tests/test-gadgetstock.R
In gadget-framework/rgadget: Tools to Create and Maintain Gadget Models
library(Rgadget)
library(unittest, quietly = TRUE)
library(magrittr)
ver_string <- paste("; Generated by Rgadget", utils::packageVersion("Rgadget"))
# Read all files in a directory
dir_list <- function (dir) {
files <- sort(list.files(dir, full.names = FALSE, recursive = TRUE), method = 'radix')
structure(
lapply(files, function (f) readLines(file.path(dir, f), n = -1)),
names = files
)
}
# Is vector (snippet) part of (full)?
part_of <- function(full, snippet) {
# If positions of each part of snippet make an ordered list from start
if (!is.na(match(snippet[[1]], full)) && identical(
match(snippet, full),
seq.int(match(snippet[[1]], full), along.with=snippet))) {
return(TRUE)
}
# Fall back to ut_cmp_identical, which will show some difference
ut_cmp_identical(full, snippet)
}
# Write string into temporary directory and read it back again as a gadget file
read.gadget.string <- function(..., file_type = "generic") {
dir <- tempfile()
dir.create(dir)
writeLines(c(...), con = file.path(dir, "wibble"))
read.gadget.file(dir, "wibble", file_type = file_type)
}
ok_group("Can create new stocks with some default content", {
path <- tempfile()
# MFDB data should look roughly like this
data <- structure(
data.frame(
year = 1998,
step = 1,
area = rep(c('A', 'B'), each = 4, times = 1),
age = rep(c('1', '9'), each = 1, times = 4),
length = rep(c('len100', 'len200'), each = 1, times = 4),
number = 10:17,
mean = 20:27,
stringsAsFactors = TRUE),
area = list(A = 1:3, B = 4:6),
length = list(
len100 = structure(call("seq", 100, 200 - 1), min = 100, max = 200),
len200 = structure(call("seq", 200, 300 - 1), min = 200, max = 300)))
gadgetstock('codimm', path, missingOkay = TRUE) %>% # Create a skeleton if missing
gadget_update('stock', minage = 2, maxage = 4) %>%
gadget_update('doeseat', maxconsumption = 100, halffeedingvalue = 70) %>%
gadget_update('doesrenew', number = data) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.rec.number" = c(
ver_string,
"; -- data --",
"; year\tstep\tarea\tage\tlength\tnumber\tweight",
"1998\t1\tA\t1\t100\t10\t20",
"1998\t1\tA\t9\t200\t11\t21",
"1998\t1\tA\t1\t100\t12\t22",
"1998\t1\tA\t9\t200\t13\t23",
"1998\t1\tB\t1\t100\t14\t24",
"1998\t1\tB\t9\t200\t15\t25",
"1998\t1\tB\t1\t100\t16\t26",
"1998\t1\tB\t9\t200\t17\t27",
NULL),
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t2",
"maxage\t4",
"minlength\t",
"maxlength\t",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t#codimm.M\t#codimm.M\t#codimm.M",
"iseaten\t0",
"doeseat\t1", "maxconsumption\t100", "halffeedingvalue\t70",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t1", "minlength\t100", "maxlength\t300", "dl\t100", "numberfile\tModelfiles/codimm.rec.number",
"doesspawn\t0", "doesstray\t0",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "Wrote out stock file")
gadgetstock('codimm', path, missingOkay = FALSE) %>%
gadget_update('stock', maxage = 6, minlength = 10, maxlength = 20) %>%
gadget_update('renewal', 0) %>% # Doesn't renew anymore, we use component name alias
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.rec.number" = c( # NB: We don't tidy up old files (yet)
ver_string,
"; -- data --",
"; year\tstep\tarea\tage\tlength\tnumber\tweight",
"1998\t1\tA\t1\t100\t10\t20",
"1998\t1\tA\t9\t200\t11\t21",
"1998\t1\tA\t1\t100\t12\t22",
"1998\t1\tA\t9\t200\t13\t23",
"1998\t1\tB\t1\t100\t14\t24",
"1998\t1\tB\t9\t200\t15\t25",
"1998\t1\tB\t1\t100\t16\t26",
"1998\t1\tB\t9\t200\t17\t27",
NULL),
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t2",
"maxage\t6",
"minlength\t10",
"maxlength\t20",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M", # NB: Now with extra defaults
"iseaten\t0",
"doeseat\t1", "maxconsumption\t100", "halffeedingvalue\t70",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0", "doesspawn\t0", "doesstray\t0",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "Updated existing stock file")
gadgetstock('codmat', path, missingOkay = TRUE) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.rec.number" = c(
ver_string,
"; -- data --",
"; year\tstep\tarea\tage\tlength\tnumber\tweight",
"1998\t1\tA\t1\t100\t10\t20",
"1998\t1\tA\t9\t200\t11\t21",
"1998\t1\tA\t1\t100\t12\t22",
"1998\t1\tA\t9\t200\t13\t23",
"1998\t1\tB\t1\t100\t14\t24",
"1998\t1\tB\t9\t200\t15\t25",
"1998\t1\tB\t1\t100\t16\t26",
"1998\t1\tB\t9\t200\t17\t27",
NULL),
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t2",
"maxage\t6",
"minlength\t10",
"maxlength\t20",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M",
"iseaten\t0",
"doeseat\t1", "maxconsumption\t100", "halffeedingvalue\t70",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0", "doesspawn\t0", "doesstray\t0",
NULL),
codmat = c(
ver_string,
"stockname\tcodmat",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t",
"maxlength\t",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codmat.Linf\t(* 0.001 #codmat.k)\t#codmat.walpha\t#codmat.wbeta", "beta\t(* 10 #codmat.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0", "doeseat\t0",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0", "doesspawn\t0", "doesstray\t0",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodmat\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "Added new stock file, left old one alone")
gadgetstock('codmat', path, missingOkay = TRUE) %>%
gadget_update('doesmigrate',
yearstepfile = gadgetfile('data/yearstepfile', components = list(
data.frame(year = 1998, step = 1:4, matrix = 'codmat-migration'))),
definematrices = gadgetfile('data/migratematrix', components = list(
migrationmatrix = list(name = 'codmat-migration'),
data.frame(1:4, 1:4, 1:4, 1:4)))) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.rec.number" = c(
ver_string,
"; -- data --",
"; year\tstep\tarea\tage\tlength\tnumber\tweight",
"1998\t1\tA\t1\t100\t10\t20",
"1998\t1\tA\t9\t200\t11\t21",
"1998\t1\tA\t1\t100\t12\t22",
"1998\t1\tA\t9\t200\t13\t23",
"1998\t1\tB\t1\t100\t14\t24",
"1998\t1\tB\t9\t200\t15\t25",
"1998\t1\tB\t1\t100\t16\t26",
"1998\t1\tB\t9\t200\t17\t27",
NULL),
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t2",
"maxage\t6",
"minlength\t10",
"maxlength\t20",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M",
"iseaten\t0",
"doeseat\t1", "maxconsumption\t100", "halffeedingvalue\t70",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0", "doesspawn\t0", "doesstray\t0",
NULL),
codmat = c(
ver_string,
"stockname\tcodmat",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t",
"maxlength\t",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codmat.Linf\t(* 0.001 #codmat.k)\t#codmat.walpha\t#codmat.wbeta", "beta\t(* 10 #codmat.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t1", "yearstepfile\tdata/yearstepfile", "definematrices\tdata/migratematrix",
"doesmature\t0", "doesmove\t0",
"doesrenew\t0", "doesspawn\t0", "doesstray\t0",
NULL),
"data/migratematrix" = c(
ver_string,
"[migrationmatrix]",
"name\tcodmat-migration",
"; -- data --",
"; X1.4\tX1.4.1\tX1.4.2\tX1.4.3",
"1\t1\t1\t1",
"2\t2\t2\t2",
"3\t3\t3\t3",
"4\t4\t4\t4",
NULL),
"data/yearstepfile" = c(
ver_string,
"; -- data --",
"; year\tstep\tmatrix",
"1998\t1\tcodmat-migration",
"1998\t2\tcodmat-migration",
"1998\t3\tcodmat-migration",
"1998\t4\tcodmat-migration",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodmat\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "Added new stock file, left old one alone")
})
ok_group("Can detect some GADGET errors", {
path <- tempfile()
s <- gadgetstock('codimm', path, missingOkay = TRUE)
ok(ut_cmp_error(
gadget_update(s, 'idontexist', minage = 2, maxage = 4),
"idontexist.*stock.*doesmigrate"), "Noticed bad stock name, suggested proper ones")
})
ok_group("Can populate naturalmortality", {
path <- tempfile()
gadgetstock('codimm', path, missingOkay = TRUE) %>% # Create a skeleton if missing
gadget_update('stock', minage = 2, maxage = 10) %>%
gadget_update('naturalmortality', c(0.5, 0.8)) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t2",
"maxage\t10",
"minlength\t",
"maxlength\t",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t0.5\t0.8\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0",
"doesspawn\t0", "doesstray\t0",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "naturalmortality as long as age-groups, values given at start")
})
ok_group("Doesgrow defaults", {
path <- tempfile()
gadgetstock('codimm', path, missingOkay = TRUE) %>% # Create a skeleton if missing
gadget_update('stock', minage = 2, maxage = 10) %>%
gadget_update('doesgrow', 1) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path)$codimm, c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t2",
"maxage\t10",
"minlength\t",
"maxlength\t",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1",
"growthfunction\tlengthvbsimple",
"growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta",
"beta\t(* 10 #codimm.bbin)",
"maxlengthgroupgrowth\t15",
"naturalmortality\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0",
"doesspawn\t0", "doesstray\t0",
NULL)
), "Default values for doesgrow filled in")
})
ok_group("Refweight from a data.frame", {
path <- tempfile()
gadgetstock('codimm', path, missingOkay = TRUE) %>% # Create a skeleton if missing
gadget_update('refweight', data = data.frame(length = c(2,4,6,8,10), weight = 11:15)) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.refwgt" = c(
ver_string,
"; -- data --",
"; length\tweight",
"2\t11", "4\t12", "6\t13", "8\t14", "10\t15",
NULL),
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t2",
"maxlength\t10",
"dl\t2",
"refweightfile\tModelfiles/codimm.refwgt",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0",
"doesspawn\t0", "doesstray\t0",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "refweight tables both create table and update min/max/dl")
gadgetstock('codimm', path, missingOkay = TRUE) %>% # Create a skeleton if missing
gadget_update('refweight', length = seq(10,28,3), alpha = 4, beta = 2) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.refwgt" = c(
ver_string,
"; -- data --",
"; length\tweight",
"10\t400", "13\t676", "16\t1024", "19\t1444", "22\t1936", "25\t2500", "28\t3136",
NULL),
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t10",
"maxlength\t28",
"dl\t3",
"refweightfile\tModelfiles/codimm.refwgt",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0",
"doesspawn\t0", "doesstray\t0",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "refweight tables can be derived from alpha/beta")
})
ok_group("Refweight from an MFDB data.frame", {
path <- tempfile()
# MFDB data should look roughly like this
data <- structure(
data.frame(
area = rep(c('A', 'B'), each = 4, times = 1),
length = rep(c('len100', 'len200'), each = 1, times = 4),
number = 10:17,
mean = 20:27,
stringsAsFactors = TRUE),
area = list(A = 1:3, B = 4:6),
length = list(
len100 = structure(call("seq", 100, 200 - 1), min = 100, max = 200),
len200 = structure(call("seq", 200, 300 - 1), min = 200, max = 300)))
gadgetstock('codimm', path, missingOkay = TRUE) %>% # Create a skeleton if missing
gadget_update('refweight', data = data) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.refwgt" = c(
ver_string,
"; -- data --",
"; length\tweight",
"100\t20", "100\t22", "100\t24", "100\t26", "200\t21", "200\t23", "200\t25", "200\t27",
NULL),
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t100",
"maxlength\t300",
"dl\t100",
"refweightfile\tModelfiles/codimm.refwgt",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0",
"doesspawn\t0", "doesstray\t0",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "refweight tables both create table and update min/max/dl, using attributes")
gadgetstock('codimm', path, missingOkay = TRUE) %>% # Create a skeleton if missing
gadget_update('refweight', length = seq(10,28,3), alpha = 4, beta = 2) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.refwgt" = c(
ver_string,
"; -- data --",
"; length\tweight",
"10\t400", "13\t676", "16\t1024", "19\t1444", "22\t1936", "25\t2500", "28\t3136",
NULL),
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t10",
"maxlength\t28",
"dl\t3",
"refweightfile\tModelfiles/codimm.refwgt",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0",
"doesspawn\t0", "doesstray\t0",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "refweight tables can be derived from alpha/beta")
})
ok_group("initialconditions from MFDB data.frame", {
path <- tempfile()
# MFDB data should look roughly like this
data <- structure(
data.frame(
area = rep(c('A', 'B'), each = 4, times = 1),
age = rep(c('age5', 'age10'), each = 2, times = 2),
length = rep(c('len100', 'len200'), each = 1, times = 4),
number = 10:17,
weight = 20:27,
stringsAsFactors = TRUE),
area = list(A = 1:3, B = 4:6),
age = list(age5 = c(5:9), age10 = c(10:15)),
length = list(
len100 = structure(call("seq", 100, 200 - 1), min = 100, max = 200),
len200 = structure(call("seq", 200, 300 - 1), min = 200, max = 300)))
gadgetstock('codimm', path, missingOkay = TRUE) %>%
gadget_update('initialconditions', number = data) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.init.number" = c(
ver_string,
"; -- data --",
"; age\tarea\tlength\tnumber\tweight",
"age5\tA\t100\t10\t20",
"age5\tA\t200\t11\t21",
"age10\tA\t100\t12\t22",
"age10\tA\t200\t13\t23",
"age5\tB\t100\t14\t24",
"age5\tB\t200\t15\t25",
"age10\tB\t100\t16\t26",
"age10\tB\t200\t17\t27",
NULL),
"codimm" = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t",
"maxlength\t",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1",
"growthfunction\tlengthvbsimple",
"growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta",
"beta\t(* 10 #codimm.bbin)",
"maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"minage\t5",
"maxage\t15",
"minlength\t100",
"maxlength\t300",
"dl\t100",
"numberfile\tModelfiles/codimm.init.number",
"doesmigrate\t0",
"doesmature\t0",
"doesmove\t0",
"doesrenew\t0",
"doesspawn\t0",
"doesstray\t0",
NULL),
"main" = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "Generate initialconditions from MFDB data")
})
ok_group("Generate maturation files", {
path <- tempfile()
gadgetstock('codimm', path, missingOkay = TRUE) %>% # Create a skeleton if missing
gadget_update(
'maturation',
maturityfunction = 'constant',
maturestocksandratios = c('codimm', 0.9, 'codmat', 0.1),
coefficients = c(0.24, 0.25, 0.15, 0.25)) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path)$codimm, c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t",
"maxlength\t",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1",
"growthfunction\tlengthvbsimple",
"growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta",
"beta\t(* 10 #codimm.bbin)",
"maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t0",
"doesmature\t1", "maturityfunction\tconstant", "maturityfile\tModelfiles/codimm.maturity",
"doesmove\t0",
"doesrenew\t0",
"doesspawn\t0", "doesstray\t0",
NULL)
), "Filled in doesmature")
ok(ut_cmp_identical(dir_list(path)[['Modelfiles/codimm.maturity']], c(
ver_string,
"maturestocksandratios\tcodimm\t0.9\tcodmat\t0.1",
"coefficients\t0.24\t0.25\t0.15\t0.25",
NULL)
), "Rest of parameters went into maturity file")
})
ok_group("Numeric recruitment from MFDB data.frame", {
path <- tempfile()
# MFDB data should look roughly like this
data <- structure(
data.frame(
year = 1998,
step = 'all',
area = rep(c('A', 'B'), each = 4, times = 1),
age = rep(c('age5', 'age10'), each = 2, times = 2),
length = rep(c('len100', 'len200'), each = 1, times = 4),
number = 10:17,
mean = 20:27,
stringsAsFactors = TRUE),
year = list("1998" = 1998),
step = list(all = 1:4),
area = list(A = 1:3, B = 4:6),
age = list(age5 = c(5:9), age10 = c(10:15)),
length = list(
len100 = structure(call("seq", 100, 200 - 1), min = 100, max = 200),
len200 = structure(call("seq", 200, 300 - 1), min = 200, max = 300)))
gadgetstock('codimm', path, missingOkay = TRUE) %>%
gadget_update('doesrenew', number = data) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.rec.number" = c(
ver_string,
"; -- data --",
"; year\tstep\tarea\tage\tlength\tnumber\tweight",
"1998\tall\tA\tage5\t100\t10\t20",
"1998\tall\tA\tage5\t200\t11\t21",
"1998\tall\tA\tage10\t100\t12\t22",
"1998\tall\tA\tage10\t200\t13\t23",
"1998\tall\tB\tage5\t100\t14\t24",
"1998\tall\tB\tage5\t200\t15\t25",
"1998\tall\tB\tage10\t100\t16\t26",
"1998\tall\tB\tage10\t200\t17\t27",
NULL),
"codimm" = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t",
"maxlength\t",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1",
"growthfunction\tlengthvbsimple",
"growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta",
"beta\t(* 10 #codimm.bbin)",
"maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t0",
"doesmature\t0",
"doesmove\t0",
"doesrenew\t1", "minlength\t100", "maxlength\t300", "dl\t100", "numberfile\tModelfiles/codimm.rec.number",
"doesspawn\t0",
"doesstray\t0",
NULL),
"main" = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "Generate recruitment from MFDB data")
})
ok_group("Multiple suitability functions", {
path <- tempfile()
gadgetstock('simple_stock', path, missingOkay = TRUE) %>%
gadget_update('doeseat',
suitability = list(
prey = list(type='function',suit_func = 'constant', alpha = 1),
otherfood = list(type='function',suit_func = 'constant', alpha = 1e5)),
preference = list(prey = 0.75,otherfood = 0.25),
maxconsumption = list(m0=1,m1=0,m2=0,m3=0,m4=0),
halffeedingvalue = 0.5) %>%
write.gadget.file(path)
ok(part_of(dir_list(path)$simple_stock, c(
"suitability",
"prey\tfunction\tconstant\t1",
"otherfood\tfunction\tconstant\t1e+05",
"preference\t0.75\t0.25",
"maxconsumption\t1\t0\t0\t0\t0",
"halffeedingvalue\t0.5")), "suitibility functions each in a sub-section")
})
gadget-framework/rgadget documentation built on July 20, 2022, 12:16 p.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library(Rgadget)
library(unittest, quietly = TRUE)
library(magrittr)
ver_string <- paste("; Generated by Rgadget", utils::packageVersion("Rgadget"))
# Read all files in a directory
dir_list <- function (dir) {
files <- sort(list.files(dir, full.names = FALSE, recursive = TRUE), method = 'radix')
structure(
lapply(files, function (f) readLines(file.path(dir, f), n = -1)),
names = files
)
}
# Is vector (snippet) part of (full)?
part_of <- function(full, snippet) {
# If positions of each part of snippet make an ordered list from start
if (!is.na(match(snippet[[1]], full)) && identical(
match(snippet, full),
seq.int(match(snippet[[1]], full), along.with=snippet))) {
return(TRUE)
}
# Fall back to ut_cmp_identical, which will show some difference
ut_cmp_identical(full, snippet)
}
# Write string into temporary directory and read it back again as a gadget file
read.gadget.string <- function(..., file_type = "generic") {
dir <- tempfile()
dir.create(dir)
writeLines(c(...), con = file.path(dir, "wibble"))
read.gadget.file(dir, "wibble", file_type = file_type)
}
ok_group("Can create new stocks with some default content", {
path <- tempfile()
# MFDB data should look roughly like this
data <- structure(
data.frame(
year = 1998,
step = 1,
area = rep(c('A', 'B'), each = 4, times = 1),
age = rep(c('1', '9'), each = 1, times = 4),
length = rep(c('len100', 'len200'), each = 1, times = 4),
number = 10:17,
mean = 20:27,
stringsAsFactors = TRUE),
area = list(A = 1:3, B = 4:6),
length = list(
len100 = structure(call("seq", 100, 200 - 1), min = 100, max = 200),
len200 = structure(call("seq", 200, 300 - 1), min = 200, max = 300)))
gadgetstock('codimm', path, missingOkay = TRUE) %>% # Create a skeleton if missing
gadget_update('stock', minage = 2, maxage = 4) %>%
gadget_update('doeseat', maxconsumption = 100, halffeedingvalue = 70) %>%
gadget_update('doesrenew', number = data) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.rec.number" = c(
ver_string,
"; -- data --",
"; year\tstep\tarea\tage\tlength\tnumber\tweight",
"1998\t1\tA\t1\t100\t10\t20",
"1998\t1\tA\t9\t200\t11\t21",
"1998\t1\tA\t1\t100\t12\t22",
"1998\t1\tA\t9\t200\t13\t23",
"1998\t1\tB\t1\t100\t14\t24",
"1998\t1\tB\t9\t200\t15\t25",
"1998\t1\tB\t1\t100\t16\t26",
"1998\t1\tB\t9\t200\t17\t27",
NULL),
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t2",
"maxage\t4",
"minlength\t",
"maxlength\t",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t#codimm.M\t#codimm.M\t#codimm.M",
"iseaten\t0",
"doeseat\t1", "maxconsumption\t100", "halffeedingvalue\t70",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t1", "minlength\t100", "maxlength\t300", "dl\t100", "numberfile\tModelfiles/codimm.rec.number",
"doesspawn\t0", "doesstray\t0",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "Wrote out stock file")
gadgetstock('codimm', path, missingOkay = FALSE) %>%
gadget_update('stock', maxage = 6, minlength = 10, maxlength = 20) %>%
gadget_update('renewal', 0) %>% # Doesn't renew anymore, we use component name alias
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.rec.number" = c( # NB: We don't tidy up old files (yet)
ver_string,
"; -- data --",
"; year\tstep\tarea\tage\tlength\tnumber\tweight",
"1998\t1\tA\t1\t100\t10\t20",
"1998\t1\tA\t9\t200\t11\t21",
"1998\t1\tA\t1\t100\t12\t22",
"1998\t1\tA\t9\t200\t13\t23",
"1998\t1\tB\t1\t100\t14\t24",
"1998\t1\tB\t9\t200\t15\t25",
"1998\t1\tB\t1\t100\t16\t26",
"1998\t1\tB\t9\t200\t17\t27",
NULL),
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t2",
"maxage\t6",
"minlength\t10",
"maxlength\t20",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M", # NB: Now with extra defaults
"iseaten\t0",
"doeseat\t1", "maxconsumption\t100", "halffeedingvalue\t70",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0", "doesspawn\t0", "doesstray\t0",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "Updated existing stock file")
gadgetstock('codmat', path, missingOkay = TRUE) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.rec.number" = c(
ver_string,
"; -- data --",
"; year\tstep\tarea\tage\tlength\tnumber\tweight",
"1998\t1\tA\t1\t100\t10\t20",
"1998\t1\tA\t9\t200\t11\t21",
"1998\t1\tA\t1\t100\t12\t22",
"1998\t1\tA\t9\t200\t13\t23",
"1998\t1\tB\t1\t100\t14\t24",
"1998\t1\tB\t9\t200\t15\t25",
"1998\t1\tB\t1\t100\t16\t26",
"1998\t1\tB\t9\t200\t17\t27",
NULL),
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t2",
"maxage\t6",
"minlength\t10",
"maxlength\t20",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M",
"iseaten\t0",
"doeseat\t1", "maxconsumption\t100", "halffeedingvalue\t70",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0", "doesspawn\t0", "doesstray\t0",
NULL),
codmat = c(
ver_string,
"stockname\tcodmat",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t",
"maxlength\t",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codmat.Linf\t(* 0.001 #codmat.k)\t#codmat.walpha\t#codmat.wbeta", "beta\t(* 10 #codmat.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0", "doeseat\t0",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0", "doesspawn\t0", "doesstray\t0",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodmat\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "Added new stock file, left old one alone")
gadgetstock('codmat', path, missingOkay = TRUE) %>%
gadget_update('doesmigrate',
yearstepfile = gadgetfile('data/yearstepfile', components = list(
data.frame(year = 1998, step = 1:4, matrix = 'codmat-migration'))),
definematrices = gadgetfile('data/migratematrix', components = list(
migrationmatrix = list(name = 'codmat-migration'),
data.frame(1:4, 1:4, 1:4, 1:4)))) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.rec.number" = c(
ver_string,
"; -- data --",
"; year\tstep\tarea\tage\tlength\tnumber\tweight",
"1998\t1\tA\t1\t100\t10\t20",
"1998\t1\tA\t9\t200\t11\t21",
"1998\t1\tA\t1\t100\t12\t22",
"1998\t1\tA\t9\t200\t13\t23",
"1998\t1\tB\t1\t100\t14\t24",
"1998\t1\tB\t9\t200\t15\t25",
"1998\t1\tB\t1\t100\t16\t26",
"1998\t1\tB\t9\t200\t17\t27",
NULL),
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t2",
"maxage\t6",
"minlength\t10",
"maxlength\t20",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M",
"iseaten\t0",
"doeseat\t1", "maxconsumption\t100", "halffeedingvalue\t70",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0", "doesspawn\t0", "doesstray\t0",
NULL),
codmat = c(
ver_string,
"stockname\tcodmat",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t",
"maxlength\t",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codmat.Linf\t(* 0.001 #codmat.k)\t#codmat.walpha\t#codmat.wbeta", "beta\t(* 10 #codmat.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t1", "yearstepfile\tdata/yearstepfile", "definematrices\tdata/migratematrix",
"doesmature\t0", "doesmove\t0",
"doesrenew\t0", "doesspawn\t0", "doesstray\t0",
NULL),
"data/migratematrix" = c(
ver_string,
"[migrationmatrix]",
"name\tcodmat-migration",
"; -- data --",
"; X1.4\tX1.4.1\tX1.4.2\tX1.4.3",
"1\t1\t1\t1",
"2\t2\t2\t2",
"3\t3\t3\t3",
"4\t4\t4\t4",
NULL),
"data/yearstepfile" = c(
ver_string,
"; -- data --",
"; year\tstep\tmatrix",
"1998\t1\tcodmat-migration",
"1998\t2\tcodmat-migration",
"1998\t3\tcodmat-migration",
"1998\t4\tcodmat-migration",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodmat\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "Added new stock file, left old one alone")
})
ok_group("Can detect some GADGET errors", {
path <- tempfile()
s <- gadgetstock('codimm', path, missingOkay = TRUE)
ok(ut_cmp_error(
gadget_update(s, 'idontexist', minage = 2, maxage = 4),
"idontexist.*stock.*doesmigrate"), "Noticed bad stock name, suggested proper ones")
})
ok_group("Can populate naturalmortality", {
path <- tempfile()
gadgetstock('codimm', path, missingOkay = TRUE) %>% # Create a skeleton if missing
gadget_update('stock', minage = 2, maxage = 10) %>%
gadget_update('naturalmortality', c(0.5, 0.8)) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t2",
"maxage\t10",
"minlength\t",
"maxlength\t",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t0.5\t0.8\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0",
"doesspawn\t0", "doesstray\t0",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "naturalmortality as long as age-groups, values given at start")
})
ok_group("Doesgrow defaults", {
path <- tempfile()
gadgetstock('codimm', path, missingOkay = TRUE) %>% # Create a skeleton if missing
gadget_update('stock', minage = 2, maxage = 10) %>%
gadget_update('doesgrow', 1) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path)$codimm, c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t2",
"maxage\t10",
"minlength\t",
"maxlength\t",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1",
"growthfunction\tlengthvbsimple",
"growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta",
"beta\t(* 10 #codimm.bbin)",
"maxlengthgroupgrowth\t15",
"naturalmortality\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M\t#codimm.M",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0",
"doesspawn\t0", "doesstray\t0",
NULL)
), "Default values for doesgrow filled in")
})
ok_group("Refweight from a data.frame", {
path <- tempfile()
gadgetstock('codimm', path, missingOkay = TRUE) %>% # Create a skeleton if missing
gadget_update('refweight', data = data.frame(length = c(2,4,6,8,10), weight = 11:15)) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.refwgt" = c(
ver_string,
"; -- data --",
"; length\tweight",
"2\t11", "4\t12", "6\t13", "8\t14", "10\t15",
NULL),
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t2",
"maxlength\t10",
"dl\t2",
"refweightfile\tModelfiles/codimm.refwgt",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0",
"doesspawn\t0", "doesstray\t0",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "refweight tables both create table and update min/max/dl")
gadgetstock('codimm', path, missingOkay = TRUE) %>% # Create a skeleton if missing
gadget_update('refweight', length = seq(10,28,3), alpha = 4, beta = 2) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.refwgt" = c(
ver_string,
"; -- data --",
"; length\tweight",
"10\t400", "13\t676", "16\t1024", "19\t1444", "22\t1936", "25\t2500", "28\t3136",
NULL),
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t10",
"maxlength\t28",
"dl\t3",
"refweightfile\tModelfiles/codimm.refwgt",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0",
"doesspawn\t0", "doesstray\t0",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "refweight tables can be derived from alpha/beta")
})
ok_group("Refweight from an MFDB data.frame", {
path <- tempfile()
# MFDB data should look roughly like this
data <- structure(
data.frame(
area = rep(c('A', 'B'), each = 4, times = 1),
length = rep(c('len100', 'len200'), each = 1, times = 4),
number = 10:17,
mean = 20:27,
stringsAsFactors = TRUE),
area = list(A = 1:3, B = 4:6),
length = list(
len100 = structure(call("seq", 100, 200 - 1), min = 100, max = 200),
len200 = structure(call("seq", 200, 300 - 1), min = 200, max = 300)))
gadgetstock('codimm', path, missingOkay = TRUE) %>% # Create a skeleton if missing
gadget_update('refweight', data = data) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.refwgt" = c(
ver_string,
"; -- data --",
"; length\tweight",
"100\t20", "100\t22", "100\t24", "100\t26", "200\t21", "200\t23", "200\t25", "200\t27",
NULL),
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t100",
"maxlength\t300",
"dl\t100",
"refweightfile\tModelfiles/codimm.refwgt",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0",
"doesspawn\t0", "doesstray\t0",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "refweight tables both create table and update min/max/dl, using attributes")
gadgetstock('codimm', path, missingOkay = TRUE) %>% # Create a skeleton if missing
gadget_update('refweight', length = seq(10,28,3), alpha = 4, beta = 2) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.refwgt" = c(
ver_string,
"; -- data --",
"; length\tweight",
"10\t400", "13\t676", "16\t1024", "19\t1444", "22\t1936", "25\t2500", "28\t3136",
NULL),
codimm = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t10",
"maxlength\t28",
"dl\t3",
"refweightfile\tModelfiles/codimm.refwgt",
"growthandeatlengths\t",
"doesgrow\t1", "growthfunction\tlengthvbsimple", "growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta", "beta\t(* 10 #codimm.bbin)", "maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t0", "doesmature\t0", "doesmove\t0",
"doesrenew\t0",
"doesspawn\t0", "doesstray\t0",
NULL),
main = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "refweight tables can be derived from alpha/beta")
})
ok_group("initialconditions from MFDB data.frame", {
path <- tempfile()
# MFDB data should look roughly like this
data <- structure(
data.frame(
area = rep(c('A', 'B'), each = 4, times = 1),
age = rep(c('age5', 'age10'), each = 2, times = 2),
length = rep(c('len100', 'len200'), each = 1, times = 4),
number = 10:17,
weight = 20:27,
stringsAsFactors = TRUE),
area = list(A = 1:3, B = 4:6),
age = list(age5 = c(5:9), age10 = c(10:15)),
length = list(
len100 = structure(call("seq", 100, 200 - 1), min = 100, max = 200),
len200 = structure(call("seq", 200, 300 - 1), min = 200, max = 300)))
gadgetstock('codimm', path, missingOkay = TRUE) %>%
gadget_update('initialconditions', number = data) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.init.number" = c(
ver_string,
"; -- data --",
"; age\tarea\tlength\tnumber\tweight",
"age5\tA\t100\t10\t20",
"age5\tA\t200\t11\t21",
"age10\tA\t100\t12\t22",
"age10\tA\t200\t13\t23",
"age5\tB\t100\t14\t24",
"age5\tB\t200\t15\t25",
"age10\tB\t100\t16\t26",
"age10\tB\t200\t17\t27",
NULL),
"codimm" = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t",
"maxlength\t",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1",
"growthfunction\tlengthvbsimple",
"growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta",
"beta\t(* 10 #codimm.bbin)",
"maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"minage\t5",
"maxage\t15",
"minlength\t100",
"maxlength\t300",
"dl\t100",
"numberfile\tModelfiles/codimm.init.number",
"doesmigrate\t0",
"doesmature\t0",
"doesmove\t0",
"doesrenew\t0",
"doesspawn\t0",
"doesstray\t0",
NULL),
"main" = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "Generate initialconditions from MFDB data")
})
ok_group("Generate maturation files", {
path <- tempfile()
gadgetstock('codimm', path, missingOkay = TRUE) %>% # Create a skeleton if missing
gadget_update(
'maturation',
maturityfunction = 'constant',
maturestocksandratios = c('codimm', 0.9, 'codmat', 0.1),
coefficients = c(0.24, 0.25, 0.15, 0.25)) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path)$codimm, c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t",
"maxlength\t",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1",
"growthfunction\tlengthvbsimple",
"growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta",
"beta\t(* 10 #codimm.bbin)",
"maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t0",
"doesmature\t1", "maturityfunction\tconstant", "maturityfile\tModelfiles/codimm.maturity",
"doesmove\t0",
"doesrenew\t0",
"doesspawn\t0", "doesstray\t0",
NULL)
), "Filled in doesmature")
ok(ut_cmp_identical(dir_list(path)[['Modelfiles/codimm.maturity']], c(
ver_string,
"maturestocksandratios\tcodimm\t0.9\tcodmat\t0.1",
"coefficients\t0.24\t0.25\t0.15\t0.25",
NULL)
), "Rest of parameters went into maturity file")
})
ok_group("Numeric recruitment from MFDB data.frame", {
path <- tempfile()
# MFDB data should look roughly like this
data <- structure(
data.frame(
year = 1998,
step = 'all',
area = rep(c('A', 'B'), each = 4, times = 1),
age = rep(c('age5', 'age10'), each = 2, times = 2),
length = rep(c('len100', 'len200'), each = 1, times = 4),
number = 10:17,
mean = 20:27,
stringsAsFactors = TRUE),
year = list("1998" = 1998),
step = list(all = 1:4),
area = list(A = 1:3, B = 4:6),
age = list(age5 = c(5:9), age10 = c(10:15)),
length = list(
len100 = structure(call("seq", 100, 200 - 1), min = 100, max = 200),
len200 = structure(call("seq", 200, 300 - 1), min = 200, max = 300)))
gadgetstock('codimm', path, missingOkay = TRUE) %>%
gadget_update('doesrenew', number = data) %>%
write.gadget.file(path)
ok(ut_cmp_identical(dir_list(path), list(
"Modelfiles/codimm.rec.number" = c(
ver_string,
"; -- data --",
"; year\tstep\tarea\tage\tlength\tnumber\tweight",
"1998\tall\tA\tage5\t100\t10\t20",
"1998\tall\tA\tage5\t200\t11\t21",
"1998\tall\tA\tage10\t100\t12\t22",
"1998\tall\tA\tage10\t200\t13\t23",
"1998\tall\tB\tage5\t100\t14\t24",
"1998\tall\tB\tage5\t200\t15\t25",
"1998\tall\tB\tage10\t100\t16\t26",
"1998\tall\tB\tage10\t200\t17\t27",
NULL),
"codimm" = c(
ver_string,
"stockname\tcodimm",
"livesonareas\t",
"minage\t",
"maxage\t",
"minlength\t",
"maxlength\t",
"dl\t",
"refweightfile\t",
"growthandeatlengths\t",
"doesgrow\t1",
"growthfunction\tlengthvbsimple",
"growthparameters\t#codimm.Linf\t(* 0.001 #codimm.k)\t#codimm.walpha\t#codimm.wbeta",
"beta\t(* 10 #codimm.bbin)",
"maxlengthgroupgrowth\t15",
"naturalmortality\t",
"iseaten\t0",
"doeseat\t0",
"initialconditions",
"doesmigrate\t0",
"doesmature\t0",
"doesmove\t0",
"doesrenew\t1", "minlength\t100", "maxlength\t300", "dl\t100", "numberfile\tModelfiles/codimm.rec.number",
"doesspawn\t0",
"doesstray\t0",
NULL),
"main" = c(
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tcodimm",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL)
)), "Generate recruitment from MFDB data")
})
ok_group("Multiple suitability functions", {
path <- tempfile()
gadgetstock('simple_stock', path, missingOkay = TRUE) %>%
gadget_update('doeseat',
suitability = list(
prey = list(type='function',suit_func = 'constant', alpha = 1),
otherfood = list(type='function',suit_func = 'constant', alpha = 1e5)),
preference = list(prey = 0.75,otherfood = 0.25),
maxconsumption = list(m0=1,m1=0,m2=0,m3=0,m4=0),
halffeedingvalue = 0.5) %>%
write.gadget.file(path)
ok(part_of(dir_list(path)$simple_stock, c(
"suitability",
"prey\tfunction\tconstant\t1",
"otherfood\tfunction\tconstant\t1e+05",
"preference\t0.75\t0.25",
"maxconsumption\t1\t0\t0\t0\t0",
"halffeedingvalue\t0.5")), "suitibility functions each in a sub-section")
})
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