Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add LPD to CAST #75

Merged
merged 10 commits into from
Feb 7, 2024
Merged

Add LPD to CAST #75

merged 10 commits into from
Feb 7, 2024

Conversation

fab-scm
Copy link
Contributor

@fab-scm fab-scm commented Jan 16, 2024 •
edited
Loading

This pull request features the full LPD functionalities implemeneted in the scope of the bachelor thesis: "Development of a local data point density approach to assess the area of applicability of spatial prediction models".

Modified functions:

  • aoa: possibility to calculate the LPD of the prediction data aoa(newdata, model, LPD = TRUE, maxLPD = 1
  • trainDI: possibility to calculate the LPD of the training data aoa(model, LPD = TRUE)
  • DItoErrormetric: possibility to derive the relationship between LPD and error from the training data DItoErrormetric(model, aoa, variable = "LPD")

fab-scm and others added 2 commits January 16, 2024 12:05
@fab-scm
Prepare branch for PR (#16)
f4fd2bd 
* implement quantitative density layer

* document parameter k

* comments

* just spaces to be in sync with qmd scripts

* change QD to LPD

* update validation and maxLPD derivation

* update plot and print (#2)

* add exploreAOA function (#3)

* update plot and print

* add exploreAOA to package

* add message for trainLPD calculation

* Dev (#4)

* update plot and print

* add exploreAOA to package

* add message for trainLPD calculation

* update explore AOA docs

* shift package to description

* update exploreAOA docs

* update exploreAOA docs and add xmark

* update aoa, trainDI and exploreAOA docs

* update aoa docs

* change order of print.aoa

* update aoa.Rd

* update DESCRIPTION

* Dev (#6)

* update plot and print

* add exploreAOA to package

* add message for trainLPD calculation

* update explore AOA docs

* shift package to description

* update exploreAOA docs

* update exploreAOA docs and add xmark

* update aoa, trainDI and exploreAOA docs

* update aoa docs

* change order of print.aoa

* update aoa.Rd

* update DESCRIPTION

* update aoa & trainDI

* add trainDat upload options

* raster to terra and new layout (#5)

* update plot function

* update exploreAOA

* update exploreAOA

* fix error

* fix error

* fix crs bounding box issue

* rm commented code

* update plot.aoa & exploreAOA

* fix error in trainLPD calculation

* fix MD calculation

* fix order in print.aoa & message in aoa()

* add predictors tif to CAST package

* add countryboundaries

* add elevation

* Dev (#12)

* update plot and print

* add exploreAOA to package

* add message for trainLPD calculation

* update explore AOA docs

* shift package to description

* update exploreAOA docs

* update exploreAOA docs and add xmark

* update aoa, trainDI and exploreAOA docs

* update aoa docs

* change order of print.aoa

* update aoa.Rd

* update DESCRIPTION

* update aoa & trainDI

* add trainDat upload options

* raster to terra and new layout (#5)

* update plot function

* update exploreAOA

* update exploreAOA

* fix error

* fix error

* fix crs bounding box issue

* rm commented code

* update plot.aoa & exploreAOA

* fix error in trainLPD calculation

* fix MD calculation

* fix order in print.aoa & message in aoa()

* add predictors tif to CAST package

* add countryboundaries

* add elevation

* Change `maxLPD` parameter handling & enable `trainLPD` calculation with only training data provided (no model) (#7)

* add to maxLPD percantages

* update maxLPD parameter validation

* enable trainLPD calc with only trainDat (no model)

* minor change in maxLPD setting

* Add `LPDtoErrormetric` functionality (#8)

* add LPDtoErrormetric and adjust plot functions

* small change

* minor changes on docs and comments

* major docs update

* update DItoErrormetric and LPDtoErrormetric

* New calculation methods for LPD of training data and LPD of prediction data, add DI_LPDtoErrormetric  (#9)

* update trainLPD implementation in trainDI

* add DI_LPDtoErrormetric

* update docs

* update `toErrormetric` functions

* update `...toErrormetric` functions

* update CAST docs

* change legend position in exploreAOA

* update aoa and .knndist - enhance performance of LPD calculation

* update trainDI - add progress bars and messages

* update DI_LPDtoErrormetric & LPDtoErrormetric to enable multiCV

* Feat train di new (#11)

* Dev (#6)

* update plot and print

* add exploreAOA to package

* add message for trainLPD calculation

* update explore AOA docs

* shift package to description

* update exploreAOA docs

* update exploreAOA docs and add xmark

* update aoa, trainDI and exploreAOA docs

* update aoa docs

* change order of print.aoa

* update aoa.Rd

* update DESCRIPTION

* update aoa & trainDI

* add trainDat upload options

* raster to terra and new layout (#5)

* update plot function

* update exploreAOA

* update exploreAOA

* fix error

* fix error

* fix crs bounding box issue

* rm commented code

* update plot.aoa & exploreAOA

* fix error in trainLPD calculation

* fix MD calculation

* fix order in print.aoa & message in aoa()

* add predictors tif to CAST package

* add countryboundaries

* add elevation

* update trainLPD implementation in trainDI

* add DI_LPDtoErrormetric

* update docs

* update `toErrormetric` functions

* update `...toErrormetric` functions

* update CAST docs

* change legend position in exploreAOA

* update aoa and .knndist - enhance performance of LPD calculation

* update trainDI - add progress bars and messages

* update DI_LPDtoErrormetric & LPDtoErrormetric to enable multiCV

* fix error in LPDtoErrormetric

* Dev (#13)

* update plot and print

* add exploreAOA to package

* add message for trainLPD calculation

* update explore AOA docs

* shift package to description

* update exploreAOA docs

* update exploreAOA docs and add xmark

* update aoa, trainDI and exploreAOA docs

* update aoa docs

* change order of print.aoa

* update aoa.Rd

* update DESCRIPTION

* update aoa & trainDI

* add trainDat upload options

* raster to terra and new layout (#5)

* update plot function

* update exploreAOA

* update exploreAOA

* fix error

* fix error

* fix crs bounding box issue

* rm commented code

* update plot.aoa & exploreAOA

* fix error in trainLPD calculation

* fix MD calculation

* fix order in print.aoa & message in aoa()

* add predictors tif to CAST package

* add countryboundaries

* add elevation

* Change `maxLPD` parameter handling & enable `trainLPD` calculation with only training data provided (no model) (#7)

* add to maxLPD percantages

* update maxLPD parameter validation

* enable trainLPD calc with only trainDat (no model)

* minor change in maxLPD setting

* Add `LPDtoErrormetric` functionality (#8)

* add LPDtoErrormetric and adjust plot functions

* small change

* minor changes on docs and comments

* major docs update

* update DItoErrormetric and LPDtoErrormetric

* New calculation methods for LPD of training data and LPD of prediction data, add DI_LPDtoErrormetric  (#9)

* update trainLPD implementation in trainDI

* add DI_LPDtoErrormetric

* update docs

* update `toErrormetric` functions

* update `...toErrormetric` functions

* update CAST docs

* change legend position in exploreAOA

* update aoa and .knndist - enhance performance of LPD calculation

* update trainDI - add progress bars and messages

* update DI_LPDtoErrormetric & LPDtoErrormetric to enable multiCV

* Feat train di new (#11)

* Dev (#6)

* update plot and print

* add exploreAOA to package

* add message for trainLPD calculation

* update explore AOA docs

* shift package to description

* update exploreAOA docs

* update exploreAOA docs and add xmark

* update aoa, trainDI and exploreAOA docs

* update aoa docs

* change order of print.aoa

* update aoa.Rd

* update DESCRIPTION

* update aoa & trainDI

* add trainDat upload options

* raster to terra and new layout (#5)

* update plot function

* update exploreAOA

* update exploreAOA

* fix error

* fix error

* fix crs bounding box issue

* rm commented code

* update plot.aoa & exploreAOA

* fix error in trainLPD calculation

* fix MD calculation

* fix order in print.aoa & message in aoa()

* add predictors tif to CAST package

* add countryboundaries

* add elevation

* update trainLPD implementation in trainDI

* add DI_LPDtoErrormetric

* update docs

* update `toErrormetric` functions

* update `...toErrormetric` functions

* update CAST docs

* change legend position in exploreAOA

* update aoa and .knndist - enhance performance of LPD calculation

* update trainDI - add progress bars and messages

* update DI_LPDtoErrormetric & LPDtoErrormetric to enable multiCV

* fix error in LPDtoErrormetric

* masking order

* adapt default degrees of freedom

* add exp and scam exp errormodels

* update docs

* update docs

* Dev (#14)

* update plot and print

* add exploreAOA to package

* add message for trainLPD calculation

* update explore AOA docs

* shift package to description

* update exploreAOA docs

* update exploreAOA docs and add xmark

* update aoa, trainDI and exploreAOA docs

* update aoa docs

* change order of print.aoa

* update aoa.Rd

* update DESCRIPTION

* update aoa & trainDI

* add trainDat upload options

* raster to terra and new layout (#5)

* update plot function

* update exploreAOA

* update exploreAOA

* fix error

* fix error

* fix crs bounding box issue

* rm commented code

* update plot.aoa & exploreAOA

* fix error in trainLPD calculation

* fix MD calculation

* fix order in print.aoa & message in aoa()

* add predictors tif to CAST package

* add countryboundaries

* add elevation

* Change `maxLPD` parameter handling & enable `trainLPD` calculation with only training data provided (no model) (#7)

* add to maxLPD percantages

* update maxLPD parameter validation

* enable trainLPD calc with only trainDat (no model)

* minor change in maxLPD setting

* Add `LPDtoErrormetric` functionality (#8)

* add LPDtoErrormetric and adjust plot functions

* small change

* minor changes on docs and comments

* major docs update

* update DItoErrormetric and LPDtoErrormetric

* New calculation methods for LPD of training data and LPD of prediction data, add DI_LPDtoErrormetric  (#9)

* update trainLPD implementation in trainDI

* add DI_LPDtoErrormetric

* update docs

* update `toErrormetric` functions

* update `...toErrormetric` functions

* update CAST docs

* change legend position in exploreAOA

* update aoa and .knndist - enhance performance of LPD calculation

* update trainDI - add progress bars and messages

* update DI_LPDtoErrormetric & LPDtoErrormetric to enable multiCV

* Feat train di new (#11)

* Dev (#6)

* update plot and print

* add exploreAOA to package

* add message for trainLPD calculation

* update explore AOA docs

* shift package to description

* update exploreAOA docs

* update exploreAOA docs and add xmark

* update aoa, trainDI and exploreAOA docs

* update aoa docs

* change order of print.aoa

* update aoa.Rd

* update DESCRIPTION

* update aoa & trainDI

* add trainDat upload options

* raster to terra and new layout (#5)

* update plot function

* update exploreAOA

* update exploreAOA

* fix error

* fix error

* fix crs bounding box issue

* rm commented code

* update plot.aoa & exploreAOA

* fix error in trainLPD calculation

* fix MD calculation

* fix order in print.aoa & message in aoa()

* add predictors tif to CAST package

* add countryboundaries

* add elevation

* update trainLPD implementation in trainDI

* add DI_LPDtoErrormetric

* update docs

* update `toErrormetric` functions

* update `...toErrormetric` functions

* update CAST docs

* change legend position in exploreAOA

* update aoa and .knndist - enhance performance of LPD calculation

* update trainDI - add progress bars and messages

* update DI_LPDtoErrormetric & LPDtoErrormetric to enable multiCV

* fix error in LPDtoErrormetric

* masking order

* adapt default degrees of freedom

* add exp and scam exp errormodels

* update docs

* update docs

* Dev (#15)

* update plot and print

* add exploreAOA to package

* add message for trainLPD calculation

* update explore AOA docs

* shift package to description

* update exploreAOA docs

* update exploreAOA docs and add xmark

* update aoa, trainDI and exploreAOA docs

* update aoa docs

* change order of print.aoa

* update aoa.Rd

* update DESCRIPTION

* update aoa & trainDI

* add trainDat upload options

* raster to terra and new layout (#5)

* update plot function

* update exploreAOA

* update exploreAOA

* fix error

* fix error

* fix crs bounding box issue

* rm commented code

* update plot.aoa & exploreAOA

* fix error in trainLPD calculation

* fix MD calculation

* fix order in print.aoa & message in aoa()

* add predictors tif to CAST package

* add countryboundaries

* add elevation

* Change `maxLPD` parameter handling & enable `trainLPD` calculation with only training data provided (no model) (#7)

* add to maxLPD percantages

* update maxLPD parameter validation

* enable trainLPD calc with only trainDat (no model)

* minor change in maxLPD setting

* Add `LPDtoErrormetric` functionality (#8)

* add LPDtoErrormetric and adjust plot functions

* small change

* minor changes on docs and comments

* major docs update

* update DItoErrormetric and LPDtoErrormetric

* New calculation methods for LPD of training data and LPD of prediction data, add DI_LPDtoErrormetric  (#9)

* update trainLPD implementation in trainDI

* add DI_LPDtoErrormetric

* update docs

* update `toErrormetric` functions

* update `...toErrormetric` functions

* update CAST docs

* change legend position in exploreAOA

* update aoa and .knndist - enhance performance of LPD calculation

* update trainDI - add progress bars and messages

* update DI_LPDtoErrormetric & LPDtoErrormetric to enable multiCV

* Feat train di new (#11)

* Dev (#6)

* update plot and print

* add exploreAOA to package

* add message for trainLPD calculation

* update explore AOA docs

* shift package to description

* update exploreAOA docs

* update exploreAOA docs and add xmark

* update aoa, trainDI and exploreAOA docs

* update aoa docs

* change order of print.aoa

* update aoa.Rd

* update DESCRIPTION

* update aoa & trainDI

* add trainDat upload options

* raster to terra and new layout (#5)

* update plot function

* update exploreAOA

* update exploreAOA

* fix error

* fix error

* fix crs bounding box issue

* rm commented code

* update plot.aoa & exploreAOA

* fix error in trainLPD calculation

* fix MD calculation

* fix order in print.aoa & message in aoa()

* add predictors tif to CAST package

* add countryboundaries

* add elevation

* update trainLPD implementation in trainDI

* add DI_LPDtoErrormetric

* update docs

* update `toErrormetric` functions

* update `...toErrormetric` functions

* update CAST docs

* change legend position in exploreAOA

* update aoa and .knndist - enhance performance of LPD calculation

* update trainDI - add progress bars and messages

* update DI_LPDtoErrormetric & LPDtoErrormetric to enable multiCV

* fix error in LPDtoErrormetric

* masking order

* adapt default degrees of freedom

* add exp and scam exp errormodels

* update docs

* update docs
@fab-scm
check if datapoint is used for testing in more than one fold (LPD)
55bc355
@fab-scm fab-scm changed the title PR: Add LPD to CAST Add LPD to CAST Jan 16, 2024
@HannaMeyer HannaMeyer merged commit 555e071 into HannaMeyer:master Feb 7, 2024
2 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@fab-scm @HannaMeyer