Package index • vectra

Data sources

Open files for lazy query execution

tbl(): Create a lazy table reference from a .vtr file
tbl_csv(): Create a lazy table reference from a delimited text file
tbl_sqlite(): Create a lazy table reference from a SQLite database
tbl_tiff(): Create a lazy table reference from a GeoTIFF raster
tbl_xlsx(): Create a lazy table reference from an Excel (.xlsx) file
tbl_fasta(): Create a lazy table reference from a FASTA file
tbl_fastq(): Create a lazy table reference from a FASTQ file
tbl_bed(): Create a lazy table reference from a BED file

Data sinks

Write query results or data.frames to disk

write_vtr(): Write data to a .vtr file
write_csv(): Write query results or a data.frame to a CSV file
write_sqlite(): Write query results or a data.frame to a SQLite table
write_tiff(): Write query results to a GeoTIFF file
st_write(<vectra_node>): Stream a vectra node's geometry to a vector file

Single-table verbs

Transform, filter, and reshape

filter(): Filter rows of a vectra query
select(): Select columns from a vectra query
mutate(): Add or transform columns
transmute(): Keep only columns from mutate expressions
rename(): Rename columns
relocate(): Relocate columns
arrange(): Sort rows by column values
desc(): Mark a column for descending sort order
distinct(): Keep distinct/unique rows
slice_head() slice_tail() slice_min() slice_max(): Select first or last rows
slice(): Select rows by position
pull(): Extract a single column as a vector
head(<vectra_node>): Limit results to first n rows

Grouping and aggregation

group_by(): Group a vectra query by columns
summarise() summarize(): Summarise grouped data
ungroup(): Remove grouping from a vectra query
count() tally(): Count observations by group
reframe(): Summarise with variable-length output per group
across(): Apply a function across multiple columns

Time series

Snap datetimes to a calendar grid and aggregate over time windows

floor_time(): Floor a datetime column to a calendar grid
resample(): Resample a time series to a calendar grid
roll_sum() roll_mean() roll_min() roll_max() roll_n(): Time-based rolling aggregates

Biological sequences

k-mer spectra and per-row sequence functions

kmer(): k-mer spectrum of a sequence column
seq_expressions: Biological-sequence functions inside mutate(), filter(), and summarise()

Joins

left_join() inner_join() right_join() full_join() semi_join() anti_join(): Join two vectra tables
cross_join(): Cross join two vectra tables
fuzzy_join(): Fuzzy join two vectra tables by string distance
interval_join(): Interval (range overlap) join of two vectra tables

Star schema

Define linked dimension tables and look up columns without explicit joins

vtr_schema(): Create a star schema over linked vectra tables
link(): Define a link between a fact table and a dimension table
lookup(): Look up columns from linked dimension tables

Combining tables

bind_rows() bind_cols(): Bind rows or columns from multiple vectra tables

Block operations

In-memory materialization and lookup

materialize(): Materialize a vectra node into a reusable in-memory block
block_lookup(): Probe a materialized block by column value
block_fuzzy_lookup(): Fuzzy-match query keys against a materialized block

Streaming consumption

Reduce or feed a query one batch at a time, for larger-than-RAM results

collect_chunked(): Fold a function over a query, one batch at a time
chunk_feeder(): Turn a query into a resettable chunk generator

Offloading

Spill a query to disk and stream it back, for out-of-core fits

offload(): Spill a query to disk and stream it back (the offload functor)
group_map() group_modify(): Apply a function to each shard of a partition

File operations

Incremental updates to .vtr files

append_vtr(): Append rows or columns to an existing .vtr file
delete_vtr(): Logically delete rows from a .vtr file
diff_vtr(): Compute the logical diff between two .vtr files
create_index(): Create a hash index on a .vtr file column
has_index(): Check whether a .vtr column has a usable hash index

Diagnostics

explain(): Print the execution plan for a vectra query
collect(): Execute a lazy query and return a data.frame
glimpse(): Get a glimpse of a vectra table
dim(<vectra_node>): Dimensions of a lazy query
print(<vectra_node>): Print a vectra query node
vectra_mem(): Resolve the vectra memory budget

Raster data cubes

Read and write .vec rasters and time cubes out of core

vec_open_raster(): Open a .vec raster
vec_close_raster(): Close a .vec raster handle
vec_raster_layout(): Tile layout of an open .vec raster
vec_raster_times(): Distinct time stamps stored in a .vec time cube
vec_read_window(): Read a window of pixels from a .vec raster
vec_read_time_slice(): Read a single time slice from a .vec time cube
vec_read_pixel_series(): Read the full time series at a single pixel from a .vec time cube
vec_extract_points(): Extract band values at (x, y) points from a .vec raster
vec_build_overviews(): Build overview pyramids for a .vec raster
vec_write_raster(): Write a raster matrix or 3D array to a .vec raster file
vec_write_time_cube(): Write a 4D time-cube raster to .vec
vec_to_tiff(): Export a .vec raster to GeoTIFF

GeoTIFF helpers

Metadata and point-sampling for GeoTIFF rasters

tiff_extract_points(): Extract raster values at point coordinates
tiff_metadata(): Read GDAL_METADATA from a GeoTIFF
tiff_band_names(): Read per-band names from a GeoTIFF
tiff_crs(): Read CRS metadata from a GeoTIFF

Spatial operations

Stream sf vector operations one batch at a time, for vector data larger than RAM

spatial_map(): Stream a query through an sf transform
spatial_join(): Spatial join a streamed query against a resident sf object
grid(): Define a uniform grid for a partitioned spatial join
spatial_filter(): Keep streamed rows by their spatial relation to a resident layer
spatial_clip(): Clip or erase a streamed layer against a resident mask
spatial_dissolve(): Dissolve geometries by group
spatial_overlay(): Self-overlay a polygon layer into disjoint pieces (QGIS-style Union)
rasterize(): Rasterize a streamed point layer onto a fixed grid
polygonize(): Vectorise a raster into polygons
contours(): Extract contour iso-lines from a streamed raster
zonal(): Summarise raster values within zones
focal(): Moving-window (focal) statistics over a streamed raster
terrain(): Terrain derivatives from a streamed elevation raster
warp(): Resample or reproject a streamed raster onto a target grid
mask(): Mask a streamed raster to a polygon layer
mosaic(): Merge aligned rasters onto a common grid
rast_calc(): Cellwise calculation over aligned rasters (map algebra)
proximity(): Euclidean distance to the nearest feature (proximity)
collect_sf(): Materialize a spatial query as an sf object
geom_expressions: Geometry functions inside mutate(), filter(), and summarise()

Geometry construction and cleaning

Reshape, repair, simplify, and snap streamed vector geometry

spatial_construct(): Build a set-wise geometry construction, optionally per group
spatial_explode(): Explode multipart geometries into single-part features
spatial_line_merge(): Merge contiguous line segments into maximal lines
spatial_simplify(): Simplify a polygon coverage without tearing shared edges
spatial_smooth(): Smooth streamed line and polygon geometry
spatial_snap(): Snap a streamed layer toward a resident reference layer
spatial_snap_grid(): Snap a streamed layer's coordinates to a fixed grid
spatial_eliminate(): Merge sliver polygons into a neighbour
spatial_split(): Split a streamed layer by a resident blade, or return its crossing points
spatial_centerline(): Trace the centerline (medial axis) of streamed polygons

Coverage and topology

Shared-edge topology and polygonal faces of polygon coverages

spatial_topology(): Build the shared-edge topology of a polygon coverage
spatial_polygonize(): Build polygonal faces from a line network

Spatial networks

Build routable graphs and solve shortest paths over line layers

spatial_network(): Build a routable network graph from a line layer
spatial_route(): Shortest paths and origin-destination costs over a network
spatial_service_area(): Service areas and isochrones over a network

Spatial queries

Nearest neighbours and linear referencing

spatial_knn(): k nearest neighbours of a streamed layer, with distances
spatial_locate(): Locate streamed points along a resident line layer

Feature space

Embedding columns and nearest neighbours in predictor space

as_embedding(): Encode vectors as an embedding column
cosine() l2() dot(): Embedding distance functions
feature_knn(): Nearest neighbours of a streamed layer in predictor space
rast_feature_distance(): Predictor-space nearest-neighbour distance surface over a raster