sensitivity analysis branch by JoeWaddell · Pull Request #1913 · RuminantFarmSystems/RuFaS

JoeWaddell · 2024-08-10T17:01:38Z

Context

Issue(s) closed by this pull request: closes #

The changelog has been updated.

How big are the changes in the PR? Would you nominate it for a major version upgrade?

Yes
No

What

Why

How

Test plan

This reverts commit ed9260f.

…nto sobol

krb78 · 2025-01-30T18:54:48Z

input/data/tasks/sobol1k_128_tasks.json

not the kind of input you are asking for, but this seems like a tight boundary. I'd expand to at least 400, probably even 440, as the upper bound

krb78 · 2025-01-30T18:55:47Z

input/data/tasks/sobol1k_128_tasks.json

and this one is a little aggressively low - tighten up a bit. 200-230 is probably the set of bounds you want here.

krb78 · 2025-01-30T18:56:50Z

input/data/tasks/sobol1k_128_tasks.json

is this one in here twice?

krb78 · 2025-01-30T18:58:58Z

input/data/tasks/sobol1k_128_tasks.json

why include this one if you are running conventional semen instead of sexed?

krb78 · 2025-01-30T20:19:07Z

input/data/tasks/sobol1k_128_tasks.json

1?! wowie you are very optimistic haha. maybe 0.6 would be a better upper limit, or 0.7 if you really want to push it in the adult herd.

krb78 · 2025-01-30T20:19:33Z

input/data/tasks/sobol1k_128_tasks.json

probably reasonable to expand this to 30

krb78 · 2025-01-30T20:19:56Z

input/data/tasks/sobol1k_128_tasks.json

28 to 40 would be better

krb78 · 2025-01-30T20:21:20Z

input/data/tasks/sobol1k_128_tasks.json

why keep these so small? don't they impact nutrient requirements of the cows? some cows walk 0.25-0.5 miles to the parlor on dry lot dairies

krb78 · 2025-01-30T20:24:10Z

model_evaluation/sensitivity_analysis/analyze_SA_analysis_main.py

hehe, I wondered what ME was :) makes perfect sense now!

matthew7838 · 2025-01-31T06:05:56Z

RUFAS/routines/animal/life_cycle/cow.py

If there's no linked issue to this, either the issue should be created or the comment should be deleted.

matthew7838 · 2025-01-31T06:08:41Z

RUFAS/routines/animal/life_cycle/cow.py

I think you're trying to catch division by zero error here. that could be more specific in the except statement.

matthew7838 · 2025-01-31T06:10:52Z

model_evaluation/sensitivity_analysis/SA_helpers.py

Is there a particular reason for leaving this here?

matthew7838 · 2025-01-31T06:14:25Z

model_evaluation/sensitivity_analysis/SA_helpers.py

Suggested change

intnames = [str(x).replace("(", "") for x in intnames]

intnames = [str(x).replace(")", "") for x in intnames]

intnames = [str(x).replace(",", "*") for x in intnames]

intnames = [str(x).replace(" ", "") for x in intnames]

trans_table = str.maketrans({"(": "", ")": "", ",": "*", " ": ""})

intnames = [str(x).translate(trans_table) for x in intnames]

matthew7838 · 2025-01-31T06:15:15Z

model_evaluation/sensitivity_analysis/SA_helpers.py

Suggested change

# print(a)

for i in a:

# print(i)

for i in a:

matthew7838 · 2025-01-31T06:28:40Z

model_evaluation/sensitivity_analysis/analyze_SA_analysis_main.py

Suggested change

pass

matthew7838 · 2025-01-31T06:34:52Z

model_evaluation/sensitivity_analysis/analyze_SA_analysis_main.py

Using str.startwith() is a lot safer to check if it actually starts with a particular pattern.

…nto sobol

JoeWaddell and others added 30 commits May 5, 2024 17:33

tasks updated

a0aab1c

added sobol sampler

30e440e

sobol1k run

b5c7ef1

analytical methods and new input files

828b889

analysis updates

40c8fba

analysis updates only inputs

3acd668

inputs_to_collate analysis

d5b4db0

outputs_to_collate

538b81a

analysis updates- bugfix

693747f

analyze SA updates

c6be8cc

Merge branch 'main' into sobol

3577b42

updated inputs

908bfd1

morris analysis

1f90393

input bound updates

7e22e0d

removed cull params from inputs, updated task manager metadata

e29dee3

tasks update

28d49e9

added minimum new stall size of 1

3e949b8

updated minimums in test sobol animal tasks

9bc9c32

minimum daily milk of 1 kg

159d605

added Catastrophic ration formulation error

f9ff78b

added bound clipping

7a32110

analysis updates

570c8b4

ration fixes from other branches

0f45153

another task file

0ddee70

exploratory analysis updates

af726fc

fix for gestation_length - AnimalBase.config["days_in_preg_when_dry"]

96054f8

try_catch

f46ef5a

try_catch

35de46f

return

ed9260f

Revert "return"

338b782

This reverts commit ed9260f.

JoeWaddell and others added 20 commits August 28, 2024 12:45

updated tasks file and metadata

46c9785

analytical updates

22169d9

updated and reorganized analysis scripts

b7d6afc

updated for benchmarking

c4e0c9f

updated names, balancing

e5c338f

Merge branch 'dev' into sobol

df11084

moved analytical scripts, archived old input sheets

712a151

brought feed back to dev

4cd1cc0

reverting defaults

c467424

Merge c467424 into 72cb550

bafd5ba

Apply Black Formatting

776ba0e

Update badges on README

5ae3cae

updated useful analytical scripts, removed deprecated

6598021

Merge branch 'sobol' of https://github.com/RuminantFarmSystems/MASM i…

45f70a4

…nto sobol

Merge 45f70a4 into 72cb550

7d6a2e7

Apply Black Formatting

ef45950

removed debugging statements

09540e1

Merge branch 'sobol' of https://github.com/RuminantFarmSystems/MASM i…

66c8a3b

…nto sobol

Merge 66c8a3b into 72cb550

ba5349c

Apply Black Formatting

67b5aa6

krb78 reviewed Jan 30, 2025

View reviewed changes

matthew7838 reviewed Jan 31, 2025

View reviewed changes

JoeWaddell added 2 commits February 4, 2025 17:19

updating bounds

cdddff5

Merge branch 'sobol' of https://github.com/RuminantFarmSystems/MASM i…

a684903

…nto sobol

PooyaHekmati force-pushed the sobol branch from 4c44295 to a684903 Compare June 19, 2025 03:43

PooyaHekmati force-pushed the dev branch from 71e0926 to be3db89 Compare June 19, 2025 03:47

PooyaHekmati closed this Jun 19, 2025

PooyaHekmati deleted the sobol branch June 19, 2025 03:50

PooyaHekmati restored the sobol branch June 19, 2025 03:57

PooyaHekmati reopened this Jun 19, 2025

-    intnames = [str(x).replace("(", "") for x in intnames]
-    intnames = [str(x).replace(")", "") for x in intnames]
-    intnames = [str(x).replace(",", "*") for x in intnames]
-    intnames = [str(x).replace(" ", "") for x in intnames]
+    trans_table = str.maketrans({"(": "", ")": "", ",": "*", " ": ""})
+    intnames = [str(x).translate(trans_table) for x in intnames]

-        # print(a)
-        for i in a:
-            # print(i)
+        for i in a:

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JoeWaddell commented Aug 10, 2024 •

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