Timon
dc7c346854
updated whole workflow and architercutre md
2026-01-12 09:34:13 +01:00
Timon
d22dc2f96e
commit all stuff
2026-01-06 14:17:37 +01:00
Timon
d5fd4bb463
Add KPI reporting system and deployment documentation
...
Major Changes:
- NEW: Scripts 09 & 10 for KPI calculation and enhanced reporting
- NEW: Shell script wrappers (01-10) for easier execution
- NEW: R packages flextable and officer for enhanced Word reports
- NEW: DEPLOYMENT_README.md with complete deployment guide
- RENAMED: Numbered R scripts (02, 03, 04) for clarity
- REMOVED: Old package management scripts (using renv only)
- UPDATED: Workflow now uses scripts 09->10 instead of 05
Files Changed: 90+ files
New Packages: flextable, officer
New Scripts: 09_run_calculate_kpis.sh, 10_run_kpi_report.sh
Documentation: DEPLOYMENT_README.md, EMAIL_TO_ADMIN.txt
See DEPLOYMENT_README.md for full deployment instructions.
2025-10-14 11:49:30 +02:00
Martin Folkerts
d258a2bf2e
cleaned the folders, made some parameters
2025-09-05 15:23:41 +02:00
Martin Folkerts
77d67c36ca
Merge branch 'code-improvements'
2025-06-25 11:03:33 +02:00
Timon
a6aa002d33
minor visualistion chagnes
2025-06-25 11:01:37 +02:00
Martin Folkerts
0e7f5cf11d
Merge branch 'code-improvements'
2025-06-25 10:47:11 +02:00
Timon
ea6842af48
minor visualistion chagnes
2025-06-25 10:39:26 +02:00
Martin Folkerts
cc6b9392d6
Merge branch 'code-improvements'
2025-06-25 09:35:19 +02:00
Timon
b2fcd66d2b
klaar voor testen, wat plaatjes e.d. aangepast
2025-06-24 21:02:54 +02:00
Timon
4d6439d5e0
Add reproducible R package management system
...
- Add renv.lock with exact package versions for reproducibility
- Add package_manager.R for automated package installation/updates
- Add extract_current_versions.R for package discovery
- Configure renv environment for team collaboration
All team members can now run source('r_app/package_manager.R') to get identical package environment
2025-06-24 14:51:22 +02:00
Martin Folkerts
a316b30afc
Merge branch 'code-improvements'
2025-06-24 09:58:56 +02:00
Timon
6efcc8cfec
Fix CI report pipeline: update tmap v4 syntax, add continuous color scales, fix formatting
...
- Updated all CI maps to use tm_scale_continuous() for proper tmap v4 compatibility
- Added fixed color scale limits (1-8 for CI, -3 to +3 for differences) for consistent field comparison
- Fixed YAML header formatting issues in CI_report_dashboard_planet.Rmd
- Positioned RGB map before CI overview map as requested
- Removed all obsolete use_breaks parameter references
- Enhanced error handling and logging throughout the pipeline
- Added new experimental analysis scripts and improvements to mosaic creation
2025-06-19 20:37:20 +02:00
Timon
bb2a599075
Enhanced SmartCane executive summary report with explanatory text and fixed priority map coloring
...
Added explanatory text for all visualizations
Fixed priority map color scheme (red=high priority, green=low priority)
Improved error handling in farm health data calculations
Added fallback mechanisms for missing data
2025-04-23 09:47:19 +02:00
Timon
2bed5949fa
Refactor CI plotting functions to use proper parameterization
...
- Refactored ci_plot and cum_ci_plot functions to accept explicit parameters
- Added default values for backward compatibility
- Updated CI_report_dashboard_planet.Rmd to pass explicit parameters
- Added input validation for better error handling
- Added parameter documentation in function headers
- Removed reliance on global variables for better maintainability
2025-04-22 21:41:18 +02:00
Timon
07aee7bed1
[200~Improve CI report visualization and migrate to terra package
...
- Replace raster package with terra throughout the codebase
- Update map visualizations with better layout and legends
- Add descriptive headers to report sections
- Improve map legend positioning and sizing
- Enhance error handling for missing data
- Remove redundant legends in field-specific visualizations
- Optimize figure dimensions to prevent page overflow
- Expand documentation of CI index and report components
- Update package dependencies in packages.
2025-04-22 20:55:02 +02:00
Timon
fbc8f5e11b
wip
2025-04-22 17:43:11 +02:00
Martin Folkerts
eb9803fbf1
Removed yieldprediction from CI_report_dashboard_planet.Rmd edited online with Bitbucket
2025-04-02 12:53:29 +00:00
Martin Folkerts
ddad4240d5
added conditional to not run prediction if requirements are not met
2025-03-25 16:09:31 +01:00
Timon
29e2867b41
adding docx
2025-03-25 10:42:04 +01:00
Martin Folkerts
dd1ee2b1a0
adjusted dates to iso dates
2025-01-07 14:24:38 +01:00
Timon
d0ff25acf9
timely save
2024-12-16 16:26:34 +01:00
Martin Folkerts
9b29dc4d57
updated signature of cum ci plot
2024-12-03 09:32:04 +01:00
Martin Folkerts
3bfa7e1750
some update to get mkulazi to work
2024-11-18 13:41:58 +01:00
Martin Folkerts
576250982c
fixed plot colouring and made ci_extraction resilient against none file;
2024-11-11 20:55:59 +01:00
Martin Folkerts
c8ef406545
added Catalog package with config and changed iteration to use available_slots
2024-11-11 10:26:02 +01:00
Martin Folkerts
db68fd8e83
removed column for plot colors
2024-11-07 11:43:09 +01:00
Martin Folkerts
3093c86e3a
okay
2024-10-31 22:35:59 +01:00
Timon
c1a32bf6ad
Refactor cum_ci_plot function for enhanced plotting options; added parameters for plot type and season filtering; improved x-axis labeling and updated ggplot aesthetics. Also, continued work on yield prediction in R.
2024-10-31 11:21:39 +01:00
Martin Folkerts
ddb4fdbc02
updated date format for excel
2024-10-28 15:57:23 +01:00
Martin Folkerts
f08da04c3b
added DownloadCreditsCommand some updates
2024-10-23 09:34:52 +02:00
Martin Folkerts
056b8dd67b
okay
2024-09-17 14:56:33 +02:00
Martin Folkerts
4beca30d2e
okay
2024-08-30 16:27:32 +02:00
Martin Folkerts
7bf4f0930d
added log as project file;
2024-08-30 16:16:26 +02:00
Martin Folkerts
499744db6d
moved logging arroudn
2024-08-30 12:09:13 +02:00
Martin Folkerts
7d671ba69c
moved end_date and added a is.na wrapping to set when running in R_Studio
2024-08-30 10:37:02 +02:00
Timon
4dd84b10a5
source(utils) aangepast voor online versie
2024-08-30 09:52:02 +02:00
Timon
bd9b7d4ab0
adjusted all functions and cleaned scripts incl rmd file
2024-08-29 16:48:24 +02:00
Timon
611bc17017
adjusted all functions and cleaned scripts
2024-08-29 16:35:59 +02:00
Martin Folkerts
ad2f41482f
updated create_report.sh to have borders option
2024-08-28 14:52:42 +02:00
Martin Folkerts
2598306643
removed chemba as a option from parameters so it is treathed as a regular project
2024-08-28 10:18:53 +02:00
Martin Folkerts
23ba088434
added logging to getTifsAsZip
2024-08-27 11:46:34 +02:00
Martin Folkerts
509f924c58
me
2024-08-26 16:23:52 +02:00
Martin Folkerts
c5f9c8e3ca
okay
2024-08-26 16:19:22 +02:00
Martin Folkerts
dce7344947
updated project
2024-08-26 14:01:57 +02:00
Martin Folkerts
64a576d638
okay
2024-08-20 17:01:58 +02:00
Martin Folkerts
fcd900075b
toch niet
2024-07-19 15:59:28 +02:00
Martin Folkerts
3e74c72da0
okay
2024-07-19 15:54:00 +02:00
Martin Folkerts
3a081bf72a
wip;
2024-07-19 15:08:14 +02:00
Martin Folkerts
7fc9f552ab
okay
2024-07-19 15:04:23 +02:00
Martin Folkerts
3813c40ac6
okay
2024-07-19 14:49:05 +02:00
Martin Folkerts
86532128aa
okay
2024-07-19 14:45:41 +02:00
Martin Folkerts
14dee6def4
olay
2024-07-19 14:42:03 +02:00
Martin Folkerts
861244fec1
okay
2024-07-19 14:38:50 +02:00
Martin Folkerts
0109a57b04
run with one day of
2024-07-19 14:10:49 +02:00
Martin Folkerts
591a30d2a8
wip
2024-07-19 14:02:37 +02:00
Martin Folkerts
19e3f79371
wip
2024-07-19 13:28:14 +02:00
Martin Folkerts
8bac58b121
okay
2024-07-19 10:57:50 +02:00
Martin Folkerts
24cbea7b0b
wip
2024-07-18 15:57:13 +02:00
Martin Folkerts
5645ad83e5
changes
2024-07-17 14:53:46 +02:00
Martin Folkerts
0b1826dccb
wip
2024-07-15 11:45:21 +02:00
Martin Folkerts
2988516db2
added conditional to skip field/subfield when no downloads available in current rds
2024-07-15 10:41:13 +02:00
Martin Folkerts
3ea7eec68e
some more work
2024-07-09 15:47:53 +02:00
Martin Folkerts
1de6dd4edf
wip
2024-07-04 21:16:12 +02:00
Martin Folkerts
d9fafcea43
wip
2024-07-02 16:51:55 +02:00
Martin Folkerts
1f194c5670
wip
2024-07-01 13:39:21 +02:00
guillaume91
3f7043199b
okay
2024-06-26 13:00:22 +02:00
guillaume91
ea38c952ba
Split 2_CI_data_prep.R into 2 files (+3 utils files)
2024-06-26 12:07:21 +02:00
Martin Folkerts
af1135e52a
wip
2024-06-25 13:37:45 +02:00
Martin Folkerts
607a221028
changed mosaic r script to work with end_date and offset instead of week
2024-06-24 11:39:47 +02:00
Martin Folkerts
1e841a0aa6
wip
2024-06-18 09:17:57 +02:00
Martin Folkerts
e2138a378a
some updates
2024-05-13 19:35:17 +02:00
Martin Folkerts
95633a553c
fixed whitespace issue in subchunkify
2024-05-06 11:46:51 +02:00
Timon
b6c576ca57
working rmd file, removed renv because it messed up my R and could not get it to work
2024-04-18 16:19:17 +02:00
Martin Folkerts
5886f59bd8
wip
2024-04-18 13:43:14 +02:00
Martin Folkerts
4051b802e2
wip
2024-04-18 11:11:24 +02:00
Martin Folkerts
d2fa24fc6c
added some changes to timons merged branch
2024-03-18 11:55:35 +01:00
Timon
88d871d865
updated harvest datata stadnadr
2024-03-14 13:01:19 +01:00
Timon
4053de50df
updated harvest datata stadnadr
2024-03-14 13:00:02 +01:00
Timon
66d6f80532
adjusted scripts to be more generalised
2024-03-13 10:27:10 +01:00
Timon
238520ff89
parameterised harvestdata etc
2024-03-12 22:18:57 +01:00
Martin Folkerts
62b9942a53
wip
2024-03-12 12:09:29 +01:00
Martin Folkerts
25715ddef6
wip
2024-03-11 10:36:47 +01:00
Martin Folkerts
f7d660356c
okay;
2024-03-10 21:53:20 +01:00
Martin Folkerts
e996a274db
merged testing
2024-03-05 09:40:46 +01:00
Martin Folkerts
c222314950
wip
2024-03-05 09:15:46 +01:00
Timon
952700f2c4
forgot to save last R file
2024-03-04 17:22:08 +01:00
Timon
6c00c57b37
changed CI extract to extract all sat images if parameter new_project_question is set to TRUE, to add when new project start
2024-03-04 17:12:20 +01:00
Timon
86f4a49d30
minor changes in script to get it running on my device
2024-03-04 12:15:23 +01:00
Timon
07a54eab25
minor changes
2024-03-01 16:32:53 +01:00
Timon
a976350ce5
first commit test
2024-03-01 14:41:55 +01:00
Martin Folkerts
645929ae4e
fixed build-report refactored enum status and HasStatusTrait
2024-02-14 21:01:15 +01:00
Martin Folkerts
a7a333fb0f
worked with timon to harmonize report output
2024-02-08 17:06:35 +01:00
Martin Folkerts
3a18e3b8a7
okeay
2024-01-31 11:58:01 +01:00
Martin Folkerts
0cfd8ad8bf
fix
2024-01-31 11:54:02 +01:00
Martin Folkerts
9f60d3db8a
added leading zero to weeknumbers so mosaics van be found for week numbers smaller then 9
2024-01-31 11:47:56 +01:00
Martin Folkerts
a19e7667e6
wip
2024-01-30 15:17:26 +01:00
Martin Folkerts
e224080232
added leading zero to weeknumber in file name format
2024-01-30 15:14:28 +01:00
Martin Folkerts
33cb0dd7da
wip
2024-01-24 21:46:08 +01:00
Martin Folkerts
d3c2c18918
revised report
2024-01-16 14:43:22 +01:00
Martin Folkerts
3eaf471f05
wip
2024-01-10 21:42:32 +01:00
Martin Folkerts
da9d94880f
wip
2024-01-09 10:49:25 +01:00
Martin Folkerts
4c22ab6758
wip
2024-01-03 22:06:03 +01:00
Martin Folkerts
3fb55ddcce
added rule for missing mergedTifs;
2023-12-24 18:02:17 +01:00
Martin Folkerts
bd4ac224ad
added CI graphs to pdf
2023-12-12 16:37:47 +01:00
Martin Folkerts
36d74ed2af
working version of all python scripts and r-scripts
2023-12-12 14:58:44 +01:00
Martin Folkerts
c40ff0c79f
updated scripts
2023-12-12 11:20:05 +01:00
Martin Folkerts
3fe61f8ab8
wip
2023-11-06 12:14:13 +01:00
Martin Folkerts
dbc8a13600
wip\
2023-10-31 15:03:32 +01:00
Martin Folkerts
0b7294340c
updated r_app/.gitignore to reflect install strategy.
...
removed renv and .Rprofile from project so every instance should run its own enviroment based on installPackages.R.
2023-10-31 14:12:12 +01:00
Martin Folkerts
2a872cf8a3
wip
2023-10-17 11:08:44 +02:00
Martin Folkerts
3ce436b6a0
added renv::restore() and renv::activate()
2023-10-16 17:34:11 +02:00
Martin Folkerts
dda9ad8871
build version of r.lock
2023-10-16 17:20:46 +02:00
Martin Folkerts
568565bc76
wip
2023-10-16 15:45:52 +02:00
Martin Folkerts
78e6567182
wip
2023-10-10 17:02:35 +02:00
Timon
