R Under development (unstable) (2026-01-23 r89325 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64

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> library(mfdb)
> library(unittest, quietly = TRUE)
> helpers <- c('utils/helpers.R', 'tests/utils/helpers.R') ; source(helpers[file.exists(helpers)])
> 
> all_components <- c(
+         "penalty",
+         "understocking",
+         "catchdistribution",
+         "catchstatistics",
+         "stockdistribution",
+         "surveydistribution",
+         "stomachcontent",
+         "migrationpenalty",
+         "catchinkilos",
+         NULL)
> 
> ok_group("Can generate gadget_likelihood_component objects", {
+     expect_error(
+         gadget_likelihood_component("aardvark"),
+         "aardvark")
+ 
+     expect_error(
+         gadget_likelihood_component("e12 ; bobby tables"),
+         "e12 ; bobby tables")
+ 
+     expect_equal(
+         class(gadget_likelihood_component("penalty")),
+         c("gadget_penalty_component", "gadget_likelihood_component"))
+ })
# Can generate gadget_likelihood_component objects
ok - Error contained 'aardvark'
ok - Error contained 'e12 ; bobby tables'
ok - class(gadget_likelihood_compon == c("gadget_penalty_component", 
> 
> ok_group("Can use as.character on gadget_likelihood_components", {
+     comp <- gadget_likelihood_component("penalty", name = "wibble", weight = 0.5)
+     expect_equal(comp$name, "wibble")
+     expect_equal(comp$weight, 0.5)
+     expect_equal(comp$type, "penalty")
+ })
# Can use as.character on gadget_likelihood_components
ok - comp$name == "wibble"
ok - comp$weight == 0.5
ok - comp$type == "penalty"
> 
> ok_group("Can nest data.frame in a list", {
+     df <- data.frame(year = 1, step = 1, area = 1, fleet = 1, total_weight = 1)
+ 
+     comp <- gadget_likelihood_component("catchinkilos", data = df)
+     ok(cmp(comp$datafile$data, df), "Data included with regular data.frame")
+ 
+     comp <- gadget_likelihood_component("catchinkilos", data = list(df))
+     ok(cmp(comp$datafile$data, df), "Data included with nested data.frame")
+ 
+     ok(cmp_error(
+         gadget_likelihood_component("catchinkilos", data = list(df, df)),
+         "list"), "More than one item causes an error")
+ })
# Can nest data.frame in a list
ok - Data included with regular data.frame
ok - Data included with nested data.frame
ok - More than one item causes an error
> 
> for (type in all_components) {
+     if (type == "catchstatistics") {
+         default_opts <- list(type,
+             data = data.frame(), data_function = "customfunction")
+     } else if (type == "catchdistribution") {
+         default_opts <- list(type,
+             data = data.frame(year = 1, step = 1, area = 1, age = 1, length = 1, number = 1))
+     } else if (type == "stockdistribution") {
+         default_opts <- list(type,
+             data = data.frame(year = 1, step = 1, area = 1, aardvark = 1, age = 1, length = 1, number = 1))
+     } else if (type == "surveydistribution") {
+         default_opts <- list(type,
+             data = data.frame(year = 1, step = 1, area = 1, age = 1, length = 1, number = 1))
+     } else if (type == "stomachcontent") {
+         default_opts <- list(type,
+             data = data.frame(year = 1, step = 1, area = 1, predator_length = 'pred100', prey_length = 'prey10', ratio = 1),
+             predator_length = list('pred100' = 'pred100'),
+             prey_length = list('prey10' = 'prey10'),
+             prey_labels = list('prey10' = 'Prey 10'))
+     } else if (type == "catchinkilos") {
+         default_opts <- list(type,
+             data = data.frame(year = 1, step = 1, area = 1, fleet = 1, total_weight = 1))
+     } else {
+         default_opts <- list(type)
+     }
+ 
+     ok_group(paste("Name, type and weight for component", type), {
+         comp <- do.call(gadget_likelihood_component, default_opts)
+ 
+         # Class should match type
+         ok(cmp(class(comp), c(
+             paste0("gadget_", type, "_component"),
+             "gadget_likelihood_component")), "Has correct class")
+ 
+         # Type and name should match the name we gave
+         ok(cmp(comp$type, type), "Type set")
+         ok(cmp(comp$name, type), "Default name same as type")
+         ok(cmp(comp$weight, 0), "Weight defaults to 0")
+ 
+         # Can customise name & weight
+         comp <- do.call(gadget_likelihood_component, c(
+             default_opts,
+             list(name = "gerald", weight = 0.542),
+             NULL))
+         ok(cmp(comp$name, "gerald"), "Can set name")
+         ok(cmp(comp$weight, 0.542), "Can set weight")
+     })
+ 
+     ok_group(paste("Filenames for component", type), {
+         contains <- function(pattern, x) {
+             if(length(grep(pattern, x, value = FALSE)) > 0) {
+                 TRUE
+             } else {
+                  paste0(x, " does not contain ", pattern)
+             }
+         }
+ 
+         comp <- do.call(gadget_likelihood_component, c(
+             default_opts,
+             list(name = "gerald", weight = 0.542),
+             NULL))
+         for (key in names(comp)) {
+             if ("gadget_file" %in% class(comp[[key]]) && comp$type != "penalty") {
+                 ok(contains(
+                     paste0("^Data/", comp$type, "\\.", comp$name, "\\."),
+                     comp$datafile$filename), "Filename starts with name and type")
+             }
+         }
+     })
+ }
# Name, type and weight for component penalty
ok - Has correct class
ok - Type set
ok - Default name same as type
ok - Weight defaults to 0
ok - Can set name
ok - Can set weight
# Filenames for component penalty
# Name, type and weight for component understocking
ok - Has correct class
ok - Type set
ok - Default name same as type
ok - Weight defaults to 0
ok - Can set name
ok - Can set weight
# Filenames for component understocking
# Name, type and weight for component catchdistribution
ok - Has correct class
ok - Type set
ok - Default name same as type
ok - Weight defaults to 0
ok - Can set name
ok - Can set weight
# Filenames for component catchdistribution
ok - Filename starts with name and type
ok - Filename starts with name and type
ok - Filename starts with name and type
ok - Filename starts with name and type
# Name, type and weight for component catchstatistics
ok - Has correct class
ok - Type set
ok - Default name same as type
ok - Weight defaults to 0
ok - Can set name
ok - Can set weight
# Filenames for component catchstatistics
ok - Filename starts with name and type
ok - Filename starts with name and type
ok - Filename starts with name and type
# Name, type and weight for component stockdistribution
ok - Has correct class
ok - Type set
ok - Default name same as type
ok - Weight defaults to 0
ok - Can set name
ok - Can set weight
# Filenames for component stockdistribution
ok - Filename starts with name and type
ok - Filename starts with name and type
ok - Filename starts with name and type
ok - Filename starts with name and type
# Name, type and weight for component surveydistribution
ok - Has correct class
ok - Type set
ok - Default name same as type
ok - Weight defaults to 0
ok - Can set name
ok - Can set weight
# Filenames for component surveydistribution
ok - Filename starts with name and type
ok - Filename starts with name and type
ok - Filename starts with name and type
ok - Filename starts with name and type
# Name, type and weight for component stomachcontent
ok - Has correct class
ok - Type set
ok - Default name same as type
ok - Weight defaults to 0
ok - Can set name
ok - Can set weight
# Filenames for component stomachcontent
ok - Filename starts with name and type
ok - Filename starts with name and type
ok - Filename starts with name and type
ok - Filename starts with name and type
# Name, type and weight for component migrationpenalty
ok - Has correct class
ok - Type set
ok - Default name same as type
ok - Weight defaults to 0
ok - Can set name
ok - Can set weight
# Filenames for component migrationpenalty
# Name, type and weight for component catchinkilos
ok - Has correct class
ok - Type set
ok - Default name same as type
ok - Weight defaults to 0
ok - Can set name
ok - Can set weight
# Filenames for component catchinkilos
ok - Filename starts with name and type
ok - Filename starts with name and type
> 
> ok_group("Can write likelihood components", {
+     # Create a temporary directory, starts off empty
+     dir <- tempfile()
+     gd <- gadget_directory(dir)
+     expect_equal(list.files(dir), character(0))
+ 
+     # Create some components
+     gadget_dir_write(gd, gadget_likelihood_component("understocking", name="head-bone", weight = 0.3))
+     expect_equal(list.files(dir), c("likelihood", "main"))
+     expect_equal(
+         gadget_dir_read(gd, "likelihood")$components,
+         list(
+             list(),
+             component = structure(list(name = "head-bone", weight = 0.3, type = "understocking"), preamble = list(""))))
+     ok(cmp_file(gd, "main",
+         ver_string,
+         "timefile\t",
+         "areafile\t",
+         "printfiles\t; Required comment",
+         "[stock]",
+         "[tagging]",
+         "[otherfood]",
+         "[fleet]",
+         "[likelihood]",
+         "likelihoodfiles\tlikelihood"))
+ 
+     gadget_dir_write(gd, gadget_likelihood_component("penalty", name="neck-bone", weight = 0.5))
+     ok(cmp(
+         list.files(dir, recursive = TRUE),
+         c("Data/neck-bone.penaltyfile", "likelihood", "main")), "Created penaltyfile")
+     expect_equal(
+         gadget_dir_read(gd, "likelihood")$components,
+         list(
+             list(),
+             component = structure(list(name = "head-bone", weight = 0.3, type = "understocking"), preamble = list("")),
+             component = structure(list(name = "neck-bone", weight = 0.5, type = "penalty", datafile = "Data/neck-bone.penaltyfile"), preamble = list(""))))
+     ok(cmp_file(gd, "main",
+         ver_string,
+         "timefile\t",
+         "areafile\t",
+         "printfiles\t; Required comment",
+         "[stock]",
+         "[tagging]",
+         "[otherfood]",
+         "[fleet]",
+         "[likelihood]",
+         "likelihoodfiles\tlikelihood"))
+ 
+     # Override one, add another
+     gadget_dir_write(gd, gadget_likelihood_component("understocking", name="head-bone", weight = 0.8))
+     gadget_dir_write(gd, gadget_likelihood_component("understocking", name="shoulder-bone", weight = 0.2))
+     expect_equal(
+         gadget_dir_read(gd, "likelihood")$components,
+         list(
+             list(),
+             component = structure(list(name = "head-bone", weight = 0.8, type = "understocking"), preamble = list("")),
+             component = structure(list(name = "neck-bone", weight = 0.5, type = "penalty", datafile = "Data/neck-bone.penaltyfile"), preamble = list("")),
+             component = structure(list(name = "shoulder-bone", weight = 0.2, type = "understocking"), preamble = list(""))))
+     ok(cmp_file(gd, "main",
+         ver_string,
+         "timefile\t",
+         "areafile\t",
+         "printfiles\t; Required comment",
+         "[stock]",
+         "[tagging]",
+         "[otherfood]",
+         "[fleet]",
+         "[likelihood]",
+         "likelihoodfiles\tlikelihood"))
+ 
+     # Add one to a new likelihood file
+     gadget_dir_write(gd, gadget_likelihood_component("understocking", likelihoodfile="dahood", name="bad-to-the-bone", weight = 0.8))
+     ok(cmp_file(gd, "main",
+         ver_string,
+         "timefile\t",
+         "areafile\t",
+         "printfiles\t; Required comment",
+         "[stock]",
+         "[tagging]",
+         "[otherfood]",
+         "[fleet]",
+         "[likelihood]",
+         "likelihoodfiles\tlikelihood\tdahood"))
+     ok(cmp_file(gd, "dahood",
+         ver_string,
+         "; ",
+         "[component]",
+         "name\tbad-to-the-bone",
+         "weight\t0.8",
+         "type\tunderstocking",
+         NULL))
+ })
# Can write likelihood components
ok - list.files(dir) == character(0)
ok - list.files(dir) == c("likelihood", "main")
ok - gadget_dir_read(gd, "likelihoo == list(list(), component = strucgadget_dir_read(gd, "likelihoo ==  type = "understocking"), prea
ok - cmp_file(gd, "main", ver_string, "timefile\t", "areafile\t",
ok - Created penaltyfile
ok - gadget_dir_read(gd, "likelihoo == list(list(), component = strucgadget_dir_read(gd, "likelihoo ==  type = "understocking"), preagadget_dir_read(gd, "likelihoo ==  weight = 0.5, type = "penaltygadget_dir_read(gd, "likelihoo ==  preamble = list("")))
ok - cmp_file(gd, "main", ver_string, "timefile\t", "areafile\t",
ok - gadget_dir_read(gd, "likelihoo == list(list(), component = strucgadget_dir_read(gd, "likelihoo ==  type = "understocking"), preagadget_dir_read(gd, "likelihoo ==  weight = 0.5, type = "penaltygadget_dir_read(gd, "likelihoo ==  preamble = list("")), componegadget_dir_read(gd, "likelihoo ==  weight = 0.2, type = "underst
ok - cmp_file(gd, "main", ver_string, "timefile\t", "areafile\t",
ok - cmp_file(gd, "main", ver_string, "timefile\t", "areafile\t",
ok - cmp_file(gd, "dahood", ver_string, "; ", "[component]", "nam
> 
> ###############################################################################
> ok_group("Can generate an understocking component with default parameters", {
+     comp <- gadget_likelihood_component("understocking")
+     expect_equal(comp$name, "understocking")
+     expect_equal(comp$weight, 0)
+     expect_equal(comp$type, "understocking")
+ })
# Can generate an understocking component with default parameters
ok - comp$name == "understocking"
ok - comp$weight == 0
ok - comp$type == "understocking"
> 
> ok_group("Can customise it", {
+     comp <- gadget_likelihood_component("understocking", name = "alfred", weight = 0.3)
+     expect_equal(comp$name, "alfred")
+     expect_equal(comp$weight, 0.3)
+     expect_equal(comp$type, "understocking")
+ })
# Can customise it
ok - comp$name == "alfred"
ok - comp$weight == 0.3
ok - comp$type == "understocking"
> 
> ###############################################################################
> ok_group("Function either provided explicitly or based on generator", {
+     expect_error(
+         gadget_likelihood_component("catchstatistics"),
+         "No data provided")
+     expect_error(
+         gadget_likelihood_component("catchstatistics", data = data.frame()),
+         "Cannot work out the required function, and data_function not provided")
+     expect_error(
+         gadget_likelihood_component("catchstatistics", data = structure(data.frame(), generator = "camel")),
+         "Unknown generator function camel")
+ 
+     expect_equal(
+         gadget_likelihood_component("catchstatistics",
+             data = data.frame(), data_function = "customfunction")[['function']],
+         "customfunction")
+ 
+     ok(cmp(
+         gadget_likelihood_component("catchstatistics", data = structure(
+             data.frame(year = 1990, step = 1, area = 1, age = 1, number = 1, mean = 1, stddev = 1),
+             generator = "mfdb_sample_meanlength_stddev"))[['function']],
+         "lengthgivenstddev"), "Guessed function given generator")
+ 
+     ok(cmp_error(
+         gadget_likelihood_component("catchstatistics", data = structure(
+             data.frame(),
+             generator = "mfdb_sample_meanlength_stddev")),
+         "data given to gadget_catchstatistics_component is empty"), "Noticed missing data")
+ 
+     ok(cmp_error(
+         gadget_likelihood_component("catchstatistics", data = structure(
+             data.frame(year = 1990, step = 1, area = 1, age = 1, number = 1, mean = 1),
+             generator = "mfdb_sample_meanlength_stddev")),
+         "stddev"), "Noticed missing column")
+ })
# Function either provided explicitly or based on generator
ok - Error contained 'No data provided'
ok - Error contained 'Cannot work out the required function, and data_function not provided'
ok - Error contained 'Unknown generator function camel'
ok - gadget_likelihood_component("c == "customfunction" data_function = "customfuncti == "customfunction"
ok - Guessed function given generator
ok - Noticed missing data
ok - Noticed missing column
> 
> ###############################################################################
> ok_group("Aggregation files", {
+     cmp_agg <- function (agg_type, agg, ...) {
+         gd <- gadget_directory(tempfile())
+         agg_summ <- agg_summary(fake_mdb(), agg, 'c.col', 'col', data.frame(col = 1:5), 0)
+         gadget_dir_write(gd, gadget_likelihood_component(
+             "catchdistribution",
+             name="cd",
+             weight = 0.8,
+             data = structure(
+                 data.frame(year = 1, step = 1, area = 1, age = 1, length = 1, number = 1),
+                 area = if (agg_type == 'area') agg_summ else NULL,
+                 age = if (agg_type == 'age') agg_summ else NULL,
+                 length = if (agg_type == 'len') agg_summ else NULL,
+                 generator = "mfdb_sample_meanlength")
+             ))
+         do.call(cmp_file, c(
+             list(gd, paste0("Aggfiles/catchdistribution.cd.", agg_type, ".agg")),
+             list(...)))
+     }
+ 
+     ok(cmp_agg('area', list(divA = c('x', 't'), divB = c('s', 'r')),
+         ver_string,
+         "divA\t1",
+         "divB\t2",
+         NULL), "Area aggregation file has subdivisions hidden")
+ 
+     ok(cmp_agg('age', list(young = 1:4, old = 5:8),
+         ver_string,
+         "young\t1\t2\t3\t4",
+         "old\t5\t6\t7\t8",
+         NULL), "Age aggregation matches input")
+ 
+     ok(cmp_agg('age', 1:4,
+         ver_string,
+         "1\t1",
+         "2\t2",
+         "3\t3",
+         "4\t4",
+         NULL), "1:4 converted into 1 group for each")
+ 
+     ok(cmp_agg('age', mfdb_unaggregated(),
+         ver_string,
+         "1\t1",
+         "2\t2",
+         "3\t3",
+         "4\t4",
+         "5\t5",
+         NULL), "mfdb_unaggregated")
+ 
+     ok(cmp_agg('len', mfdb_interval("len", seq(0, 50, by = 10)),
+         ver_string,
+         "len0\t0\t10",
+         "len10\t10\t20",
+         "len20\t20\t30",
+         "len30\t30\t40",
+         "len40\t40\t50",
+         NULL), "mfdb_interval (with len, so min/max)")
+ 
+     ok(cmp_agg('len', mfdb_step_interval("len", to = 30, by = 5),
+         ver_string,
+         "len0\t0\t5",
+         "len5\t5\t10",
+         "len10\t10\t15",
+         "len15\t15\t20",
+         "len20\t20\t25",
+         "len25\t25\t30",
+         NULL), "mfdb_step_interval (with len, so min/max)")
+ 
+     ok(cmp_agg('age', mfdb_interval("age", seq(0, 20, by = 10)),
+         ver_string,
+         "age0\t0\t1\t2\t3\t4\t5\t6\t7\t8\t9",
+         "age10\t10\t11\t12\t13\t14\t15\t16\t17\t18\t19",
+         NULL), "mfdb_interval (with age, so discrete numbers)")
+ 
+     ok(cmp_agg('age', mfdb_step_interval("age", to = 30, by = 5),
+         ver_string,
+         "age0\t0\t1\t2\t3\t4",
+         "age5\t5\t6\t7\t8\t9",
+         "age10\t10\t11\t12\t13\t14",
+         "age15\t15\t16\t17\t18\t19",
+         "age20\t20\t21\t22\t23\t24",
+         "age25\t25\t26\t27\t28\t29",
+         NULL), "mfdb_step_interval (with age, so discrete numbers)")
+ 
+     ok(cmp_agg('age', mfdb_step_interval("age", to = 5, by = 1),
+         ver_string,
+         "age0\t0",
+         "age1\t1",
+         "age2\t2",
+         "age3\t3",
+         "age4\t4",
+         NULL), "mfdb_step_interval (with age, so discrete numbers)")
+ 
+ })
# Aggregation files
ok - Area aggregation file has subdivisions hidden
ok - Age aggregation matches input
ok - 1:4 converted into 1 group for each
ok - mfdb_unaggregated
ok - mfdb_interval (with len, so min/max)
ok - mfdb_step_interval (with len, so min/max)
ok - mfdb_interval (with age, so discrete numbers)
ok - mfdb_step_interval (with age, so discrete numbers)
ok - mfdb_step_interval (with age, so discrete numbers)
> 
> ###############################################################################
> ok_group("surveyindices", {
+     cmp_component <- function (comp, ...) {
+         gd <- gadget_directory(tempfile())
+         gadget_dir_write(gd, comp)
+         cmp_file(gd, "likelihood", ...)
+     }
+ 
+     component <- gadget_likelihood_component('surveyindices', name = 'si', sitype = 'lengths', fittype = 'linearfit',
+         data = structure(
+             data.frame(year = 1998, step = 1:2, area = 101, length = c(100,200), number = c(2,4)),
+             area = list(all = 101),
+             length = list(len100 = c(100,500))))
+     ok(cmp(class(component)[[1]], 'gadget_surveyindices_component'), "Made lengths sitype")
+     ok(cmp_component(component,
+         ver_string,
+         "; ",
+         "[component]",
+         "name\tsi",
+         "weight\t0",
+         "type\tsurveyindices",
+         "datafile\tData/surveyindices.si.lengths",
+         "sitype\tlengths",
+         "biomass\t0",
+         "areaaggfile\tAggfiles/surveyindices.si.area.agg",
+         "lenaggfile\tAggfiles/surveyindices.si.len.agg",
+         "fittype\tlinearfit",
+         NULL), "Wrote component with lengths sitype")
+ 
+     component <- gadget_likelihood_component('surveyindices', name = 'si', sitype = 'ages', fittype = 'linearfit',
+         data = structure(
+             data.frame(year = 1998, step = 1:2, area = 101, age = c(100,200), number = c(2,4)),
+             area = list(all = 101),
+             age = list(age100 = c(100,500))))
+     ok(cmp(class(component)[[1]], 'gadget_surveyindices_component'), "Made ages sitype")
+     ok(cmp_component(component,
+         ver_string,
+         "; ",
+         "[component]",
+         "name\tsi",
+         "weight\t0",
+         "type\tsurveyindices",
+         "datafile\tData/surveyindices.si.ages",
+         "sitype\tages",
+         "biomass\t0",
+         "areaaggfile\tAggfiles/surveyindices.si.area.agg",
+         "ageaggfile\tAggfiles/surveyindices.si.age.agg",
+         "fittype\tlinearfit",
+         NULL), "Wrote component with ages sitype")
+ 
+     component <- gadget_likelihood_component('surveyindices', name = 'si', sitype = 'fleets', fittype = 'linearfit',
+         data = structure(
+             data.frame(year = 1998, step = 1:2, area = 101, length = c(100,200), number = c(2,4)),
+             area = list(all = 101),
+             length = list(len100 = c(100,500))),
+         fleetnames = c("cuthbert", "dibble"))
+     ok(cmp(class(component)[[1]], 'gadget_surveyindices_component'), "Made fleets sitype")
+     ok(cmp_component(component,
+         ver_string,
+         "; ",
+         "[component]",
+         "name\tsi",
+         "weight\t0",
+         "type\tsurveyindices",
+         "datafile\tData/surveyindices.si.fleets",
+         "sitype\tfleets",
+         "biomass\t0",
+         "areaaggfile\tAggfiles/surveyindices.si.area.agg",
+         "lenaggfile\tAggfiles/surveyindices.si.len.agg",
+         "fleetnames\tcuthbert\tdibble",
+         "fittype\tlinearfit",
+         NULL), "Wrote component with fleets sitype")
+ 
+     component <- gadget_likelihood_component('surveyindices', name = 'si', sitype = 'acoustic', fittype = 'linearfit',
+         data = structure(
+             data.frame(year = 1998, step = 1:2, area = 101, survey = c(100,200), acoustic = c(2,4)),
+             area = list(all = 101)),
+         surveynames = c("cuthbert", "dibble"))
+     ok(cmp(class(component)[[1]], 'gadget_surveyindices_component'), "Made acoustic sitype")
+     ok(cmp_component(component,
+         ver_string,
+         "; ",
+         "[component]",
+         "name\tsi",
+         "weight\t0",
+         "type\tsurveyindices",
+         "datafile\tData/surveyindices.si.acoustic",
+         "sitype\tacoustic",
+         "biomass\t0",
+         "areaaggfile\tAggfiles/surveyindices.si.area.agg",
+         "surveynames\tcuthbert\tdibble",
+         "fittype\tlinearfit",
+         NULL), "Wrote component with acoustic sitype")
+ 
+     component <- gadget_likelihood_component('surveyindices', name = 'si', sitype = 'effort', fittype = 'linearfit',
+         data = structure(
+             data.frame(year = 1998, step = 1:2, area = 101, fleet = c(100,200), effort = c(2,4)),
+             area = list(all = 101)),
+         fleetnames = c("cuthbert", "dibble"))
+     ok(cmp(class(component)[[1]], 'gadget_surveyindices_component'), "Made effort sitype")
+     ok(cmp_component(component,
+         ver_string,
+         "; ",
+         "[component]",
+         "name\tsi",
+         "weight\t0",
+         "type\tsurveyindices",
+         "datafile\tData/surveyindices.si.effort",
+         "sitype\teffort",
+         "biomass\t0",
+         "areaaggfile\tAggfiles/surveyindices.si.area.agg",
+         "fleetnames\tcuthbert\tdibble",
+         "fittype\tlinearfit",
+         NULL), "Wrote component with effort sitype")
+ 
+ })
# surveyindices
ok - Made lengths sitype
ok - Wrote component with lengths sitype
ok - Made ages sitype
ok - Wrote component with ages sitype
ok - Made fleets sitype
ok - Wrote component with fleets sitype
ok - Made acoustic sitype
ok - Wrote component with acoustic sitype
ok - Made effort sitype
ok - Wrote component with effort sitype
> 
> ###############################################################################
> ok_group("surveydistribution", {
+     component <- gadget_likelihood_component('surveydistribution', name = 'sd',
+         data = structure(
+             data.frame(year = 1998, step = 1:2, area = 101, age = c(1,2), length = c(3,4), number = c(100,200)),
+             area = list(all = 101),
+             age = list(all = 1:20),
+             length = list(all = 1:10)),
+         stocknames = c('frank', 'barbara'),
+         fittype = 'linearfit',
+         parameters = c(2, 4),
+         suitability = "function woo",
+         epsilon = 10,
+         likelihoodtype = 'multinomial')
+     ok(cmp(class(component)[[1]], 'gadget_surveydistribution_component'), "Made effort sitype")
+     ok(cmp_component(component,
+         ver_string,
+         "; ",
+         "[component]",
+         "name\tsd",
+         "weight\t0",
+         "type\tsurveydistribution",
+         "datafile\tData/surveydistribution.sd.",
+         "areaaggfile\tAggfiles/surveydistribution.sd.area.agg",
+         "lenaggfile\tAggfiles/surveydistribution.sd.len.agg",
+         "ageaggfile\tAggfiles/surveydistribution.sd.age.agg",
+         "stocknames\tfrank\tbarbara",
+         "fittype\tlinearfit",
+         "parameters\t2\t4",
+         "function woo",
+         "epsilon\t10",
+         "likelihoodtype\tmultinomial",
+         NULL), "Wrote component with effort sitype")
+ })
# surveydistribution
ok - Made effort sitype
ok - Wrote component with effort sitype
> 
> ###############################################################################
> ok_group("stomachcontent - matching of prey to labels", {
+     # Create a temporary directory, starts off empty
+     dir <- tempfile()
+     gd <- gadget_directory(dir)
+     expect_equal(list.files(dir), character(0))
+ 
+     sample_data <- data.frame(year = 1, step = 1, area = 1:3, predator_length = 'pred100',
+         prey_length = c('cod', 'anacoda', 'cod.imm'),
+         ratio = 1)
+ 
+     # Default to get assigned eveywhere
+     gadget_dir_write(gd, gadget_likelihood_component(
+         'stomachcontent',
+         data = sample_data,
+         prey_length = list(cod = 10:20, anacoda = 1:5, "cod.imm" = 1:10),
+         prey_labels = 'Prey 10'))
+     ok(cmp_file(gd, gadget_dir_read(gd, "likelihood")$components[[2]]$preyaggfile,
+         ver_string,
+         "; ",
+         "cod\t",
+         "Prey 10\t",
+         "lengths\t10\t20",
+         "digestioncoefficients\t",
+         "; ",
+         "anacoda\t",
+         "Prey 10\t",
+         "lengths\t1\t5",
+         "digestioncoefficients\t",
+         "; ",
+         "cod.imm\t",
+         "Prey 10\t",
+         "lengths\t1\t10",
+         "digestioncoefficients\t",
+         NULL))
+ 
+     # The first match in the list wins, we match from the start
+     gadget_dir_write(gd, gadget_likelihood_component(
+         'stomachcontent',
+         data = sample_data,
+         prey_length = list(cod = 10:20, anacoda = 1:5, "cod.imm" = 1:10),
+         prey_labels = list("cod" = "all.cod", "cod.imm" = "immature.cod", "other"),
+         prey_digestion_coefficients = list("cod.imm" = c(1,1,1), "cod" = c(3,3,3), c(9,9,9))))
+     ok(cmp_file(gd, gadget_dir_read(gd, "likelihood")$components[[2]]$preyaggfile,
+         ver_string,
+         "; ",
+         "cod\t",
+         "all.cod\t",
+         "lengths\t10\t20",
+         "digestioncoefficients\t3\t3\t3",
+         "; ",
+         "anacoda\t",
+         "other\t",
+         "lengths\t1\t5",
+         "digestioncoefficients\t9\t9\t9",
+         "; ",
+         "cod.imm\t",
+         "all.cod\t",
+         "lengths\t1\t10",
+         "digestioncoefficients\t1\t1\t1",
+         NULL))
+     gadget_dir_write(gd, gadget_likelihood_component(
+         'stomachcontent',
+         data = sample_data,
+         prey_length = list(cod = 10:20, anacoda = 1:5, "cod.imm" = 1:10),
+         prey_labels = list("cod.imm" = "immature.cod", "cod" = "all.cod", "other"),
+         prey_digestion_coefficients = list("cod" = c(3,3,3), "cod.imm" = c(1,1,1), c(9,9,9))))
+     ok(cmp_file(gd, gadget_dir_read(gd, "likelihood")$components[[2]]$preyaggfile,
+         ver_string,
+         "; ",
+         "cod\t",
+         "all.cod\t",
+         "lengths\t10\t20",
+         "digestioncoefficients\t3\t3\t3",
+         "; ",
+         "anacoda\t",
+         "other\t",
+         "lengths\t1\t5",
+         "digestioncoefficients\t9\t9\t9",
+         "; ",
+         "cod.imm\t",
+         "immature.cod\t",
+         "lengths\t1\t10",
+         "digestioncoefficients\t3\t3\t3",
+         NULL))
+ })
# stomachcontent - matching of prey to labels
ok - list.files(dir) == character(0)
ok - cmp_file(gd, gadget_dir_read(gd, "likelihood")$components[[2
ok - cmp_file(gd, gadget_dir_read(gd, "likelihood")$components[[2
ok - cmp_file(gd, gadget_dir_read(gd, "likelihood")$components[[2
> 
> ###############################################################################
> ok_group("catchinkilos", {
+     # aggregationlevel = 0
+     comp <- gadget_likelihood_component(
+         'catchinkilos',
+         data = data.frame(year = 1, step = 1:3, area = 1, fleet = 1, total_weight = 11:13))
+     ok(cmp(names(comp$datafile$data), c("year", "step", "area", "fleet", "total_weight")), "Has step column")
+ 
+     # aggregationlevel = 1
+     comp <- gadget_likelihood_component(
+         'catchinkilos',
+         data = structure(data.frame(year = 1, step = 1, area = 1, fleet = 1, total_weight = 11:13),
+             step = mfdb_timestep_yearly))
+     ok(cmp(names(comp$datafile$data), c("year", "area", "fleet", "total_weight")), "step column removed")
+ })
# catchinkilos
ok - Has step column
ok - step column removed
> 
> proc.time()
   user  system elapsed 
   1.40    0.31    1.73 
1..135
# Looks like you passed all 135 tests.