Nothing
demo/inttest-stockfile.R
In mfdb: MareFrame DB Querying Library
# This script demonstrates creating stock files
#
# ok and ok_group are there so we can run this code and verify it is correct,
# and not needed every-day use.
#
# NB: if you want to run this, you must be using mfdb-workspace, also be warned
# any data stored in your database will be destroyed.
library(unittest)
library(mfdb)
source('tests/utils/helpers.R')
source('tests/utils/inttest-helpers.R')
# Empty database & rebuild
if (exists("mdb")) mfdb_disconnect(mdb)
mfdb(gsub("inttest", "inttest-stockfile", Sys.getenv('INTTEST_SCHEMA', 'inttest')), db_params = db_params, destroy_schema = TRUE)
mdb <- mfdb(gsub("inttest", "inttest-stockfile", Sys.getenv('INTTEST_SCHEMA', 'inttest')), db_params = db_params, save_temp_tables = FALSE)
# Set-up areas/divisions
mfdb_import_area(mdb, data.frame(
name = c('45G01', '45G02', '45G03'),
division = c('divA', 'divA', 'divB'),
size = c(10,200,400)))
ok_group("Stockfile example", {
# Create a temporary gadget directory
gd <- gadget_directory(tempfile())
# Import a survey for the data we are interested in
mfdb_import_survey(mdb, data_source = "cod2000",
table_string("
year month areacell species maturity_stage length age weight
2000 1 45G01 COD 1 21 2 210
2000 1 45G01 COD 5 34 3 220
2000 1 45G01 COD 5 34 3 230
2000 1 45G01 COD 5 62 1 320
2000 1 45G01 COD 5 53 1 330
2000 1 45G01 COD 5 54 2 430
2000 1 45G01 COD 1 28 2 210
2000 1 45G01 COD 5 34 3 220
2000 1 45G01 COD 1 24 3 230
2000 1 45G01 COD 1 12 1 320
2000 1 45G01 COD 5 44 1 330
2000 1 45G01 COD 1 14 2 430
"))
# Query min/max age, and average weight for our length groups (Immature cod)
imm_data <- mfdb_sample_meanweight(mdb, c('age', 'length'), list(
age = NULL, # This means the age column will have "all", but aggfile will have min & max
length = mfdb_step_interval('', 10, to = 100),
species = 'COD',
maturity_stage = '1',
null = NULL))
# Write both min/max and refweighfile into our gadget directory
gadget_dir_write(gd, gadget_stockfile_extremes('cod.imm', imm_data[[1]]))
gadget_dir_write(gd, gadget_stockfile_refweight('cod.imm', imm_data[[1]]))
# Do the same for mature cod
mat_data <- mfdb_sample_meanweight(mdb, c('age', 'length'), list(
age = NULL, # This means the age column will have "all", but aggfile will have min & max
length = mfdb_step_interval('len', 10, to = 100),
species = 'COD',
maturity_stage = '5',
null = NULL))
gadget_dir_write(gd, gadget_stockfile_extremes('cod.mat', mat_data[[1]]))
gadget_dir_write(gd, gadget_stockfile_refweight('cod.mat', mat_data[[1]]))
# Stockfiles mentioned in the mainfile
ok(cmp_file(gd, "main",
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tModelfiles/cod.imm\tModelfiles/cod.mat",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL), "Mainfile mentions both new stockfiles")
ok(cmp_file(gd, "Modelfiles/cod.imm",
ver_string,
"stockname\tcod.imm",
"minage\t1",
"maxage\t2",
"minlength\t0",
"maxlength\t100",
"dl\t10",
"refweightfile\tModelfiles/cod.imm.refwgt",
NULL), "Immature cod stockfile")
ok(cmp_file(gd, "Modelfiles/cod.imm.refwgt",
ver_string,
"; -- data --",
"; length\tweight",
"10\t375",
"20\t216.666666666667",
NULL), "Immature cod stock refweightfile")
ok(cmp_file(gd, "Modelfiles/cod.mat",
ver_string,
"stockname\tcod.mat",
"minage\t3",
"maxage\t3",
"minlength\t0",
"maxlength\t100",
"dl\t10",
"refweightfile\tModelfiles/cod.mat.refwgt",
NULL), "Mature cod stockfile")
ok(cmp_file(gd, "Modelfiles/cod.mat.refwgt",
ver_string,
"; -- data --",
"; length\tweight",
"30\t223.333333333333",
"40\t330",
"50\t380",
"60\t320",
NULL), "Mature cod stock refweightfile")
})
ok_group("Stockfile example - initialconditions", {
# Add initialconditions to existing directory
mat_data <- mfdb_sample_meanweight(mdb, c('age', 'length'), list(
area = NULL,
age = NULL, # This means the age column will have "all", but aggfile will have min & max
length = mfdb_step_interval('len', 5, to = 50),
species = 'COD',
maturity_stage = '5',
null = NULL))
gadget_dir_write(gd, gadget_stockfile_initialconditions('cod.mat', mat_data[[1]]))
ok(cmp_file(gd, "Modelfiles/cod.mat",
ver_string,
"stockname\tcod.mat",
"minage\t3",
"maxage\t3",
"minlength\t0",
"maxlength\t100",
"dl\t10",
"refweightfile\tModelfiles/cod.mat.refwgt",
"initialconditions",
"minage\t3",
"maxage\t3",
"minlength\t0",
"maxlength\t50",
"dl\t5",
"numberfile\tModelfiles/cod.mat.init.number",
NULL), "Mature cod stockfile now has initialconditions")
ok(cmp_file(gd, "Modelfiles/cod.mat.init.number",
ver_string,
"; -- data --",
"; area\tage\tlength\tnumber\tweight",
"all\tall\t30\t3\t223.333333333333",
"all\tall\t40\t1\t330",
NULL), "Mature cod stockfile initialconditions")
})
ok_group("Stockfile example - recruitment", {
# Add recruitment to existing directory
mat_data <- mfdb_sample_meanweight(mdb, c('age', 'length'), list(
year = 2000:2003,
step = mfdb_timestep_quarterly,
area = mfdb_unaggregated(),
age = NULL, # This means the age column will have "all", but aggfile will have min & max
length = mfdb_step_interval('len', 5, from = 50, to = 100),
species = 'COD',
maturity_stage = '5',
null = NULL))
gadget_dir_write(gd, gadget_stockfile_recruitment('cod.mat', mat_data[[1]]))
ok(cmp_file(gd, "Modelfiles/cod.mat",
ver_string,
"stockname\tcod.mat",
"minage\t3",
"maxage\t3",
"minlength\t0",
"maxlength\t100",
"dl\t10",
"refweightfile\tModelfiles/cod.mat.refwgt",
"initialconditions",
"minage\t3",
"maxage\t3",
"minlength\t0",
"maxlength\t50",
"dl\t5",
"numberfile\tModelfiles/cod.mat.init.number",
"doesrenew\t1",
"minlength\t50",
"maxlength\t100",
"dl\t5",
"numberfile\tModelfiles/cod.mat.rec.number",
NULL), "Mature cod stockfile")
ok(cmp_file(gd, "Modelfiles/cod.mat.rec.number",
ver_string,
"; -- data --",
"; year\tstep\tarea\tage\tlength\tnumber\tweight",
"2000\t1\t45G01\tall\t50\t2\t380",
"2000\t1\t45G01\tall\t60\t1\t320",
NULL), "Mature cod stockfile initialconditions")
})
ok_group("refweight files are always continuous and in length order", {
# Create a temporary gadget directory
gd <- gadget_directory(tempfile())
# Write out refweight for mature cod, purposefully shuffling
mat_data <- mfdb_sample_meanweight(mdb, c('age', 'length'), list(
age = NULL, # This means the age column will have "all", but aggfile will have min & max
length = mfdb_step_interval('len', 10, to = 100),
species = 'COD',
maturity_stage = '5',
null = NULL))
gadget_dir_write(gd, gadget_stockfile_refweight('cod.mat', shuffle_df(mat_data[[1]])))
# Got sorted
ok(cmp_file(gd, "Modelfiles/cod.mat.refwgt",
ver_string,
"; -- data --",
"; length\tweight",
"30\t223.333333333333",
"40\t330",
"50\t380",
"60\t320",
NULL), "Mature cod stock refweightfile")
})
ok_group("Stockfile updates don't wreck existing files", {
# Create a temporary gadget directory, populate mature cod file
gd <- gadget_directory(tempfile())
mat_data <- mfdb_sample_meanweight(mdb, c('age', 'length'), list(
age = NULL, # This means the age column will have "all", but aggfile will have min & max
length = mfdb_step_interval('len', 10, to = 100),
species = 'COD',
maturity_stage = '5',
null = NULL))
gadget_dir_write(gd, gadget_stockfile_extremes('cod.mat', mat_data[[1]]))
gadget_dir_write(gd, gadget_stockfile_refweight('cod.mat', mat_data[[1]]))
mat_data <- mfdb_sample_meanweight(mdb, c('age', 'length'), list(
year = 2000:2003,
step = mfdb_timestep_quarterly,
area = mfdb_unaggregated(),
age = NULL, # This means the age column will have "all", but aggfile will have min & max
length = mfdb_step_interval('len', 5, from = 50, to = 100),
species = 'COD',
maturity_stage = '5',
null = NULL))
gadget_dir_write(gd, gadget_stockfile_recruitment('cod.mat', mat_data[[1]]))
# File should now have a bunch of content
ok(cmp_file(gd, "Modelfiles/cod.mat",
ver_string,
"stockname\tcod.mat",
"minage\t3",
"maxage\t3",
"minlength\t0",
"maxlength\t100",
"dl\t10",
"refweightfile\tModelfiles/cod.mat.refwgt",
"doesrenew\t1",
"minlength\t50",
"maxlength\t100",
"dl\t5",
"numberfile\tModelfiles/cod.mat.rec.number",
NULL), "Stockfile has initial content")
# Manually open file and tinker with iseaten
gf <- gadget_dir_read(gd, "Modelfiles/cod.mat", file_type = c("bare_component", implicit_component = "^(growthandeatlengths|doesgrow|naturalmortality|iseaten|doeseat|doesmigrate|doesmature|doesmove|doesrenew|doesspawn|doesstray)$"))
gf$components$iseaten <- list(iseaten = 1, lots = "yes-is-tasty")
gadget_dir_write(gd, gf)
ok(cmp_file(gd, "Modelfiles/cod.mat",
ver_string,
"stockname\tcod.mat",
"minage\t3",
"maxage\t3",
"minlength\t0",
"maxlength\t100",
"dl\t10",
"refweightfile\tModelfiles/cod.mat.refwgt",
"doesrenew\t1",
"minlength\t50",
"maxlength\t100",
"dl\t5",
"numberfile\tModelfiles/cod.mat.rec.number",
"iseaten\t1",
"lots\tyes-is-tasty",
NULL), "iseaten added to end")
# Write new recruitment, iseaten not affected
mat_data <- mfdb_sample_meanweight(mdb, c('age', 'length'), list(
year = 2000:2003,
step = mfdb_timestep_quarterly,
area = mfdb_unaggregated(),
age = NULL, # This means the age column will have "all", but aggfile will have min & max
length = mfdb_step_interval('len', 2, from = 50, to = 70),
species = 'COD',
maturity_stage = '5',
null = NULL))
gadget_dir_write(gd, gadget_stockfile_recruitment('cod.mat', mat_data[[1]]))
ok(cmp_file(gd, "Modelfiles/cod.mat",
ver_string,
"stockname\tcod.mat",
"minage\t3",
"maxage\t3",
"minlength\t0",
"maxlength\t100",
"dl\t10",
"refweightfile\tModelfiles/cod.mat.refwgt",
"doesrenew\t1",
"minlength\t50",
"maxlength\t70",
"dl\t2",
"numberfile\tModelfiles/cod.mat.rec.number",
"iseaten\t1",
"lots\tyes-is-tasty",
NULL), "iseaten still at end, only doesrenew changed")
})
mfdb_disconnect(mdb)
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mfdb documentation built on June 21, 2022, 5:07 p.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# This script demonstrates creating stock files
#
# ok and ok_group are there so we can run this code and verify it is correct,
# and not needed every-day use.
#
# NB: if you want to run this, you must be using mfdb-workspace, also be warned
# any data stored in your database will be destroyed.
library(unittest)
library(mfdb)
source('tests/utils/helpers.R')
source('tests/utils/inttest-helpers.R')
# Empty database & rebuild
if (exists("mdb")) mfdb_disconnect(mdb)
mfdb(gsub("inttest", "inttest-stockfile", Sys.getenv('INTTEST_SCHEMA', 'inttest')), db_params = db_params, destroy_schema = TRUE)
mdb <- mfdb(gsub("inttest", "inttest-stockfile", Sys.getenv('INTTEST_SCHEMA', 'inttest')), db_params = db_params, save_temp_tables = FALSE)
# Set-up areas/divisions
mfdb_import_area(mdb, data.frame(
name = c('45G01', '45G02', '45G03'),
division = c('divA', 'divA', 'divB'),
size = c(10,200,400)))
ok_group("Stockfile example", {
# Create a temporary gadget directory
gd <- gadget_directory(tempfile())
# Import a survey for the data we are interested in
mfdb_import_survey(mdb, data_source = "cod2000",
table_string("
year month areacell species maturity_stage length age weight
2000 1 45G01 COD 1 21 2 210
2000 1 45G01 COD 5 34 3 220
2000 1 45G01 COD 5 34 3 230
2000 1 45G01 COD 5 62 1 320
2000 1 45G01 COD 5 53 1 330
2000 1 45G01 COD 5 54 2 430
2000 1 45G01 COD 1 28 2 210
2000 1 45G01 COD 5 34 3 220
2000 1 45G01 COD 1 24 3 230
2000 1 45G01 COD 1 12 1 320
2000 1 45G01 COD 5 44 1 330
2000 1 45G01 COD 1 14 2 430
"))
# Query min/max age, and average weight for our length groups (Immature cod)
imm_data <- mfdb_sample_meanweight(mdb, c('age', 'length'), list(
age = NULL, # This means the age column will have "all", but aggfile will have min & max
length = mfdb_step_interval('', 10, to = 100),
species = 'COD',
maturity_stage = '1',
null = NULL))
# Write both min/max and refweighfile into our gadget directory
gadget_dir_write(gd, gadget_stockfile_extremes('cod.imm', imm_data[[1]]))
gadget_dir_write(gd, gadget_stockfile_refweight('cod.imm', imm_data[[1]]))
# Do the same for mature cod
mat_data <- mfdb_sample_meanweight(mdb, c('age', 'length'), list(
age = NULL, # This means the age column will have "all", but aggfile will have min & max
length = mfdb_step_interval('len', 10, to = 100),
species = 'COD',
maturity_stage = '5',
null = NULL))
gadget_dir_write(gd, gadget_stockfile_extremes('cod.mat', mat_data[[1]]))
gadget_dir_write(gd, gadget_stockfile_refweight('cod.mat', mat_data[[1]]))
# Stockfiles mentioned in the mainfile
ok(cmp_file(gd, "main",
ver_string,
"timefile\t",
"areafile\t",
"printfiles\t; Required comment",
"[stock]",
"stockfiles\tModelfiles/cod.imm\tModelfiles/cod.mat",
"[tagging]",
"[otherfood]",
"[fleet]",
"[likelihood]",
NULL), "Mainfile mentions both new stockfiles")
ok(cmp_file(gd, "Modelfiles/cod.imm",
ver_string,
"stockname\tcod.imm",
"minage\t1",
"maxage\t2",
"minlength\t0",
"maxlength\t100",
"dl\t10",
"refweightfile\tModelfiles/cod.imm.refwgt",
NULL), "Immature cod stockfile")
ok(cmp_file(gd, "Modelfiles/cod.imm.refwgt",
ver_string,
"; -- data --",
"; length\tweight",
"10\t375",
"20\t216.666666666667",
NULL), "Immature cod stock refweightfile")
ok(cmp_file(gd, "Modelfiles/cod.mat",
ver_string,
"stockname\tcod.mat",
"minage\t3",
"maxage\t3",
"minlength\t0",
"maxlength\t100",
"dl\t10",
"refweightfile\tModelfiles/cod.mat.refwgt",
NULL), "Mature cod stockfile")
ok(cmp_file(gd, "Modelfiles/cod.mat.refwgt",
ver_string,
"; -- data --",
"; length\tweight",
"30\t223.333333333333",
"40\t330",
"50\t380",
"60\t320",
NULL), "Mature cod stock refweightfile")
})
ok_group("Stockfile example - initialconditions", {
# Add initialconditions to existing directory
mat_data <- mfdb_sample_meanweight(mdb, c('age', 'length'), list(
area = NULL,
age = NULL, # This means the age column will have "all", but aggfile will have min & max
length = mfdb_step_interval('len', 5, to = 50),
species = 'COD',
maturity_stage = '5',
null = NULL))
gadget_dir_write(gd, gadget_stockfile_initialconditions('cod.mat', mat_data[[1]]))
ok(cmp_file(gd, "Modelfiles/cod.mat",
ver_string,
"stockname\tcod.mat",
"minage\t3",
"maxage\t3",
"minlength\t0",
"maxlength\t100",
"dl\t10",
"refweightfile\tModelfiles/cod.mat.refwgt",
"initialconditions",
"minage\t3",
"maxage\t3",
"minlength\t0",
"maxlength\t50",
"dl\t5",
"numberfile\tModelfiles/cod.mat.init.number",
NULL), "Mature cod stockfile now has initialconditions")
ok(cmp_file(gd, "Modelfiles/cod.mat.init.number",
ver_string,
"; -- data --",
"; area\tage\tlength\tnumber\tweight",
"all\tall\t30\t3\t223.333333333333",
"all\tall\t40\t1\t330",
NULL), "Mature cod stockfile initialconditions")
})
ok_group("Stockfile example - recruitment", {
# Add recruitment to existing directory
mat_data <- mfdb_sample_meanweight(mdb, c('age', 'length'), list(
year = 2000:2003,
step = mfdb_timestep_quarterly,
area = mfdb_unaggregated(),
age = NULL, # This means the age column will have "all", but aggfile will have min & max
length = mfdb_step_interval('len', 5, from = 50, to = 100),
species = 'COD',
maturity_stage = '5',
null = NULL))
gadget_dir_write(gd, gadget_stockfile_recruitment('cod.mat', mat_data[[1]]))
ok(cmp_file(gd, "Modelfiles/cod.mat",
ver_string,
"stockname\tcod.mat",
"minage\t3",
"maxage\t3",
"minlength\t0",
"maxlength\t100",
"dl\t10",
"refweightfile\tModelfiles/cod.mat.refwgt",
"initialconditions",
"minage\t3",
"maxage\t3",
"minlength\t0",
"maxlength\t50",
"dl\t5",
"numberfile\tModelfiles/cod.mat.init.number",
"doesrenew\t1",
"minlength\t50",
"maxlength\t100",
"dl\t5",
"numberfile\tModelfiles/cod.mat.rec.number",
NULL), "Mature cod stockfile")
ok(cmp_file(gd, "Modelfiles/cod.mat.rec.number",
ver_string,
"; -- data --",
"; year\tstep\tarea\tage\tlength\tnumber\tweight",
"2000\t1\t45G01\tall\t50\t2\t380",
"2000\t1\t45G01\tall\t60\t1\t320",
NULL), "Mature cod stockfile initialconditions")
})
ok_group("refweight files are always continuous and in length order", {
# Create a temporary gadget directory
gd <- gadget_directory(tempfile())
# Write out refweight for mature cod, purposefully shuffling
mat_data <- mfdb_sample_meanweight(mdb, c('age', 'length'), list(
age = NULL, # This means the age column will have "all", but aggfile will have min & max
length = mfdb_step_interval('len', 10, to = 100),
species = 'COD',
maturity_stage = '5',
null = NULL))
gadget_dir_write(gd, gadget_stockfile_refweight('cod.mat', shuffle_df(mat_data[[1]])))
# Got sorted
ok(cmp_file(gd, "Modelfiles/cod.mat.refwgt",
ver_string,
"; -- data --",
"; length\tweight",
"30\t223.333333333333",
"40\t330",
"50\t380",
"60\t320",
NULL), "Mature cod stock refweightfile")
})
ok_group("Stockfile updates don't wreck existing files", {
# Create a temporary gadget directory, populate mature cod file
gd <- gadget_directory(tempfile())
mat_data <- mfdb_sample_meanweight(mdb, c('age', 'length'), list(
age = NULL, # This means the age column will have "all", but aggfile will have min & max
length = mfdb_step_interval('len', 10, to = 100),
species = 'COD',
maturity_stage = '5',
null = NULL))
gadget_dir_write(gd, gadget_stockfile_extremes('cod.mat', mat_data[[1]]))
gadget_dir_write(gd, gadget_stockfile_refweight('cod.mat', mat_data[[1]]))
mat_data <- mfdb_sample_meanweight(mdb, c('age', 'length'), list(
year = 2000:2003,
step = mfdb_timestep_quarterly,
area = mfdb_unaggregated(),
age = NULL, # This means the age column will have "all", but aggfile will have min & max
length = mfdb_step_interval('len', 5, from = 50, to = 100),
species = 'COD',
maturity_stage = '5',
null = NULL))
gadget_dir_write(gd, gadget_stockfile_recruitment('cod.mat', mat_data[[1]]))
# File should now have a bunch of content
ok(cmp_file(gd, "Modelfiles/cod.mat",
ver_string,
"stockname\tcod.mat",
"minage\t3",
"maxage\t3",
"minlength\t0",
"maxlength\t100",
"dl\t10",
"refweightfile\tModelfiles/cod.mat.refwgt",
"doesrenew\t1",
"minlength\t50",
"maxlength\t100",
"dl\t5",
"numberfile\tModelfiles/cod.mat.rec.number",
NULL), "Stockfile has initial content")
# Manually open file and tinker with iseaten
gf <- gadget_dir_read(gd, "Modelfiles/cod.mat", file_type = c("bare_component", implicit_component = "^(growthandeatlengths|doesgrow|naturalmortality|iseaten|doeseat|doesmigrate|doesmature|doesmove|doesrenew|doesspawn|doesstray)$"))
gf$components$iseaten <- list(iseaten = 1, lots = "yes-is-tasty")
gadget_dir_write(gd, gf)
ok(cmp_file(gd, "Modelfiles/cod.mat",
ver_string,
"stockname\tcod.mat",
"minage\t3",
"maxage\t3",
"minlength\t0",
"maxlength\t100",
"dl\t10",
"refweightfile\tModelfiles/cod.mat.refwgt",
"doesrenew\t1",
"minlength\t50",
"maxlength\t100",
"dl\t5",
"numberfile\tModelfiles/cod.mat.rec.number",
"iseaten\t1",
"lots\tyes-is-tasty",
NULL), "iseaten added to end")
# Write new recruitment, iseaten not affected
mat_data <- mfdb_sample_meanweight(mdb, c('age', 'length'), list(
year = 2000:2003,
step = mfdb_timestep_quarterly,
area = mfdb_unaggregated(),
age = NULL, # This means the age column will have "all", but aggfile will have min & max
length = mfdb_step_interval('len', 2, from = 50, to = 70),
species = 'COD',
maturity_stage = '5',
null = NULL))
gadget_dir_write(gd, gadget_stockfile_recruitment('cod.mat', mat_data[[1]]))
ok(cmp_file(gd, "Modelfiles/cod.mat",
ver_string,
"stockname\tcod.mat",
"minage\t3",
"maxage\t3",
"minlength\t0",
"maxlength\t100",
"dl\t10",
"refweightfile\tModelfiles/cod.mat.refwgt",
"doesrenew\t1",
"minlength\t50",
"maxlength\t70",
"dl\t2",
"numberfile\tModelfiles/cod.mat.rec.number",
"iseaten\t1",
"lots\tyes-is-tasty",
NULL), "iseaten still at end, only doesrenew changed")
})
mfdb_disconnect(mdb)
Try the mfdb package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
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