Merge pull request #221 from chenyangkang/hdf5_serialization

Add functions to read and write routes and intervals using HDF5 files.

Author: ethanplunkett

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BirdFlowR
 Title: Predict and Visualize Bird Movement
-Version: 0.1.0.9075
+Version: 0.1.0.9076
 Authors@R: 
     c(person("Ethan", "Plunkett",  email = "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-4405-2251")),

NAMESPACE

@@ -14,6 +14,9 @@ S3method(print,Routes)
 S3method(st_as_sf,BirdFlowRoutes)
 S3method(st_bbox,BirdFlow)
 S3method(st_crs,BirdFlow)
+S3method(write_routes,BirdFlowRoutes)
+S3method(write_routes,Routes)
+S3method(write_routes,default)
 export(BirdFlowIntervals)
 export(Routes)
 export(add_dynamic_mask)
@@ -93,6 +96,8 @@ export(plot_routes)
 export(preprocess_species)
 export(rasterize_distr)
 export(rc_to_i)
+export(read_intervals)
+export(read_routes)
 export(route)
 export(route_migration)
 export(row_to_y)
@@ -108,6 +113,8 @@ export(validate_BirdFlow)
 export(validate_BirdFlowIntervals)
 export(validate_BirdFlowRoutes)
 export(validate_Routes)
+export(write_intervals)
+export(write_routes)
 export(x_to_col)
 export(xy_to_i)
 export(xy_to_latlon)
@@ -133,15 +140,26 @@ importFrom(grDevices,grey)
 importFrom(grDevices,rgb)
 importFrom(methods,as)
 importFrom(methods,is)
+importFrom(rhdf5,H5Fclose)
+importFrom(rhdf5,H5Fis_hdf5)
+importFrom(rhdf5,H5Fopen)
+importFrom(rhdf5,H5Lexists)
+importFrom(rhdf5,h5closeAll)
+importFrom(rhdf5,h5createFile)
+importFrom(rhdf5,h5createGroup)
 importFrom(rhdf5,h5ls)
 importFrom(rhdf5,h5read)
+importFrom(rhdf5,h5readAttributes)
+importFrom(rhdf5,h5write)
+importFrom(rhdf5,h5writeAttribute)
 importFrom(rlang,.data)
 importFrom(sf,st_as_sf)
 importFrom(sf,st_bbox)
 importFrom(sf,st_crs)
 importFrom(stats,cor)
 importFrom(stats,median)
 importFrom(stats,predict)
+importFrom(stats,setNames)
 importFrom(terra,crs)
 importFrom(terra,ext)
 importFrom(terra,res)

NEWS.md

@@ -1,9 +1,20 @@
+# BirdFlowR 0.1.0.9076
+2025-05-25
+
+* Add read and write functions of the `Routes`, `BirdFlowRoutes`, 
+`BirdFlowIntervals` in a hdf5 serialization format:
+  * `read_Routes`, `write_Routes`
+  * `read_BirdFlowRoutes`, `write_BirdFlowRoutes`
+  * `read_BirdFlowIntervals`, `write_BirdFlowIntervals`
+  
 # BirdFlowR 0.1.0.9075
 2025-05-21
 
-* Finalize the interval based validation metrics in `calc_interval_metrics()`
-* Fixed some small documentation bugs where the arguments are not used but 
-  described.
+* Finalize the interval based validation metrics in function 
+  `calculate_interval_metrics` of file `interval_based_validation.R`.
+* Fixed some small documentation bugs where the arguments are not 
+  used but described.
+  
 
 # BirdFlowR 0.1.0.9074
 2025-05-13
@@ -157,7 +168,6 @@ Thus the flow of data is
   * `snap_to_birdflow()` no longer coerces date-time input to dates before
   aggregating, and, if the input is date-time the output will be as well.
 
->>>>>>> main
 
 # BirdFlowR 0.1.0.9069
 2024-10-17