altitude operations #191

mgross · 2023-11-09T15:37:49Z

Now it is possible to create altitude/elevation maps (data comes from package elevatr):

.

Also custom maps are now possible (user must provide longitude (x), latitude (y) and value (x) data; note that each possible x-y combination must exist, i.e. full data matrix):

Weighting inside LocatoR with said altitude map (or any other map) is possible.
We have the option to set negative weighting values to 0 and to apply inverse exponential decay weighting. In the latter case, we can apply a halftime. This can make sense when we weight with altitude for example:
For a half-time of 1000m, locations with 1000 altitude get half the probability, with 2000m 1/4 of the probability and so forth.

Using Lives 13C data with 13C -18/1 as point gives this without weighting:

However with weighting, higher altitudes are downweighted:

With negative values set to zero weight oceans and areas below sealevel get 0 weight:

mgross · 2023-11-09T15:41:51Z

@arunge : Could you check this?

arunge · 2023-11-10T09:12:58Z

@mgross Unfortunately, this feature requires a higher version of elevatr than we have currently running, that is why the checks fail:

Possibly, you need exactly version 0.99.0 of elevatr, correct?

I need to discuss with @jan-abel-inwt what way is best for our system to get the higher version into our docker container.
I will update you when we found a solution!

mgross · 2023-11-10T10:33:16Z

@arunge, I can try with 0.4.2

mgross · 2023-11-10T10:45:32Z

@arunge ok, it also works for older version

arunge

In general, the feature seems to work, I have some minor suggestions.
However, I tested to create a new elevation map from scratch. I did not upload or import any data. After naming the map and pressing Run a progress bar occurs, but nothing seems to happen after that. (The main panel remains empty.)
Checking "Saved maps" gives a new map, but it looks empty. The thumbnail seems not to be there:
https://github.com/Pandora-IsoMemo/iso-app/blob/f549072ddfb8bcd9ed7dfc1ac7144c5c41d01c97/R/04-savedMapsModule.R#L43
Only after selecting to load the map, the map becomes visible. Could we display the map directly after it was created in the main panel, without having to load the map?
Additionally, an error occured in some if-clause, could you check and fix this?

If you need some assistance regarding the display of the map, please let me know.

arunge · 2023-11-16T07:49:57Z

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MpiIsoApp
 Title: Pandora & IsoMemo spatiotemporal modeling
-Version: 23.10.1
+Version: 23.11.1


Suggested change

Version: 23.11.1

Version: 23.11.0

arunge · 2023-11-16T07:50:11Z

NEWS.md

@@ -1,6 +1,14 @@
 # MpiIsoApp development version

-## Version 23.10.0
+## Version 23.11.1


Suggested change

## Version 23.11.1

## Version 23.11.0

mgross · 2023-11-17T15:32:20Z

@arunge: should be working now

arunge

Why do you not just remove the code that is not needed for this case?

arunge · 2023-11-20T07:45:52Z

R/03-mapDiff.R

+    # mapName <- trimws(input$saveMapName)
+    # if (mapName == "") {
+    #   alert("Please provide a map name")
+    #   return()
+    # }


Please, just remove the comments if this is not needed in this case.

arunge · 2023-11-20T07:46:08Z

R/03-mapDiff.R

+    # map <- createSavedMap(
+    #   model = XPred,
+    #   predictions = XPred,
+    #   plot =  recordPlot({
+    #     plot.new()
+    #     text(
+    #       x = 0.5,
+    #       y = 0.5,
+    #       paste0("Custom map"),
+    #       cex = 5
+    #     )
+    #   }),
+    #   type = "user",
+    #   name = mapName
+    # )
+    # maps <- savedMaps()
+    # maps[[length(maps) + 1]] <- map
+    # savedMaps(maps)
+    #
+    # alert(paste0("Map '", mapName, "' was saved"))
+    # updateTextInput(session, "saveMapName", value = "")


Merge branch 'beta' into altitude_operations # Conflicts: # DESCRIPTION # NEWS.md

arunge · 2023-12-05T13:59:46Z

@mgross I merged some fixes from the beta into this feature branch. It is just open to remove the comments mentioned above. I could also do this and merge afterwards. Just let me know if you need something. 😊

Merge branch 'beta' into altitude_operations # Conflicts: # DESCRIPTION # NEWS.md

* altitude operations (#191) * altitude operations * Fix * set default differently * make data points selectable in locateR * update news * Fix for older version * fixes * fix progress message * remove comments --------- Co-authored-by: Antonia Runge <antonia.runge@inwt-statistics.de> * Fix error with mask (#208) * add new tests * extract function centerPlotData * add tryCatch to plotting of map, add data preview, add logDebugs * remove deprecated parameter 'mainfolder', add data preview * update news.md * catch failing of maskDraw if no data * update news.md * fix issue when drawing only centroids, add test * add tryCatch to left plotting functions --------- Co-authored-by: Marcus Groß <marcus.gross@inwt-statistics.de>

* altitude operations (#191) * altitude operations * Fix * set default differently * make data points selectable in locateR * update news * Fix for older version * fixes * fix progress message * remove comments --------- Co-authored-by: Antonia Runge <antonia.runge@inwt-statistics.de> * Fix error with mask (#208) * add new tests * extract function centerPlotData * add tryCatch to plotting of map, add data preview, add logDebugs * remove deprecated parameter 'mainfolder', add data preview * update news.md * catch failing of maskDraw if no data * update news.md * fix issue when drawing only centroids, add test * add tryCatch to left plotting functions * Version 24.05.0: Feat/202 contour maps (#210) * option to use simple contour map, some formatting * update news.md * Feat/169 centering of coordinates (#215) * new functions and ui input * align values * center predictions * UI to center data coordinates before modelling * add logic to center data before modelling to different modelling tabs * add logic * remove comments * update news.md * update news.md * rename input to prevent confusion with parameter from batch mode * extract processing of coordinate data * extract and apply data augmentation * fix issue with wrong default zoom when switching the map center * add more docu * more docu * update test because of new logic * add a vignette to the package about the processing of coordinate data * update news.md * fix for data augmentation * Version 24.05.2: option to select a specific color for "fixed" point colour (#216) * option to select a specific color for "fixed" point colour * new button to apply point settings and the logic * update news.md * update tests after adding new input * fix news.md * MpiIsoApp 24.05.3: Bugfix missing lat/long (#219) * BUG!! * Bugfix * update news.md --------- Co-authored-by: Antonia Runge <antonia.runge@inwt-statistics.de> * MpiIsoApp 24.05.4: fix warning (#217) * fix warning * extract updatePenalty function * update news.md --------- Co-authored-by: Antonia Runge <antonia.runge@inwt-statistics.de> * MpiIsoApp 24.05.5: optionally download savedMaps (#222) * optionally download savedMaps * format new UI * MpiIsoApp 24.05.6: option to export all plots from savedMaps (#223) * option to export all plots from savedMaps * remove not required * picker input to select savedMaps for download * shift code * update news.md * fix issue with missing thumbnail plot * return empty list if missing * cleaner return * remove option to download savedMaps objects * add docu * add param to docu * MpiIsoApp 24.05.7: Feat/224 warning if creating prob map (#225) * fix issue with missing thumbnails, fix pch value * update news.md * set pch to NA * remove warning * replace deprecated package name --------- Co-authored-by: Marcus Groß <marcus.gross@inwt-statistics.de>

mgross added 3 commits November 9, 2023 16:15

altitude operations

a300102

Fix

0390021

set default differently

9438b1a

mgross requested a review from arunge November 9, 2023 15:41

arunge self-assigned this Nov 10, 2023

arunge added enhancement New feature or request IsoMemo App labels Nov 10, 2023

mgross added 2 commits November 10, 2023 11:28

make data points selectable in locateR

d33e1e2

update news

3b5670c

Fix for older version

3b73f11

arunge requested changes Nov 16, 2023

View reviewed changes

arunge assigned mgross and unassigned arunge Nov 16, 2023

fixes

89c5f4b

fix progress message

c500c29

arunge approved these changes Nov 20, 2023

View reviewed changes

arunge added 2 commits November 28, 2023 19:11

merge fix for leaflet center from beta

e7458c3

Merge branch 'beta' into altitude_operations # Conflicts: # DESCRIPTION # NEWS.md

merge bug fix from beta

c2affdb

Merge branch 'beta' into altitude_operations # Conflicts: # DESCRIPTION # NEWS.md

arunge added 3 commits December 20, 2023 18:58

merge changes from beta

a057295

Merge branch 'beta' into altitude_operations # Conflicts: # DESCRIPTION # NEWS.md

Merge branch 'beta' into altitude_operations

714397e

remove comments

f52a935

arunge merged commit 5a66c3a into beta Dec 20, 2023
1 check passed

arunge deleted the altitude_operations branch December 20, 2023 18:40

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altitude operations #191

altitude operations #191

mgross commented Nov 9, 2023

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altitude operations #191

altitude operations #191

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