(NA, 4))]
AB.params$diet[, whiting := c(NA, NA, 0.05, 0.05, NA, 0.45, 0.01, 0.44, rep(NA, 4))]
AB.params$diet[, mackerel := c(rep(NA, 4), 0.05, 0.5, NA, NA, 0.45, rep(NA, 3))]
AB.params$diet[, anchovy := c(rep(NA, 8), 1, rep(NA, 3))]
AB.params$diet[, shrimp := c(rep(NA, 7), 1, rep(NA, 4))]
AB.params$diet[, benthos := c(rep(NA, 7), 0.1, 0.1, 0.1, 0.7, NA)]
AB.params$diet[, zooplankton := c(rep(NA, 9), 0.9, 0.1, NA)]

usethis::use_data(AB.params, overwrite = T)
135 changes: 135 additions & 0 deletions data_raw/REcosystem.R
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#R Ecosystem
#Tutorial ecosystem for teaching Rpath

library(Rpath); library(data.table); library(here)

#Groups and types for the R Ecosystem----

groups <- c('Seabirds', 'Whales', 'Seals', 'JuvRoundfish1', 'AduRoundfish1',
'JuvRoundfish2', 'AduRoundfish2', 'JuvFlatfish1', 'AduFlatfish1',
'JuvFlatfish2', 'AduFlatfish2', 'OtherGroundfish', 'Foragefish1',
'Foragefish2', 'OtherForagefish', 'Megabenthos', 'Shellfish',
'Macrobenthos', 'Zooplankton', 'Phytoplankton', 'Detritus',
'Discards', 'Trawlers', 'Midwater', 'Dredgers')
stgroups <- c(rep(NA, 3), rep('Roundfish1', 2), rep('Roundfish2', 2),
rep('Flatfish1', 2), rep('Flatfish2', 2), rep(NA, 14))

types <- c(rep(0, 19), 1, rep(2, 2), rep(3, 3))

#Model----
#Create Model File
REco.params <- create.rpath.params(group = groups, type = types, stgroup = stgroups)

biomass <- c(0.0149, 0.454, NA, NA, 1.39, NA, 5.553, NA, 5.766, NA,
0.739, 7.4, 5.1, 4.7, 5.1, NA, 7, 17.4, 23, 10, rep(NA, 5))

pb <- c(0.098, 0.031, 0.100, 2.026, 0.42, 2.1, 0.425, 1.5, 0.26, 1.1, 0.18, 0.6,
0.61, 0.65, 1.5, 0.9, 1.3, 7, 39, 240, rep(NA, 5))

qb <- c(76.750, 6.976, 34.455, NA, 2.19, NA, 3.78, NA, 1.44, NA, 1.69,
1.764, 3.52, 5.65, 3.6, 2.984, rep (NA, 9))

REco.params$model[, Biomass := biomass]
REco.params$model[, PB := pb]
REco.params$model[, QB := qb]

#EE for groups w/o biomass
REco.params$model[Group %in% c('Seals', 'Megabenthos'), EE := 0.8]

#Production to Consumption for those groups without a QB
REco.params$model[Group %in% c('Shellfish', 'Zooplankton'), ProdCons:= 0.25]
REco.params$model[Group == 'Macrobenthos', ProdCons := 0.35]

#Biomass accumulation and unassimilated production
REco.params$model[, BioAcc := c(rep(0, 22), rep(NA, 3))]
REco.params$model[, Unassim := c(rep(0.2, 18), 0.4, rep(0, 3), rep(NA, 3))]

#Detrital Fate
REco.params$model[, Detritus := c(rep(1, 20), rep(0, 5))]
REco.params$model[, Discards := c(rep(0, 22), rep(1, 3))]

#Fisheries
#Landings
trawl <- c(rep(0, 4), 0.08, 0, 0.32, 0, 0.09, 0, 0.05, 0.2, rep(0, 10), rep(NA, 3))
mid <- c(rep(0, 12), 0.3, 0.08, 0.02, rep(0, 7), rep(NA, 3))
dredge <- c(rep(0, 15), 0.1, 0.5, rep(0, 5), rep(NA, 3))
REco.params$model[, Trawlers := trawl]
REco.params$model[, Midwater := mid]
REco.params$model[, Dredgers := dredge]

#Discards
trawl.d <- c(1e-5, 1e-7, 0.001, 0.001, 0.005, 0.001, 0.009, 0.001, 0.04, 0.001,
0.01, 0.08, 0.001, 0.001, 0.001, rep(0, 7), rep(NA, 3))
mid.d <- c(rep(0, 2), 0.001, 0.001, 0.01, 0.001, 0.01, rep(0, 4), 0.05, 0.05,
0.01, 0.01, rep(0, 7), rep(NA, 3))
dredge.d <- c(rep(0, 3), 0.001, 0.05, 0.001, 0.05, 0.001, 0.05, 0.001, 0.01, 0.05,
rep(0, 3), 0.09, 0.01, 1e-4, rep(0, 4), rep(NA, 3))
REco.params$model[, Trawlers.disc := trawl.d]
REco.params$model[, Midwater.disc := mid.d]
REco.params$model[, Dredgers.disc := dredge.d]

#Stanzas----
#Calculate the multistanza biomass/consumption
#Group parameters
REco.params$stanzas$stgroups[, VBGF_Ksp := c(0.145, 0.295, 0.0761, 0.112)]
#REco.params$stanzas$stgroups[, Wmat := c(0.0769, 0.561, 0.117, 0.321)]
REco.params$stanzas$stgroups[, Wmat := c(0.0577, 0.421, 0.088, 0.241)]


#Individual stanza parameters
REco.params$stanzas$stindiv[, First := c(rep(c(0, 24), 3), 0, 48)]
REco.params$stanzas$stindiv[, Last := c(rep(c(23, 400), 3), 47, 400)]
REco.params$stanzas$stindiv[, Z := c(2.026, 0.42, 2.1, 0.425, 1.5,
0.26, 1.1, 0.18)]
REco.params$stanzas$stindiv[, Leading := rep(c(F, T), 4)]

REco.params <- rpath.stanzas(REco.params)

#Diet File----
REco.params$diet[, Seabirds := c(rep(NA, 11), 0.1, 0.25, 0.2, 0.15,
rep(NA, 6), 0.3, NA)]
REco.params$diet[, Whales := c(rep(NA, 3), 0.01, NA, 0.01, NA, 0.01,
NA, 0.01, rep(NA, 4), 0.1, rep(NA, 3),
0.86, rep(NA, 4))]
REco.params$diet[, Seals := c(rep(NA, 3), 0.05, 0.1, 0.05, 0.2, 0.005,
0.05, 0.005, 0.01, 0.24, rep(0.05, 4),
0.09, rep(NA, 6))]
REco.params$diet[, JuvRoundfish1 := c(rep(NA, 3), rep(c(1e-4, NA), 4), 1e-3,
rep(NA, 2), 0.05, 1e-4, NA, .02, 0.7785,
0.1, 0.05, NA, NA)]
REco.params$diet[, AduRoundfish1 := c(rep(NA, 5), 1e-3, 0.01, 1e-3, 0.05, 1e-3,
0.01, 0.29, 0.1, 0.1, 0.347, 0.03, NA,
0.05, 0.01, rep(NA, 4))]
REco.params$diet[, JuvRoundfish2 := c(rep(NA, 3), rep(c(1e-4, NA), 4), 1e-3,
rep(NA, 2), 0.05, 1e-4, NA, .02, 0.7785,
0.1, .05, NA, NA)]
REco.params$diet[, AduRoundfish2 := c(rep(NA, 3), 1e-4, NA, 1e-4, NA, rep(1e-4, 4),
0.1, rep(0.05, 3), 0.2684, 0.01, 0.37, 0.001,
NA, 0.1, NA, NA)]
REco.params$diet[, JuvFlatfish1 := c(rep(NA, 3), rep(c(1e-4, NA), 4), rep(NA, 3),
rep(1e-4, 2), NA, 0.416, 0.4334, 0.1, 0.05,
NA, NA)]
REco.params$diet[, AduFlatfish1 := c(rep(NA, 7), rep(1e-4, 5), rep(NA, 2), 0.001,
0.05, 0.001, 0.6, 0.2475, NA, 0.1, NA, NA)]
REco.params$diet[, JuvFlatfish2 := c(rep(NA, 3), rep(c(1e-4, NA), 4), rep(NA, 3),
rep(1e-4, 2), NA, 0.416, 0.4334, 0.1, 0.05,
NA, NA)]
REco.params$diet[, AduFlatfish2 := c(rep(NA, 7), 1e-4, NA, 1e-4, rep(NA, 4),
rep(1e-4, 3), 0.44, 0.3895, NA, 0.17,
NA, NA)]
REco.params$diet[, OtherGroundfish := c(rep(NA, 3), rep(1e-4, 8), 0.05, 0.08, 0.0992,
0.3, 0.15, 0.01, 0.3, 0.01, rep(NA, 4))]
REco.params$diet[, Foragefish1 := c(rep(NA, 3), rep(c(1e-4, NA), 4), rep(NA, 7),
0.8196, 0.06, 0.12, NA, NA)]
REco.params$diet[, Foragefish2 := c(rep(NA, 3), rep(c(1e-4, NA), 4), rep(NA, 7),
0.8196, 0.06, 0.12, NA, NA)]
REco.params$diet[, OtherForagefish := c(rep(NA, 3), rep(c(1e-4, NA), 4), rep(NA, 7),
0.8196, 0.06, 0.12, NA, NA)]
REco.params$diet[, Megabenthos := c(rep(NA, 15), 0.1, 0.03, 0.55, rep(NA, 2), 0.32,
NA, NA)]
REco.params$diet[, Shellfish := c(rep(NA, 18), 0.3, 0.5, 0.2, NA, NA)]
REco.params$diet[, Macrobenthos := c(rep(NA, 16), 0.01, rep(0.2, 2), NA, 0.59,
NA, NA)]
REco.params$diet[, Zooplankton := c(rep(NA, 18), 0.2, 0.6, 0.2, NA, NA)]

usethis::use_data(REco.params, overwrite = T)
5 changes: 5 additions & 0 deletions src/RcppExports.cpp
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using namespace Rcpp;

#ifdef RCPP_USE_GLOBAL_ROSTREAM
Rcpp::Rostream<true>& Rcpp::Rcout = Rcpp::Rcpp_cout_get();
Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
#endif

// rk4_run
List rk4_run(List params, List instate, List forcing, List fishing, List stanzas, int StartYear, int EndYear);
RcppExport SEXP _Rpath_rk4_run(SEXP paramsSEXP, SEXP instateSEXP, SEXP forcingSEXP, SEXP fishingSEXP, SEXP stanzasSEXP, SEXP StartYearSEXP, SEXP EndYearSEXP) {
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