# Biological Analysis and Visualization of Weather Radar Data

## Documentation for package ‘bioRad’ version 0.6.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I M N O P R S U V W misc

## -- A --

apply_mistnet | Apply MistNet segmentation to a polar volume
as.data.frame.vp | Convert a vertical profile ('vp') or time series of vertical profiles ('vpts') to a data frame
as.data.frame.vpts | Convert a vertical profile ('vp') or time series of vertical profiles ('vpts') to a data frame
attribute_table | Extract a volume coverage pattern table with all attributes

## -- B --

beam_distance | Calculate radar beam distance
beam_height | Calculate radar beam height
beam_profile | Calculate vertical radiation profile
beam_profile_overlap | Calculate overlap between a vertical profile ('vp') of biological scatterers and the vertical radiation profile emitted by the radar
beam_range | Calculate radar beam range
beam_width | Calculate radar beam width
bind_into_vpts | Bind vertical profiles ('vp') into time series ('vpts')
bind_into_vpts.list | Bind vertical profiles ('vp') into time series ('vpts')
bind_into_vpts.vp | Bind vertical profiles ('vp') into time series ('vpts')
bind_into_vpts.vpts | Bind vertical profiles ('vp') into time series ('vpts')

## -- C --

c.vp | Concatenate vertical profiles ('vp') into a list of vertical profiles
calculate_param | Calculate a new scan parameter
calculate_param.ppi | Calculate a new scan parameter
calculate_param.pvol | Calculate a new scan parameter
calculate_param.scan | Calculate a new scan parameter
calculate_vp | Calculate a vertical profile ('vp') from a polar volume ('pvol') file
check_docker | Check if Docker is running
check_night | Check if it is night at a given time and place
check_night.default | Check if it is night at a given time and place
check_night.list | Check if it is night at a given time and place
check_night.pvol | Check if it is night at a given time and place
check_night.vp | Check if it is night at a given time and place
check_night.vpi | Check if it is night at a given time and place
check_night.vpts | Check if it is night at a given time and place
composite_ppi | Create a composite of multiple plan position indicators ('ppi')
convert_legacy | Convert legacy bioRad objects
convert_legacy.vp | Convert legacy bioRad objects
convert_legacy.vpts | Convert legacy bioRad objects

## -- D --

dbz_to_eta | Convert reflectivity factor to reflectivity
dim.ppi | Inspect a plan position indicator ('ppi')
dim.pvol | Inspect a polar volume ('pvol')
dim.scan | Inspect a scan ('scan')
dim.vp | Inspect a vertical profile ('vp')
dim.vpts | Inspect a time series of vertical profiles ('vpts')
download_basemap | Download a basemap for 'map(ppi)'
download_pvolfiles | Download polar volume ('pvol') files from the NEXRAD archive
download_vpfiles | Download vertical profile ('vp') files from the ENRAM data repository
doy | Look up day of year (doy) or night of year (noy)
doy.default | Look up day of year (doy) or night of year (noy)
doy.pvol | Look up day of year (doy) or night of year (noy)
doy.vp | Look up day of year (doy) or night of year (noy)
doy.vpi | Look up day of year (doy) or night of year (noy)
doy.vpts | Look up day of year (doy) or night of year (noy)
doy_noy | Look up day of year (doy) or night of year (noy)

## -- E --

eta_to_dbz | Convert reflectivity to reflectivity factor
example_scan | Scan ('scan') example
example_vp | Vertical profile ('vp') example
example_vpts | Time series of vertical profiles ('vpts') example

## -- F --

filter_vpts | Time and night/day selection in a time series of vertical profiles ('vpts')

## -- G --

get_elevation_angles | Get elevation angles of a polar volume ('pvol'), scan ('scan') or parameter ('param')
get_elevation_angles.param | Get elevation angles of a polar volume ('pvol'), scan ('scan') or parameter ('param')
get_elevation_angles.pvol | Get elevation angles of a polar volume ('pvol'), scan ('scan') or parameter ('param')
get_elevation_angles.scan | Get elevation angles of a polar volume ('pvol'), scan ('scan') or parameter ('param')
get_iris_raw_task | Check task of IRIS RAW file
get_odim_object_type | Check the 'data' object contained in a ODIM HDF5 file
get_param | Get a parameter ('param') from a scan ('scan')
get_quantity | Get a quantity from a vertical profile ('vp') or time series of vertical profiles ('vpts')
get_quantity.list | Get a quantity from a vertical profile ('vp') or time series of vertical profiles ('vpts')
get_quantity.vp | Get a quantity from a vertical profile ('vp') or time series of vertical profiles ('vpts')
get_quantity.vpts | Get a quantity from a vertical profile ('vp') or time series of vertical profiles ('vpts')
get_scan | Get a scan ('scan') from a polar volume ('pvol')

## -- I --

integrate_profile | Vertically integrate profiles ('vp' or 'vpts') to an integrated profile ('vpi')
integrate_profile.list | Vertically integrate profiles ('vp' or 'vpts') to an integrated profile ('vpi')
integrate_profile.vp | Vertically integrate profiles ('vp' or 'vpts') to an integrated profile ('vpi')
integrate_profile.vpts | Vertically integrate profiles ('vp' or 'vpts') to an integrated profile ('vpi')
integrate_to_ppi | Calculate a plan position indicator ('ppi') of vertically integrated density adjusted for range effects
is.param | Inspect a parameter ('param')
is.ppi | Inspect a plan position indicator ('ppi')
is.pvol | Inspect a polar volume ('pvol')
is.pvolfile | Check if a file is a polar volume ('pvol')
is.scan | Inspect a scan ('scan')
is.vp | Inspect a vertical profile ('vp')
is.vpfile | Check if a file is a vertical profile ('vp')
is.vpi | Inspect an integrated profile ('vpi')
is.vpts | Inspect a time series of vertical profiles ('vpts')

## -- M --

map | Map a plan position indicator ('ppi')
map.ppi | Map a plan position indicator ('ppi')
Math.pvol | Mathematical and arithmetic operations on param's, scan's and pvol's
Math.scan | Mathematical and arithmetic operations on param's, scan's and pvol's

## -- N --

nexrad_to_odim | Convert a NEXRAD polar volume file to an ODIM polar volume file
noy | Look up day of year (doy) or night of year (noy)
noy.default | Look up day of year (doy) or night of year (noy)
noy.pvol | Look up day of year (doy) or night of year (noy)
noy.vp | Look up day of year (doy) or night of year (noy)
noy.vpi | Look up day of year (doy) or night of year (noy)
noy.vpts | Look up day of year (doy) or night of year (noy)
nyquist_velocity | Nyquist velocity for a given pulse repetition frequency (PRF)

## -- O --

Ops.param | Mathematical and arithmetic operations on param's, scan's and pvol's
Ops.pvol | Mathematical and arithmetic operations on param's, scan's and pvol's
Ops.scan | Mathematical and arithmetic operations on param's, scan's and pvol's

## -- P --

plot.ppi | Plot a plan position indicator ('ppi')
plot.scan | Plot a scan ('scan') in polar coordinates
plot.vp | Plot a vertical profile ('vp')
plot.vpi | Plot an integrated profile ('vpi')
plot.vpts | Plot a time series of vertical profiles ('vpts')
project_as_ppi | Project a scan ('scan') or parameter ('param') to a plan position indicator ('ppi')
project_as_ppi.param | Project a scan ('scan') or parameter ('param') to a plan position indicator ('ppi')
project_as_ppi.scan | Project a scan ('scan') or parameter ('param') to a plan position indicator ('ppi')

## -- R --

rcs | Get radar cross section
rcs.list | Get radar cross section
rcs.vp | Get radar cross section
rcs.vpi | Get radar cross section
rcs.vpts | Get radar cross section
rcs<- | Set radar cross section
rcs<-.list | Set radar cross section
rcs<-.vp | Set radar cross section
rcs<-.vpi | Set radar cross section
rcs<-.vpts | Set radar cross section
read_cajun | Read a vertical profile ('vp') from UMASS Cajun text file
read_pvolfile | Read a polar volume ('pvol') from file
read_vpfiles | Read a vertical profile ('vp') or a list of vertical profiles ('vp') from files
read_vpts | Read a time series of vertical profiles ('vpts') from file
regularize_vpts | Regularize a time series of vertical profiles ('vpts') on a regular time grid

## -- S --

scan_to_raster | convert a polar scan into a raster
scan_to_spatial | convert a polar scan into a spatial object.
sd_vvp_threshold | Get threshold of the radial velocity standard deviation
sd_vvp_threshold.list | Get threshold of the radial velocity standard deviation
sd_vvp_threshold.vp | Get threshold of the radial velocity standard deviation
sd_vvp_threshold.vpts | Get threshold of the radial velocity standard deviation
sd_vvp_threshold<- | Set threshold of the radial velocity standard deviation
sd_vvp_threshold<-.list | Set threshold of the radial velocity standard deviation
sd_vvp_threshold<-.vp | Set threshold of the radial velocity standard deviation
sd_vvp_threshold<-.vpts | Set threshold of the radial velocity standard deviation
select_vpfiles | Select vertical profile ('vp') files from computer
summary.param | Inspect a parameter ('param')
summary.ppi | Inspect a plan position indicator ('ppi')
summary.pvol | Inspect a polar volume ('pvol')
summary.scan | Inspect a scan ('scan')
summary.vp | Inspect a vertical profile ('vp')
summary.vpi | Inspect an integrated profile ('vpi')
summary.vpts | Inspect a time series of vertical profiles ('vpts')
sunrise | Calculate sunrise or sunset for a time and place
sunrise_sunset | Calculate sunrise or sunset for a time and place
sunset | Calculate sunrise or sunset for a time and place

## -- U --

update_docker | Update Docker image from Docker hub

## -- V --

vol2bird_version | Check version of the vol2bird algorithm used by bioRad

## -- W --

write_pvolfile | Write a polar volume ('pvol') object to ODIM HDF5 file

## -- misc --

[.ppi | Subset a plan position indicator ('ppi')
[.vpts | Subset a time series of vertical profiles ('vpts')