Background reading material: the Standard Tree
Manifesto.
The recommendation is to organize data_preparation and model_runs as top
directories. There are often different people involved in data preparation vs.
model runs, and both consist of a large number of subdirectories.
The plots also becomes a top directory and is not optional. This is an
essential part of the work that is carried over to the person who will conduct
the next assessment of the stock. The plot scripts read files from
data_preparation and model_runs and are written in a clear and reproducible
format, allowing all team members to produce most (ideally all) of the figures
found in the stock assessment report. One script for each final report figure
should be a practical and general rule.
In the table below, the 5 top directories should be required and the naming
scheme for subdirectories is recommended. The 'Example contents' column,
however, will vary depending on focus topics for that assessment. Lowercase
directory names are useful to prevent OS-specific errors in scripts.
| Top dir |
Subdir |
Example contents |
| (1) data_preparation |
age_length |
|
| " |
cpue |
4region, 8region, 1region |
| " |
fisheries |
4region, 8region, 1region |
| " |
growth |
|
| " |
maturity |
|
| " |
natmort |
|
| " |
regions |
|
| " |
size_comps |
4region, 8region, 1region |
| " |
tagging |
4region, 8region, 1region |
| (2) model_runs |
setup |
basefiles, condorfiles, doitall, executable |
| " |
stepwise |
I: newexe, catchcond, initpop, reprate, dirichlet, compwts, II: revisedata, newyears, 4region |
| " |
jitter |
|
| " |
diagnostic |
|
| " |
hessian |
|
| " |
lprof |
|
| " |
retro |
|
| " |
sensitivities |
1region |
| " |
kobe_majuro |
|
| " |
impact |
|
| " |
grid |
|
| " |
projections |
|
| " |
web |
|
| (3) plots |
assessment |
|
| " |
data |
|
| " |
shiny |
|
| (4) presentations |
weekly |
|
| " |
paw |
|
| " |
sc |
|
| (5) writeup |
assessment |
tables |
| " |
data_inputs |
new_cpue, regional_structure |
| Top dir |
Subdir |
Contents |
| (1) assessment |
data_preparation |
age_length, biology, cpue, fisheries, frq, length_comps, mfdgr, tagging |
| " |
model_runs |
run001, run009, ..., run535 |
| " |
projections |
|
| " |
refcase |
|
| " |
setup |
basefiles, condorfiles, doitall |
| (2) write-up |
assessment |
|
| " |
presentation |
|
| " |
working |
figs, functions, tables |
| Top dir |
Subdir |
Contents |
| (1) assessment |
data_preparation |
biology, fisheries, cpue, length_comps, growth, mfdgr, regions, tagging |
| " |
model_runs |
diagnostic, grid, hessian, lprof, retro, sensitivities |
| " |
setup |
build, condor, exe |
| (2) presentations |
|
|
| (3) write-up |
assessment |
figures, tables |
| " |
data |
|
| Top dir |
Subdir |
Contents |
| (1) 4fin |
kobe |
|
| " |
retro |
|
| (2) 4john |
s1m1d1r1g1 |
|
| " |
... |
|
| " |
s3m2d3r2g2 |
|
| " |
wcpo21 |
m1, m2 |
| (3) 4nick |
spo21_hessianfiles |
|
| (4) backccj |
alb21 |
s1m1d1r1g1, ..., s3m2d3r2g2, impact, lprof, plots, projections, retro, web |
| (5) datainputs |
catchplots |
|
| (6) fisheries_plots |
|
|
| (7) presentations |
|
|
| (8) stock_assessment_rep_2021 |
figures |
|
| " |
tables |
|
| Top dir |
Subdir |
Contents |
| (1) assessment |
data_preparation |
cpue, doitall, length_comps, mfdgr, movements, seapodym, tagging |
| " |
model_runs |
run01, ..., run500, growthvar, post_sc, projections, stepwise) |
| " |
refcase |
|
| " |
setup |
basefiles, condor, step |
| (2) write-up |
|
|
| Top dir |
Subdir |
Contents |
| (1) assessment |
data_preparation |
age_length, catch, cpue, fisheries, growth, maturity, mfdgr, tagging |
| " |
model_runs |
grid, retro, sensitivities, stepwise, web |
| " |
setup |
basefiles, build, condorfiles, exe, grid, retro |
| (2) presentations |
cpue_workshop |
|
| " |
paw |
|
| " |
sc |
|
| (3) writeup |
assessment |
|
| " |
figures |
|
| " |
inputs |
|
| " |
tables |
|
| Top dir |
Subdir |
Contents |
| (1) data_prep |
age_length |
|
| " |
cpue |
|
| " |
doitall |
|
| " |
growth |
|
| " |
maturity |
|
| " |
length_comps |
|
| " |
tagging |
|
| (2) model_runs |
condor |
|
| " |
grid |
|
| " |
lprof |
|
| " |
mfcl |
|
| " |
stepwise |
|
| (3) presentations |
weekly |
|
| (4) reports |
cpue_proposal |
|
| " |
figures |
|
| " |
inputs |
|
| " |
tables |
|
| Top dir |
Subdir |
Contents |
| (1) assessment |
data_preparation |
cpue, fisheries, growth, mfdgr, tagging |
| " |
model_runs |
diagnostic, grid, hessian, impact, kobe, lprof, projections, retro, sensitivities |
| " |
setup |
basefiles, build, condor, exe, retro |
| (2) presentations |
paw |
|
| " |
sc |
|
| (3) writeup |
assessment |
|
| " |
figures |
|
| " |
tables |
|
| Top dir |
Subdir |
Contents |
| (1) assessment |
data_preparation |
5region, 8region, cpue, lengthweight, maturity |
| " |
diagnostic |
hessian, impact, kobe, lprof |
| " |
model_runs |
grid, stepwise |
| " |
setup |
5region, 8region, condor, exe, fisheries, tags |
| (2) presentations |
progress |
|
| (3) writeup |
assessment |
|
| " |
fisheries |
|
| " |
inputs |
|
| Top dir |
Subdir |
Contents |
| (1) assessment |
data_preparation |
basefiles, cpue, mixing, mfdgr, tagging |
| " |
model_runs |
grid, hessian, impact, retro, rr |
| " |
presentations |
|
| " |
report |
figures |
| Top dir |
Subdir |
Contents |
| (1) assessment |
data_preparation |
build, check, doitall, mfdgr, regions, size, tagging |
| " |
model_runs |
run01, ..., run43, sensitivities |
| " |
refcase |
|
| " |
setup |
|
| (2) writeup |
assessment |
|
| " |
presentation |
|
| " |
figs |
|
| " |
tables |
|
| Top dir |
Subdir |
Contents |
| (1) assessment |
data_preparation |
cpue, fisheries, mfdgr, size, tagging |
| " |
model_runs |
diagnostics, grid, retro, sensitivities, stepwise, web |
| " |
setup |
basefiles, build, condor, exe |
| (2) presentations |
|
|
| (3) writeup |
cpue |
|
| " |
figures |
|
| " |
tables |
|
| Top dir |
Subdir |
Contents |
| (1) assessment |
datapreparation |
cpue, fisheries, growth, maturity, mfdgr, size, tagging |
| " |
modelruns |
diagnostic, grid, hessian, impact, kobe, lprof, retro, sensititivies, singleregion, stepwise |
| " |
setup |
basefiles, condor, exe, grid |
| (2) presentations |
progress |
|
| (3) writeup |
assessment |
|
| " |
figures |
|
| " |
inputs |
|
| " |
tables |
|