Update reference document path in report output configuration
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@ -13,7 +13,8 @@ params:
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x_axis_unit: "days"
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output:
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word_document:
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reference_docx: !expr params$ref toc: no
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reference_docx: !expr file.path("word-styles-reference-var1.docx")
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toc: no
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editor_options:
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chunk_output_type: console
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---
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@ -461,179 +461,3 @@ rmarkdown::render(
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output_dir = "laravel_app/storage/app/angata/reports"
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)
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#
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# EXPECTED OUTPUT:
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# File: SmartCane_Report_*_{PROJECT}_{DATE}.docx
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# Location: laravel_app/storage/app/{PROJECT}/reports/
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# Script execution time: 5-10 minutes
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#
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# NOTE:
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# These are R Markdown files and cannot be run directly via Rscript
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# Use rmarkdown::render() from an R interactive session or wrapper script
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# See run_full_pipeline.R for an automated example
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#
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# ============================================================================
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# ==============================================================================
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# QUICK REFERENCE: Common Workflows
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# ==============================================================================
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#
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# WORKFLOW A: Weekly Update (Most Common)
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# ─────────────────────────────────────────────────────────────────────────
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# Goal: Process latest week of data through full pipeline
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#
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# Parameters:
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# $PROJECT = "angata"
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# $END_DATE = "2026-02-04" # Today or latest date available
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# $OFFSET = 7 # One week back
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#
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# Steps:
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# 1. SKIP Python download (if you already have data)
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# 2. Run R10: & "C:\Program Files\R\R-4.4.3\bin\x64\Rscript.exe" r_app/10_create_per_field_tiffs.R angata 2026-02-04 7
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# (Argument order: [PROJECT] [END_DATE] [OFFSET])
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# 3. Run R20: & "C:\Program Files\R\R-4.4.3\bin\x64\Rscript.exe" r_app/20_ci_extraction_per_field.R angata 2026-02-04 7
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# 4. Run R30: & "C:\Program Files\R\R-4.4.3\bin\x64\Rscript.exe" r_app/30_interpolate_growth_model.R angata
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# 5. Run R21: & "C:\Program Files\R\R-4.4.3\bin\x64\Rscript.exe" r_app/21_convert_ci_rds_to_csv.R angata
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# 6. Run R40: & "C:\Program Files\R\R-4.4.3\bin\x64\Rscript.exe" r_app/40_mosaic_creation_per_field.R 2026-02-04 7 angata
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# (Argument order: [END_DATE] [OFFSET] [PROJECT])
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# 7. Run R80: & "C:\Program Files\R\R-4.4.3\bin\x64\Rscript.exe" r_app/80_calculate_kpis.R 2026-02-04 angata 7
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# (Argument order: [END_DATE] [PROJECT] [OFFSET] - DIFFERENT from R40!)
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# 8. OPTIONAL R91 (Cane Supply) - Use automated runner:
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# & "C:\Program Files\R\R-4.4.3\bin\x64\Rscript.exe" r_app/run_full_pipeline.R
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# OR from R console:
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# rmarkdown::render("r_app/91_CI_report_with_kpis_cane_supply.Rmd",
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# params=list(data_dir="angata", report_date=as.Date("2026-02-04")),
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# output_file="SmartCane_Report_cane_supply_angata_2026-02-04.docx",
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# output_dir="laravel_app/storage/app/angata/reports")
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#
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# Execution time: ~60-90 minutes total
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#
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#
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# WORKFLOW B: Initial Setup (Large Backfill)
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# ─────────────────────────────────────────────────────────────────────────
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# Goal: Process multiple weeks of historical data
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#
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# Steps:
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# 1. Python download (your entire date range)
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# 2. Run R10 with large offset to process all historical dates:
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# & "C:\Program Files\R\R-4.4.3\bin\x64\Rscript.exe" r_app/10_create_per_field_tiffs.R angata 2026-02-04 365
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# (This processes from 2025-02-04 to 2026-02-04, covering entire year)
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# 3. Run R20 with large offset to process all historical dates:
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# & "C:\Program Files\R\R-4.4.3\bin\x64\Rscript.exe" r_app/20_ci_extraction_per_field.R angata 2026-02-04 365
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# (This processes from 2025-02-04 to 2026-02-04, covering entire year)
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# 4. Run R30 once (growth model full season)
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# 5. Run R21 once (CSV export)
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# 6. Run R40 with specific week windows as needed
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# 7. Run R80 for each week you want KPIs for
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# 6. For each week, run:
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# - R40 with different END_DATE values (one per week)
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# - R80 with different WEEK/YEAR values (one per week)
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# - R91 optional (one per week report)
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#
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# Pro tip: Script R40 with offset=14 covers two weeks at once
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# Then R40 again with offset=7 for just one week
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#
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#
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# WORKFLOW C: Troubleshooting (Check Intermediate Outputs)
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# ─────────────────────────────────────────────────────────────────────────
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# Goal: Verify outputs before moving to next step
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#
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# After R10: Check field_tiles/{FIELD_ID}/ has #dates files
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# After R20: Check field_tiles_CI/{FIELD_ID}/ has same #dates files
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# After R30: Check Data/extracted_ci/cumulative_vals/ has All_pivots_*.rds
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# After R40: Check weekly_mosaic/{FIELD_ID}/ has week_WW_YYYY.tif per week
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# After R80: Check output/ has {PROJECT}_field_analysis_week*.xlsx
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#
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# ============================================================================
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# ==============================================================================
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# TROUBLESHOOTING
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# ==============================================================================
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#
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# ISSUE: R20 not processing all field_tiles files
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# ────────────────────────────────────────────────
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# Symptom: field_tiles has 496 files, field_tiles_CI only has 5
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#
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# Possible causes:
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# 1. Source files incomplete or corrupted
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# 2. Script 20 skips because CI TIFF already exists (even if incomplete)
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# 3. Partial run from previous attempt
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#
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# Solutions:
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# 1. Delete the small number of files in field_tiles_CI/{FIELD}/ (don't delete all!)
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# rm laravel_app/storage/app/angata/field_tiles_CI/{fieldnum}/*
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# 2. Re-run Script 20
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# 3. If still fails, delete field_tiles_CI completely and re-run Script 20
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# rm -r laravel_app/storage/app/angata/field_tiles_CI/
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#
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# ISSUE: Script 80 says "No per-field mosaic files found"
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# ────────────────────────────────────────────────────────
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# Symptom: R80 fails to calculate KPIs
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#
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# Possible causes:
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# 1. Script 40 hasn't run yet (weekly_mosaic doesn't exist)
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# 2. Wrong END_DATE or WEEK/YEAR combination
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# 3. weekly_mosaic/{FIELD}/ directory missing (old format?)
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#
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# Solutions:
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# 1. Ensure Script 40 has completed: Check weekly_mosaic/{FIELD}/ exists with week_WW_YYYY.tif
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# 2. Verify END_DATE is within date range of available CI data
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# 3. For current week: End date must be THIS week (same ISO week as today)
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#
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# ISSUE: Python download fails ("Not authorized")
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# ────────────────────────────────────────────────
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# Symptom: python 00_download_8band_pu_optimized.py fails with authentication error
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#
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# Cause: PLANET_API_KEY environment variable not set
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#
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# Solution:
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# 1. Save your Planet API key: $env:PLANET_API_KEY = "your_key_here"
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# 2. Verify: $env:PLANET_API_KEY (should show your key)
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# 3. Try download again
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#
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# ISSUE: R30 takes too long
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# ──────────────────────────
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# Symptom: Script 30 running for >30 minutes
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#
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# Cause: LOESS interpolation is slow with many dates/fields
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#
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# Solution:
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# 1. This is normal - large date ranges slow down interpolation
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# 2. Subsequent runs are faster (cached results)
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# 3. If needed: reduce offset or run fewer weeks at a time
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#
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# ==============================================================================
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# ==============================================================================
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# SUMMARY OF FILES CREATED BY EACH SCRIPT
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# ==============================================================================
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#
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# Script 10 creates:
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# laravel_app/storage/app/{PROJECT}/field_tiles/{FIELD}/{DATE}.tif
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#
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# Script 20 creates:
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# laravel_app/storage/app/{PROJECT}/field_tiles_CI/{FIELD}/{DATE}.tif
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# laravel_app/storage/app/{PROJECT}/Data/extracted_ci/daily_vals/{FIELD}/{DATE}.rds
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#
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# Script 30 creates:
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# laravel_app/storage/app/{PROJECT}/Data/extracted_ci/cumulative_vals/All_pivots_Cumulative_CI_quadrant_year_v2.rds
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#
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# Script 21 creates:
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# laravel_app/storage/app/{PROJECT}/ci_data_for_python.csv
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#
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# Python 31 creates:
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# laravel_app/storage/app/{PROJECT}/reports/kpis/field_stats/{PROJECT}_harvest_imminent_week_{WW}_{YYYY}.csv
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#
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# Script 40 creates:
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# laravel_app/storage/app/{PROJECT}/weekly_mosaic/{FIELD}/{DATE}/week_{WW}_{YYYY}.tif
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#
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# Script 80 creates:
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# laravel_app/storage/app/{PROJECT}/output/{PROJECT}_field_analysis_week{WW}_{YYYY}.xlsx
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# laravel_app/storage/app/{PROJECT}/output/{PROJECT}_field_analysis_week{WW}_{YYYY}.rds
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#
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# Script 90/91 creates:
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# laravel_app/storage/app/{PROJECT}/output/SmartCane_Report_week{WW}_{YYYY}.docx
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#
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# ==============================================================================
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