vignettes/incorporating-observation-data.Rmd
incorporating-observation-data.Rmd## Error in get(paste0(generic, ".", class), envir = get_method_env()) :
## object 'type_sum.accel' not foundEach run of a model will generate a likelihood score, by summing the result of any likelihood actions in the model together. To fit a model to observation data, we need to add a likelihood action that will compare observation data to the model.
To do this you either need g3l_catchdistribution() or
g3l_abundancedistribution(). As the names suggest,
g3l_catchdistribution() will compare catch data of stocks
from the provided fleets/predators,
g3l_abundancedistribution() will compare total abundance of
stocks. Otherwise they are identical.
This comparison is a 2 stage process:
function_f) is
supplied to g3l_*distribution(), to convert to a likelihood
score. For example g3l_distribution_sumofsquares(), which
compares the relative abundance of each grouping vs. the model, and sums
the square of theseWe saw the following example in
vignette("introduction-single-stock"):
# TODO: This isn't a brilliantly-named example, something else?
# Generate random data
expand.grid(year = 1990:1994, step = 3, area = 'IXa') |>
# Fill in a number column with total numbers in that year/step/area combination
mutate(number = runif(n(), min = 10000, max = 100000)) ->
dist_si_acoustic
actions_likelihood_si_acoustic <- list(
g3l_abundancedistribution(
"dist_si_acoustic",
obs_data = dist_si_acoustic,
stocks = list(fish),
function_f = g3l_distribution_surveyindices_log(alpha = NULL, beta = 1),
area_group = area_names,
report = TRUE,
nll_breakdown = TRUE),
NULL)The first step generates random observation data. We have the following columns:
There are no age or length columns, so this is total abundance within that area/time.
We use g3l_distribution_surveyindices_log(), which
calculates the likelihood score by performing a linear fit using the log
scale, the slope (beta) is fixed.
The model optimisation process will minimise the total likelihood score, and in the process fit the model to the observation data.
The function of many of gadget2’s likeihood components has been collapsed down into these 2 functions. Here is a summary of how to translate:
g3l_catchdistribution()
g3l_distribution_*() function,
e.g. g3l_distribution_sumofsquares()
g3l_abundancedistribution()
g3l_distribution_surveyindices_log() or
g3l_distribution_surveyindices_linear()
g3l_catchdistribution(function_f = g3l_distribution_sumofsquares())
gadget3 bases it’s decision on how to aggregate on the incoming data. Whilst it tries to do the “right thing” in most cases, it’s important to get the shape of this data to match what you require.
In doing so, the incoming data.frame() is converted into
an array(). We can use the
g3_distribution_preview() function to see what that array
will look like, and in doing so see how gadget3 will treat the
observation data.
Critically, your data needs to have column names it recognises. The following breaks down what can be by each column.
At least a weight or number column needs to be supplied. If a number column is present then each value will be compared to number of individuals in that group. If a weight column is present then each value will be compared to total biomass in that group.
The weight is suitable for total catches in kilos, otherwise the number column will generally be used.
If a year column is given, then catch/abundance will be aggregated by year. Gaps are allowed, if so then no comparisons will be made for that year/step.
The following observations will be compared against the total number of indivduals caught in years 1999, 2000, 2002, 2003:
g3_distribution_preview(read.table(header = TRUE, text="
year number
1999 1000
2000 1002
2002 1004
2003 1008
"))## time
## length 1999 2000 2002 2003
## 0:Inf 1000 1002 1004 1008If step is given, then it will restrict it to that step
within the year (see ?g3a_time for how to define steps in a
year).
In the following example, we will aggregate spring of 1999 & 2000, autumn of 2001. Any catch in spring of 2001, or other periods not mentioned, will be ignored:
g3_distribution_preview(read.table(header = TRUE, text="
year step number
1999 2 1020
2000 2 2040
2001 3 1902
"))## time
## length 1999-02 2000-02 2001-03
## 0:Inf 1020 2040 1902Adding a length column will aggregate catch/abundance data by the same length bins as in the observation data.
For instance:
g3_distribution_preview(read.table(header = TRUE, text="
year length number
1999 [0,10) 1023
1999 [10,20) 2938
1999 [20,30) 3948
1999 [30,40) 3855
2000 [0,10) 1023
2000 [10,20) 2938
# NB: No [10,30)
2000 [30,40) 3855
"))## time
## length 1999 2000
## 0:10 1023 1023
## 10:20 2938 2938
## 20:30 3948 NA
## 30:40 3855 3855Note that unlike with the year & step columns,
here gaps in data are preserved, in the preview output we see
NA for the missing year & length
combination. By default we will compare to 0 at this point,
this behaviour is controlled with the missing_val parameter to
?g3l_catchdistribution.
Length aggregations do not have to be hand-crafted like we do above,
a length column could be generated using dplyr::group_by()
and cut():
# Generate an unaggregated length distribution
ldist.lln.raw <- data.frame(
year = c(1999, 2000),
length = sample(10:75, 100, replace = TRUE),
number = 1,
stringsAsFactors = FALSE)
# Group length into 10-long bins
ldist.lln.raw |> dplyr::group_by(
year = year,
length = cut(length, breaks = seq(10, 100, by = 10), right = FALSE)
) |> dplyr::summarise(number = sum(number), .groups = 'keep') -> ldist.lln.agg
ldist.lln.agg## # A tibble: 14 × 3
## # Groups: year, length [14]
## year length number
## <dbl> <fct> <dbl>
## 1 1999 [10,20) 11
## 2 1999 [20,30) 5
## 3 1999 [30,40) 7
## 4 1999 [40,50) 11
## 5 1999 [50,60) 8
## 6 1999 [60,70) 7
## 7 1999 [70,80) 1
## 8 2000 [10,20) 3
## 9 2000 [20,30) 6
## 10 2000 [30,40) 14
## 11 2000 [40,50) 10
## 12 2000 [50,60) 9
## 13 2000 [60,70) 6
## 14 2000 [70,80) 2
# NB: The last 2 bins are empty, but because cut() creates a factor column,
# gadget3 knows about them even though they don't appear in the data.
g3_distribution_preview(ldist.lln.agg)## time
## length 1999 2000
## 10:20 11 3
## 20:30 5 6
## 30:40 7 14
## 40:50 11 10
## 50:60 8 9
## 60:70 7 6
## 70:80 1 2
## 80:90 NA NA
## 90:100 NA NAgadget3 will also automatically read the aggregation attributes used
by ?mfdb::mfdb_sample_count.
# Import data into a temporary database
library(mfdb)
mdb <- mfdb(tempfile(fileext=".duckdb"))
ldist.lln.raw$month <- 1
ldist.lln.raw$areacell <- 'all' # NB: We have to have an areacell mapping for MFDB
mfdb_import_area(mdb, data.frame(name = c('all'), size = c(5)))
mfdb_import_survey(mdb, ldist.lln.raw)
# Use mfdb_sample_count to extract & group in the same manner as above
ldist.lln.agg <- mfdb_sample_count(mdb, c('length'), list(
year=1999:2000,
length = mfdb_interval("len", seq(10, 100, by = 10)) ))[[1]]
g3_distribution_preview(ldist.lln.agg, area_group = c(all=1))
mfdb_disconnect(mdb)Age-length aggregations can be performed by adding an age column in a very similar manner to the length column:
We can both group by individual age values:
g3_distribution_preview(read.table(header = TRUE, text="
year age length number
1999 1 [0,10) 1026
1999 1 [10,20) 2936
1999 1 [20,30) 3962
1999 1 [30,40) 3863
1999 2 [0,10) 1026
1999 2 [10,20) 2936
1999 2 [20,30) 3962
1999 2 [30,40) 3863
"))## , , time = 1999
##
## age
## length age1 age2
## 0:10 1026 1026
## 10:20 2936 2936
## 20:30 3962 3962
## 30:40 3863 3863…or group ages together:
g3_distribution_preview(read.table(header = TRUE, text="
year age length number
1999 [1,1] [0,10) 1026
1999 [1,1] [10,20) 2936
1999 [1,1] [20,30) 3962
1999 [1,1] [30,40) 3863
1999 [2,4] [0,10) 1011
# Missing [2,4] [10,20)
1999 [2,4] [20,30) 3946
1999 [2,4] [30,40) 3872
"))## , , time = 1999
##
## age
## length 1:1 2:4
## 0:10 1026 1011
## 10:20 2936 NA
## 20:30 3962 3946
## 30:40 3863 3872As before, gaps in data are preserved, and missing_val
is used to decide what to do with them.
Again, gadget3 will also interpret aggregation generated by
group_by(age = cut(...)) or
?mfdb::mfdb_sample_count.
If a stock is divided up into multiple areas, then data can be broken down by area
area_names <- g3_areas(c('IXa', 'IXb', 'IXc'))
g3_distribution_preview(read.table(header = TRUE, text="
year area number
1999 IXa 1000
1999 IXb 4305
2000 IXa 7034
2000 IXb 2381
2001 IXb 3913
"), area_group = area_names)[length = '0:Inf',,]## area
## time IXa IXb
## 1999 1000 4305
## 2000 7034 2381
## 2001 NA 3913As before, gaps in data are preserved, and missing_val
is used to decide what to do with them.
However, if an area isn’t mentioned at all (note that
IXc does not figure in the above data), then it won’t be
compared.
If you have multiple stocks, for example because you have divided up your species into mature and immature substocks, you can use this division in likelihood components also:
st_imm <- g3_stock(c(species = 'fish', 'imm'), 1:10)
st_mat <- g3_stock(c(species = 'fish', 'mat'), 1:10)
g3_distribution_preview(read.table(header = TRUE, text="
year stock number
1999 fish_imm 1000
1999 fish_mat 4305
2000 fish_imm 7034
2000 fish_mat 2381
2001 fish_mat 3913
"), stocks = list(st_imm, st_mat))[length = '0:Inf',,]## time
## stock 1999 2000 2001
## fish_imm 1000 7034 NA
## fish_mat 4305 2381 3913The stock names have to match what gadget3 uses, or an error will be generated.
You can also use partial stock names, for example:
stocks <- list(
g3_stock(c(species = 'fish', 'imm', 'f'), 1:10),
g3_stock(c(species = 'fish', 'imm', 'm'), 1:10),
g3_stock(c(species = 'fish', 'mat', 'f'), 1:10),
g3_stock(c(species = 'fish', 'mat', 'm'), 1:10) )
drop(g3_distribution_preview(read.table(header = TRUE, text="
year stock number
1999 imm 1000
1999 mat 4305
2000 imm 7034
2000 mat 2381
"), stocks = stocks))## time
## stock 1999 2000
## imm 1000 7034
## mat 4305 2381
## attr(,"stock_map")
## fish_imm_f fish_imm_m fish_mat_f fish_mat_m
## "imm" "imm" "mat" "mat"The imm columns will compare to the sum of
fish_imm_f & fish_mat_f.
The parts do not have to be in order, the following is also valid:
drop(g3_distribution_preview(read.table(header = TRUE, text="
year stock number
1999 fish_f 1000
1999 fish_m 4305
2000 fish_f 7034
2000 fish_m 2381
"), stocks = stocks))## time
## stock 1999 2000
## fish_f 1000 7034
## fish_m 4305 2381
## attr(,"stock_map")
## fish_imm_f fish_imm_m fish_mat_f fish_mat_m
## "fish_f" "fish_m" "fish_f" "fish_m"NB: A stock can only appear in one grouping:
# NB: Wrong!
drop(g3_distribution_preview(read.table(header = TRUE, text="
year stock number
1999 f 1000
1999 imm 4305
2000 f 7034
2000 imm 2381
"), stocks = stocks))## time
## stock 1999 2000
## f 1000 7034
## imm 4305 2381
## attr(,"stock_map")
## fish_imm_f fish_imm_m fish_mat_f fish_mat_m
## "f" "imm" "f" NAfish_imm_f will only appear in the f rows,
not imm rows. In this case, multiple likelhood components
would be a better approach.
As before, gaps in data are preserved, and missing_val
is used to decide what to do with them.
fleets <- list(
g3_fleet(c('comm', country = 'se')),
g3_fleet(c('comm', country = 'fi')),
g3_fleet(c('surv', country = 'se')) )
g3_distribution_preview(read.table(header = TRUE, text="
year fleet number
1999 comm 1000
1999 surv_se 4305
2000 comm 7034
2000 surv_se 2381
2001 surv_se 3913
"), fleets = fleets)[length = '0:Inf',,]## time
## fleet 1999 2000 2001
## comm 1000 7034 NA
## surv_se 4305 2381 3913The name matching works in the same way as stocks above, and should be either the name gadget3 uses or parts of it.
As before, gaps in data are preserved, and missing_val
is used to decide what to do with them.
predators <- list(
g3_stock(c('seal', 'imm', 'f'), 10:20),
g3_stock(c('seal', 'mat', 'f'), 10:20),
g3_stock(c('seal', 'imm', 'm'), 10:20),
g3_stock(c('seal', 'mat', 'm'), 10:20) )
drop(g3_distribution_preview(read.table(header = TRUE, text="
year predator number
1999 seal_f 1000
1999 seal_m 4305
2000 seal_f 7034
2000 seal_m 2381
"), predators = predators))## time
## predator 1999 2000
## seal_f 1000 7034
## seal_m 4305 2381
## attr(,"predator_map")
## seal_imm_f seal_mat_f seal_imm_m seal_mat_m
## "seal_f" "seal_f" "seal_m" "seal_m"The name matching works in the same way as stocks above, and should be either the name gadget3 uses or parts of it.
As before, gaps in data are preserved, and missing_val
is used to decide what to do with them.