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Implement multi-site local sensitivity analysis workflow #1

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fc9f282
update config
Nov 17, 2025
1b4fae2
update template.xml
Nov 17, 2025
cb141cf
add R scripts for local sensitivity analysis
Nov 17, 2025
8fc2243
add local SA analysis script
Nov 17, 2025
68e4be6
add processed data outputs for SA
Nov 17, 2025
a38efee
add design_points_198.csv for multisite SA
Nov 17, 2025
d82f2d6
add sa_design_points.csv for SA generation
Nov 17, 2025
000c14b
add workflow scripts for local SA
Nov 17, 2025
ae7e038
Revert "add processed data outputs for SA"
Nov 18, 2025
a5c942d
Revert "add sa_design_points.csv for SA generation"
Nov 18, 2025
36370ec
made sigma configurable
Nov 18, 2025
4fe8777
update sigma_level
Nov 18, 2025
6e5489b
corrected dplyr namespace
Nov 18, 2025
b38a22a
made quantile block as first entry of sensitivity.analysis
Nov 18, 2025
ff3eafd
save regression_results as csv
Nov 18, 2025
e3ecab6
updated analyze_environmental_gradient() to fits regressions of both …
Nov 18, 2025
481d540
update local sensitivity analysis report
Nov 18, 2025
17db11a
ensure data directory exists
Nov 18, 2025
d77d112
add the data/design_points.csv path
divine7022 Nov 26, 2025
7753a3d
add process_sa_file helper function and refactor doc
divine7022 Nov 26, 2025
76a2b6a
refactored to completely drop the clustering logic and it now acts pu…
divine7022 Nov 26, 2025
10d2acf
fix indent
divine7022 Nov 26, 2025
4aba622
remove XML dependency and replaced raw XML file re-parsing with direc…
divine7022 Nov 26, 2025
9b701ae
correct design_points path
divine7022 Dec 8, 2025
8692fdc
fix sa variables extraction logic
divine7022 Dec 10, 2025
2c0b932
address review comments
divine7022 Feb 27, 2026
57865a5
cleanup unused
divine7022 Feb 27, 2026
47621d3
update comment
divine7022 Mar 5, 2026
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11 changes: 11 additions & 0 deletions 000-config.yml
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Expand Up @@ -8,8 +8,19 @@ default:
raw_data_dir: "data_raw"
cache_dir: "cache"
pecan_outdir: "/projectnb2/dietzelab/ccmmf/modelout/ccmmf_phase_2b_mixed_pfts_20250701"

@dlebauer dlebauer Feb 3, 2026

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Once we have ccmmf_dir, can we change this to use that as a variable? That way it is only necessary to change the system-specific path once. (also applies to master_design points etc. )

Suggested change
pecan_outdir: "/projectnb2/dietzelab/ccmmf/modelout/ccmmf_phase_2b_mixed_pfts_20250701"
pecan_outdir: "$ccmmf_dir/modelout/ccmmf_phase_2b_mixed_pfts_20250701"

@divine7022 divine7022 Feb 27, 2026

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I looked into this, unfortunately yaml doesn't support variable substitution like $ccmmf_dir/modelout/...
If you'd prefer we could switch to an R based config

master_design_points: "/projectnb2/dietzelab/ccmmf/data/design_points.csv"

@dlebauer dlebauer Feb 4, 2026

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nit: these are just design points ...

Suggested change
master_design_points: "/projectnb2/dietzelab/ccmmf/data/design_points.csv"
design_points: "/projectnb2/dietzelab/ccmmf/data/design_points.csv"

@divine7022 divine7022 Feb 27, 2026

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rename 👍

pecan_xml_template: "data_raw/template.xml"
sites:
design_points_file: "data_raw/sa_design_points.csv"
n_sample: 10

@dlebauer dlebauer Mar 14, 2026

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I think it would be more clear to put n_sample and any other values that will be used in dev mode into a separate 'development' chunk

sensitivity:

@dlebauer dlebauer Nov 21, 2025

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The goal with this file was to handle settings that aren't in the pecan xml. Is there a reason that these are included here rather than the template.xml?

Minimizing config options here, and providing sensible defaults in the template.xml could make it more clear to end users.

@divine7022 divine7022 Feb 27, 2026

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good point, template.xml already holds most pecan specific defaults. The items in 000-config.yml fall into two categories,
1 ) project level paths (ccmmf_dir, design_points, pecan_outdir) -- these are system specific and shouldn't live in template.xml since can change per machine

2 ) run configs (n_ensemble, n_met, start_date, end_date) -- moved these here from being hardcoded in
002_build_xml.R so users can configure them in one place. They feed into the XML building step

I have minimized config, let me know if you still have any specifics

sigma_levels: [-3, -2, -1, 1, 2, 3] # Standard
# Or use [-2, -1, 1, 2] for faster runs
# ensemble:
# size: 20
# n_met: 10
# run:
# start_date: "2016-01-01"
# end_date: "2023-12-31"
projection:
ca_albers_crs: 3310
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