remove rgdal use

[nelsopet]

Loading required package: rgdal
Please note that rgdal will be retired by the end of 2023,
plan transition to sf/stars/terra functions using GDAL and PROJ
at your earliest convenience.

[krbundy]

This is all the places that rgdal is mentioned:
55 results - 16 files

README.Rmd:
13 require(sf)
14: library(rgdal)
15 library(tidyverse)

Scripts/manual_validation.ipynb:
44 "\n",
45: "Loading required package: rgdal\n",
46 "\n",
47: "Please note that rgdal will be retired during October 2023,\n",
48 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

50 "See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution\n",
51: "rgdal: version: 1.6-7, (SVN revision 1203)\n",
52 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",

60 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n",
61: "use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.\n",
62 "\n",

Scripts/split_bonanza.ipynb:
63 "\n",
64: "Loading required package: rgdal\n",
65 "\n",
66: "Please note that rgdal will be retired during October 2023,\n",
67 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

69 "See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution\n",
70: "rgdal: version: 1.6-7, (SVN revision 1203)\n",
71 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",

79 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n",
80: "use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.\n",
81 "\n",

Scripts/Archive/7C_Visualizations_ReadKML_plot_map.R:
1: library(rgdal)
2 library(tidyverse)

Scripts/Archive/gs_revised_RF.ipynb:
66 ""package 'hsdar' was built under R version 4.2.2"\n",
67: "Loading required package: rgdal\n",
68 "\n",
69 "Warning message:\n",
70: ""package 'rgdal' was built under R version 4.2.2"\n",
71: "Please note that rgdal will be retired during 2023,\n",
72 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

74 "See https://r-spatial.org/r/2022/04/12/evolution.html and https://github.com/r-spatial/evolution\n",
75: "rgdal: version: 1.6-2, (SVN revision 1183)\n",
76 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",
77 "Loaded GDAL runtime: GDAL 3.5.2, released 2022/09/02\n",
78: "Path to GDAL shared files: C:/Users/Nelson Lab/AppData/Local/R/win-library/4.2/rgdal/gdal\n",
79 "GDAL binary built with GEOS: TRUE \n",
80 "Loaded PROJ runtime: Rel. 8.2.1, January 1st, 2022, [PJ_VERSION: 821]\n",
81: "Path to PROJ shared files: C:/Users/Nelson Lab/AppData/Local/R/win-library/4.2/rgdal/proj\n",
82 "PROJ CDN enabled: FALSE\n",

84 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n",
85: "use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.\n",
86 "\n",

Scripts/Archive/gs_xgboost.ipynb:
44 "\n",
45: "Loading required package: rgdal\n",
46 "\n",
47: "Please note that rgdal will be retired during 2023,\n",
48 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

50 "See https://r-spatial.org/r/2022/04/12/evolution.html and https://github.com/r-spatial/evolution\n",
51: "rgdal: version: 1.6-6, (SVN revision 1201)\n",
52 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",

60 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n",
61: "use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.\n",
62 "\n",

Scripts/Archive/site_specific_model_experiments.ipynb:
42 "\n",
43: "Loading required package: rgdal\n",
44 "\n",
45: "Please note that rgdal will be retired by the end of 2023,\n",
46 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

48 "\n",
49: "rgdal: version: 1.5-32, (SVN revision 1176)\n",
50 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",

58 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n",
59: "use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.\n",
60 "\n",

Scripts/Archive/tree_visualization.ipynb:
42 "\n",
43: "Loading required package: rgdal\n",
44 "\n",
45: "Please note that rgdal will be retired by the end of 2023,\n",
46 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

48 "\n",
49: "rgdal: version: 1.5-32, (SVN revision 1176)\n",
50 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",

58 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n",
59: "use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.\n",
60 "\n",

Scripts/ExploratoryDataAnalysis/7_Visualizations_Ground_and_UAS_Spectra_locations.R:
2 require(sf)
3: library(rgdal)
4 library(tidyverse)

Scripts/ExploratoryDataAnalysis/model_building.ipynb:
42 "\n",
43: "Loading required package: rgdal\n",
44 "\n",
45: "Please note that rgdal will be retired by the end of 2023,\n",
46 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

48 "\n",
49: "rgdal: version: 1.5-32, (SVN revision 1176)\n",
50 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",

58 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n",
59: "use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.\n",
60 "\n",

Scripts/TrainingDataCreation/merge_data.ipynb:
42 "\n",
43: "Loading required package: rgdal\n",
44 "\n",
45: "Please note that rgdal will be retired by the end of 2023,\n",
46 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

48 "\n",
49: "rgdal: version: 1.5-32, (SVN revision 1176)\n",
50 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",

58 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n",
59: "use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.\n",
60 "\n",

Scripts/TrainingDataCreation/speclib_processing.ipynb:
76 "\n",
77: "Loading required package: rgdal\n",
78 "\n",
79: "Please note that rgdal will be retired during October 2023,\n",
80 "plan transition to sf/stars/terra functions using GDAL and PROJ\n",

82 "See https://r-spatial.org/r/2023/05/15/evolution4.html and https://github.com/r-spatial/evolution\n",
83: "rgdal: version: 1.6-7, (SVN revision 1203)\n",
84 "Geospatial Data Abstraction Library extensions to R successfully loaded\n",

92 "To mute warnings of possible GDAL/OSR exportToProj4() degradation,\n",
93: "use options("rgdal_show_exportToProj4_warnings"="none") before loading sp or rgdal.\n",
94 "\n",

Scripts/TrainingDataCreation/Image/101_Crop_TarpWhiteRefs.R:
3 require(raster)
4: require(rgdal)
5

Scripts/TrainingDataCreation/Image/101_Crop_Training_PFT_vector.R:
3 require(raster)
4: require(rgdal)
5

Scripts/TrainingDataCreation/Image/101_Crop_Training_Quads.R:
3 require(raster)
4: require(rgdal)
5

Scripts/Utilities/install_dependenies.R:
1 lecospec_depenencies <- c(
2: "rgdal",
3 "gdalUtils",

[krbundy]

• manual_validation.ipynb DONE
• split_bonanza.ipyn DONE

So far, all are holdovers from before rgdal was removed from Functions/lecospectR.R. The notebooks simply maintain a reference to the package from before since they have not been run in a long time.

[krbundy]

These are the remaining mentions that actually need to be addressed:

• Scripts/ExploratoryDataAnalysis/7_Visualizations_Ground_and_UAS_Spectra_locations.R
• Scripts/TrainingDataCreation/Image/101_Crop_TarpWhiteRefs.R:
• Scripts/TrainingDataCreation/Image/101_Crop_Training_PFT_vector.R:
• Scripts/TrainingDataCreation/Image/101_Crop_Training_Quads.R:

Note that since I removed it from install_dependencies, the package will no longer be installed automatically.

Do you want to see if these are things that should be addressed @nelsopet ?