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Style code and document #714

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Style code and document #714

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2 changes: 0 additions & 2 deletions .github/workflows/call-calc-coverage.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,6 @@ name: call-calc_coverage
# The default is to run the workflow on every push or pull request to every branch.
on:
workflow_dispatch:
push:
on: workflow_dispatch
paths-ignore:
- .devcontainer
- .github
Expand Down
154 changes: 38 additions & 116 deletions DESCRIPTION
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Expand Up @@ -2,122 +2,44 @@ Package: FIMS
Title: The Fisheries Integrated Modeling System
Version: 0.3.0.0
Authors@R: c(
person(
role = c("aut", "cre"),
family = "Johnson",
given = c("Kelli", "F."),
email = "[email protected]",
comment = c(ORCID = "0000-0002-5149-451X")
),
person(
role = "aut",
family = "Brodziak",
given = c("Jon", "K.", "T."),
comment = c(ORCID = "0000-0001-8690-5588")
),
person(
role = "aut",
family = "Doering",
given = c("Kathryn", "L."),
comment = c(ORCID = "0000-0002-0396-7044")
),
person(
role = "aut",
family = "Havron",
given = c("Andrea", "M."),
comment = c(ORCID = "0000-0002-4080-448X")
),
person(
role = "aut",
family = "Klasky",
given = c("Ronald"),
comment = c(ORCID = "0009-0004-7563-7716")
),
person(
role = "aut",
family = "Kuriyama",
given = c("Peter", "T."),
comment = c(ORCID = "0000-0002-6971-4015")
),
person(
role = "aut",
family = "Legault",
given = c("Christopher", "M."),
comment = c(ORCID = "0000-0002-0328-1376")
),
person(
role = "aut",
family = "Li",
given = "Bai",
comment = c(ORCID = "0000-0002-8249-1442")
),
person(
role = "aut",
family = "Miller",
given = c("Timothy", "J."),
comment = c(ORCID = "0000-0003-1411-1206")
),
person(
role = "aut",
family = "Monnahan",
given = c("Cole", "C."),
comment = c(ORCID = "0000-0003-0871-6700")
),
person(
role = "aut",
family = "Oshima",
given = c("Megumi", "C."),
comment = c(ORCID = "0009-0002-2239-1594")
),
person(
role = "aut",
family = "Shertzer",
given = c("Kyle", "W."),
comment = c(ORCID = "0000-0001-7196-5959")
),
person(
role = "aut",
family = "Stawitz",
given = c("Christine", "C."),
email = "[email protected]",
comment = c(ORCID = "0000-0003-3122-4501")
),
person(
role = "aut",
family = "Sullivan",
given = c("Jane", "Y."),
comment = c(ORCID = "0000-0002-8094-1673")
),
person(
role = "aut",
family = "Supernaw",
given = "Matthew",
comment = c(ORCID = "0009-0007-3681-7433")
),
person(
role = "aut",
family = "Taylor",
given = c("Ian", "G."),
comment = c(ORCID = "0000-0002-4232-5669")
),
person(
role = "aut",
family = "Vaughan",
given = c("Nathan", "R."),
comment = c(ORCID = "0009-0000-3054-6950")
),
person(
role = "ctb",
family = "Blackhart",
given = "Kristan",
comment = c(ORCID = "0000-0003-4232-2510")
),
person(
role = "ctb",
family = "Ianelli",
given = c("James", "N."),
comment = c(ORCID = "0000-0002-7170-8677")
)
person(c("Kelli", "F."), "Johnson", , "[email protected]", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-5149-451X")),
person(c("Jon", "K.", "T."), "Brodziak", role = "aut",
comment = c(ORCID = "0000-0001-8690-5588")),
person(c("Kathryn", "L."), "Doering", role = "aut",
comment = c(ORCID = "0000-0002-0396-7044")),
person(c("Andrea", "M."), "Havron", role = "aut",
comment = c(ORCID = "0000-0002-4080-448X")),
person("Ronald", "Klasky", role = "aut",
comment = c(ORCID = "0009-0004-7563-7716")),
person(c("Peter", "T."), "Kuriyama", role = "aut",
comment = c(ORCID = "0000-0002-6971-4015")),
person(c("Christopher", "M."), "Legault", role = "aut",
comment = c(ORCID = "0000-0002-0328-1376")),
person("Bai", "Li", role = "aut",
comment = c(ORCID = "0000-0002-8249-1442")),
person(c("Timothy", "J."), "Miller", role = "aut",
comment = c(ORCID = "0000-0003-1411-1206")),
person(c("Cole", "C."), "Monnahan", role = "aut",
comment = c(ORCID = "0000-0003-0871-6700")),
person(c("Megumi", "C."), "Oshima", role = "aut",
comment = c(ORCID = "0009-0002-2239-1594")),
person(c("Kyle", "W."), "Shertzer", role = "aut",
comment = c(ORCID = "0000-0001-7196-5959")),
person(c("Christine", "C."), "Stawitz", , "[email protected]", role = "aut",
comment = c(ORCID = "0000-0003-3122-4501")),
person(c("Jane", "Y."), "Sullivan", role = "aut",
comment = c(ORCID = "0000-0002-8094-1673")),
person("Matthew", "Supernaw", role = "aut",
comment = c(ORCID = "0009-0007-3681-7433")),
person(c("Ian", "G."), "Taylor", role = "aut",
comment = c(ORCID = "0000-0002-4232-5669")),
person(c("Nathan", "R."), "Vaughan", role = "aut",
comment = c(ORCID = "0009-0000-3054-6950")),
person("Kristan", "Blackhart", role = "ctb",
comment = c(ORCID = "0000-0003-4232-2510")),
person(c("James", "N."), "Ianelli", role = "ctb",
comment = c(ORCID = "0000-0002-7170-8677"))
)
Description: The Fisheries Integrated Modeling System is a next-generation
framework of stock assessment models, assisting fishery managers with
Expand Down
20 changes: 9 additions & 11 deletions R/create_default_parameters.R
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Original file line number Diff line number Diff line change
Expand Up @@ -344,8 +344,7 @@ create_default_fleet <- function(fleets,
dplyr::arrange(dplyr::desc(type)) |>
dplyr::pull(uncertainty)

index_distribution_default <- switch(
index_distribution,
index_distribution_default <- switch(index_distribution,
"DnormDistribution" = create_default_DnormDistribution(
value = index_uncertainty,
input_type = "data",
Expand All @@ -367,8 +366,8 @@ create_default_fleet <- function(fleets,
default <- list(c(
selectivity_default,
process_default,
index_distribution_default)
)
index_distribution_default
))

names(default) <- fleet_name
return(default)
Expand Down Expand Up @@ -523,7 +522,7 @@ create_default_DlnormDistribution <- function(
}

#' Create default recruitment parameters
#'#'
#'
#' @description
#' This function sets up default parameters for a recruitment module.
#'
Expand All @@ -541,7 +540,8 @@ create_default_DlnormDistribution <- function(
create_default_recruitment <- function(
recruitment,
data,
input_type = "BevertonHoltRecruitment") {
input_type = "BevertonHoltRecruitment"
) {
# Input checks
if (!is.list(recruitment)) {
cli::cli_abort(c(
Expand All @@ -554,8 +554,7 @@ create_default_recruitment <- function(
# NOTE: All new forms of recruitment must be placed in the vector of default
# arguments for `form` and their methods but be placed below in the call to
# `switch`
process_default <- switch(
form,
process_default <- switch(form,
"BevertonHoltRecruitment" = create_default_BevertonHoltRecruitment(data)
)
names(process_default) <- paste0(form, ".", names(process_default))
Expand All @@ -564,8 +563,7 @@ create_default_recruitment <- function(
distribution_input <- recruitment[["process_distribution"]]
distribution_default <- NULL
if (!is.null(distribution_input)) {
distribution_default <- switch(
distribution_input,
distribution_default <- switch(distribution_input,
"DnormDistribution" = create_default_DnormDistribution(
data = data,
input_type = "process"
Expand Down Expand Up @@ -614,7 +612,7 @@ update_parameters <- function(current_parameters, modified_parameters) {
# Check if current_parameters is a list with required components
if (
!is.list(current_parameters) ||
!all(c("parameters", "modules") %in% names(current_parameters))
!all(c("parameters", "modules") %in% names(current_parameters))
) {
cli::cli_abort(c(
"i" = "{.var current_parameters} argument must be a list containing
Expand Down
18 changes: 9 additions & 9 deletions R/distribution_formulas.R
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ check_distribution_validity <- function(args) {
}
if (
!(family[["family"]] %in% available_distributions) ||
"unavailable data type" %in% available_distributions
"unavailable data type" %in% available_distributions
) {
ifelse_type <- ifelse(
is.null(data_type),
Expand Down Expand Up @@ -120,7 +120,7 @@ check_distribution_validity <- function(args) {
}
if (
length(sd[["estimated"]]) > 1 &&
length(sd[["value"]]) != length(sd[["estimated"]])
length(sd[["value"]]) != length(sd[["estimated"]])
) {
sd_length <- length(sd[["value"]])
est_length <- length(sd[["estimated"]])
Expand Down Expand Up @@ -236,7 +236,7 @@ get_expected_name <- function(family, data_type) {
#' ),
#' data_type = "index"
#' )
#'
#'
#' # Set up a new process distribution
#' # Create a new recruitment module
#' recruitment <- methods::new(BevertonHoltRecruitment)
Expand All @@ -263,7 +263,7 @@ initialize_data_distribution <- function(
# FIXME: Make the available families a data object
# Could also make the matrix of distributions available per type as a
# data frame where the check could use the stored object.


# validity check on user input
args <- list(
Expand Down Expand Up @@ -303,7 +303,7 @@ initialize_data_distribution <- function(

# populate logged standard deviation parameter with log of input
new_module$log_sd$resize(length(sd[["value"]]))
for (i in seq_along(sd[["value"]])){
for (i in seq_along(sd[["value"]])) {
new_module$log_sd[i]$value <- log(sd[["value"]][i])
}

Expand All @@ -318,7 +318,7 @@ initialize_data_distribution <- function(
}

if (family[["family"]] == "multinomial") {
#create new Rcpp module
# create new Rcpp module
new_module <- methods::new(DmultinomDistribution)
}

Expand Down Expand Up @@ -366,7 +366,7 @@ initialize_process_distribution <- function(
log(sd[["value"]]),
length(sd[["value"]])
)
#setup whether or not sd parameter is estimated
# setup whether or not sd parameter is estimated
if (length(sd[["value"]]) > 1 && length(sd[["estimated"]]) == 1) {
new_module$log_sd$set_all_estimable(sd[["estimated"]])
} else {
Expand All @@ -382,11 +382,11 @@ initialize_process_distribution <- function(

# populate logged standard deviation parameter with log of input
new_module$log_sd$resize(length(sd[["value"]]))
for (i in seq_along(sd[["value"]])){
for (i in seq_along(sd[["value"]])) {
new_module$log_sd[i]$value <- log(sd[["value"]][i])
}

#setup whether or not sd parameter is estimated
# setup whether or not sd parameter is estimated
if (length(sd[["value"]]) > 1 && length(sd[["estimated"]]) == 1) {
new_module$log_sd$set_all_estimable(sd[["estimated"]])
} else {
Expand Down
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