Site built with pkgdown 2.0.9.
+Site built with pkgdown 2.1.0.
- +Adriaan M. Dokter
- Source:vignettes/rad_aero_22.Rmd
+ Source: vignettes/rad_aero_22.Rmd
rad_aero_22.RmdAdriaan M.
These course materials were developed for the 4th Radar Aeroecology Training School, Jul 30 - Aug 5 2022, Fort Collins, CO, USA.
-## Attempting to load MistNet from: /home/runner/work/_temp/Library/vol2birdR/lib
-## MistNet successfully initialized.Getting started
Execute each of the code examples provided below in RStudio, and try to complete the exercises.
-+# make sure you start with a fresh R session # load the bioRad package library(bioRad) @@ -130,12 +120,12 @@Getting startedpackageVersion("bioRad")
All bioRad’s functions are documented in an extensive function reference online, as well as in manual pages within R:
-+# bring up the package general help page: ?bioRadStart by making a new directory on your local machine that you will use for this practical:
-+# make a new local directory on your machine for this practical # replace the string below with the path of that directory: HOME <- "your/personal/working/directory/" @@ -160,7 +150,7 @@Basic visualization of radar scans
The structure of polar volumes
-+# Let's first download the NEXRAD polar volume files for the KHGX radar (Houston) # for a 15 minute period in 2017: download_pvolfiles(date_min=as.POSIXct("2017-05-04 01:25:00"), date_max=as.POSIXct("2017-05-04 01:40:00"), radar="KHGX", directory="./data_pvol") @@ -178,7 +168,7 @@The structure of polar volumes
Plotting radar scans
-+# let's extract the scan collected at 1.5 degree elevation from our polar volume: my_scan <- get_scan(my_pvol, 0.5) # print some information about this scan: @@ -188,7 +178,7 @@Plotting radar scans
+# before we can plot the scan, we need to project it on a Cartesian grid, # i.e. we need to make a Plan Position Indicator (PPI) my_ppi <- project_as_ppi(my_scan) @@ -213,7 +203,7 @@Plotting radar scans
Overlaying radar scans on maps
-+# It is often informative to plot radar data on a base layer. # First choose a base layer from the list of rosm::osm.types() basemap = "osm" @@ -230,9 +220,10 @@using correlation coefficient\(\rho_{/HV}\) +data above a certain + thresholds, most commonly 0.95. -
+# Screen out the reflectivity areas with RHOHV < 0.95 my_ppi_clean <- calculate_param(my_ppi, DBZH = ifelse(RHOHV > 0.95, NA, DBZH)) # plot the original and cleaned up reflectivity: @@ -246,7 +237,7 @@using MistNet
+# apply the MistNet model to the polar volume file and load it as a polar volume (pvol): my_pvol <- apply_mistnet(my_pvolfiles[1]) # mistnet will add additional parameters to the @@ -260,22 +251,24 @@using MistNetusing depolarization ratio
Another quantity that has been proposed for distinguishing weather -and biology is the depolarization ratio (\(D_r\)), which is defined as
-\[D_r=\frac{Z_{DR}+ 1 -2 \sqrt{Z_{DR}} \ -\rho_{HV}}{Z_{DR}+ 1 +2 \sqrt{Z_{DR}} \ \rho_{HV}}\] First we add -the depolarization ratio (DR) as a parameter. We’ll express DR on a dB -scale by transforming: \[DR=10\log_{10}(D_r) -\] (see Kilambi et al. 2018, A Simple and Effective Method -for Separating Meteorological from Nonmeteorological Targets Using +and biology is the depolarization ratio +(), +which is defined as
++First we add the depolarization ratio (DR) as a parameter. We’ll express +DR on a dB scale by transforming: + +(see Kilambi et al. 2018, A Simple and Effective Method for +Separating Meteorological from Nonmeteorological Targets Using Dual-Polarization Data for more information)
-+# let's add depolarization ratio (DR) as a parameter (following Kilambi 2018): my_ppi <- calculate_param(my_ppi, DR = 10 * log10((1+ ZDR - 2 * (ZDR^0.5) * RHOHV) / (1 + ZDR+ 2 * (ZDR^0.5) * RHOHV)))Like correlation coefficient you can apply simple thresholds to its value to screen out precipitation. It has a good (potentially even better) ability to distinguish weather and biology:
-+# plot the depolarization ratio, using a viridis color palette: map(my_ppi, map = basemap, param = "DR", zlim=c(-25,-5), palette = viridis::viridis(100))MistNet adds several new parameters: *
WEATHER: a @@ -287,7 +280,7 @@using depolarization ratioCELL values equal 1 for the additional fringe, and 2 for the originally segmented precipitation area by MistNet. -
+# as before, project the scan as a ppi: my_ppi <- project_as_ppi(my_scan) # plot the probability for the WEATHER class @@ -320,7 +313,7 @@Vertical profiles
Loading processed vertical profiles
-+# Usually we would load processed vertical profiles (vp files) by: # my_vplist <- read_vpfiles("./your/directory/with/processed/profiles/goes/here") # my_vplist contains after running the command a list of vertical profile (vp) objects @@ -336,7 +329,7 @@Inspecting single vertical profiles exploring them. We will start with plotting and inspecting single vertical profiles, i.e. a single profile from the list of vp objects you have just loaded. -
+# let's extract a profile from the list, in this example the 41st profile: my_vp <- my_vplist[[41]] # print some info for this profile to the console @@ -368,7 +361,7 @@Inspecting single vertical profiles section per bird). For these two reasons, for weather radar ornithologists reflectivity
etais the more conventional unit. -+# let's plot the vertical profile, in terms of bird density plot(my_vp, quantity = "dens") # print the currently assumed radar cross section (RCS) per bird: @@ -378,7 +371,7 @@Inspecting single vertical profiles is 10 times as large, what will be the effect on the bird density profile?
The assumed radar cross section can be changed as follows:
-+# let's change the RCS to 110 cm^2 rcs(my_vp) <- 110Exercise 6: Verify your answers on the previous two @@ -391,7 +384,7 @@
Plotting vertical profile time se
We will now examine multiple vertical profiles at once that are ordered into a time series, e.g. the vertical profiles obtained from a single radar over a full day.
-+# convert the list of vertical profiles into a time series: my_vpts <- bind_into_vpts(my_vplist) # time series objects can be subsetted, just as you may be used to with vectors @@ -406,7 +399,7 @@Plotting vertical profile time se # is called plot.vpts: ?plot.vpts
Let’s make a plot for a subselection of the time series:
-+# filter our vpts for night time my_vpts_night <- filter_vpts(my_vpts, night=TRUE) # plot this smaller time series: @@ -434,8 +427,9 @@Vertical and time integration is surface density as opposed to a volume densities you have been plotting in the previous exercises: this number gives you how many migrants are aloft per square kilometer earth’s surface (unit -individuals/km\(^{2}\)), obtained by a -vertical integration of the volume densities (unit individuals/km\(^{3}\)). +individuals/km), +obtained by a vertical integration of the volume densities (unit +individuals/km).
Note that the VID quantity doesn’t depend on the speed of the migrants. A common measure that reflects both the density and speed of the migration is migration traffic rate (MTR). This is flux measure that @@ -445,7 +439,7 @@ Vertical and time integration
We will be using bioRad’s
-integrate_profile()function to calculate these quantities:+# Let's continue with the vpts object created in the previous example. # The vertically integrated quantities are calculated as follows: my_vpi <- integrate_profile(my_vpts) @@ -466,7 +460,7 @@Vertical and time integration cubic kilometer. Above 1500 meter there are no birds.
Exercise 9: What is in this case the bird’s vertically integrated density (VID)? Give your answer in units -birds/km\(^2\).
+birds/km.Exercise 10: Let’s assume that in the lower layer birds fly at 50 km/hour, and in the upper layer at 100 km/hour. What is in this case the migration traffic rate across a transect perpendicular @@ -480,7 +474,7 @@
Vertical and time integration
Both MTR, VID and MT depend on the assumed radar cross section (RCS) per bird. If you are unwilling/unable to specify RCS, alternatively you can use two closely related quantities that make no assumptions RCS:
-+# instead of vertically integrated density (VID), you can use vertically integrated reflectivity (VIR): plot(my_vpi, quantity = "vir") # instead of migration traffic rate (MTR), you can use the reflectivity traffic rate (RTR): @@ -508,7 +502,7 @@Inspecting precipitation s reflectivity (quantity DBZH), which includes everything: birds, insects and precipitation. Precipitation often has higher reflectivities than birds, and also extends to much higher altitudes. -
+# load a time series for the KBGM radar in Binghamton, NY my_vpts <- readRDS("data_vpts/KBGM20170527-20170602.rds") # print the loaded vpts time series for this radar: @@ -532,7 +526,7 @@Range bias correction
First, let’s examine the beam shape of the lowest elevation scan of the radar, which is typically around 0.5 degrees.
-- ++- +# define ranges from 0 to 2500000 meter (250 km), in steps of 100 m: range <- seq(0, 250000, 100) @@ -547,7 +541,7 @@Range bias correction
Processing a polar volume into a profile
-- ++- +# download a polar volume for the KBRO radar in Brownsville, TX download_pvolfiles(date_min=as.POSIXct("2017-05-14 05:50:00"), date_max=as.POSIXct("2017-05-14 06:00:00"), radar="KBRO", directory="./data_pvol") # Load all the polar volume filenames downloaded so far for the KBRO radar: @@ -575,7 +569,7 @@Processing a polar volume into
- +Range bias correction and vertical integration on a map
-- ++# We will use the piping operator %>% of magrittr package to # execute multiple operations in one statement: library(magrittr) @@ -626,7 +620,7 @@Processing multiple polar volumes
First we download more files, and prepare an output directory for storing the processed profiles:
-- ++@@ -95,7 +87,7 @@# First we download more data, for a total of one additional hour for the same radar: download_pvolfiles(date_min=as.POSIXct("2017-05-04 01:40:00"), date_max=as.POSIXct("2017-05-04 02:40:00"), radar="KHGX", directory="./data_pvol") # We will process all the polar volume files downloaded so far: @@ -643,7 +637,7 @@to keep going after errors with specific filesProcessing multiple polar volumestryCatch()
Having generated the profiles, we can read them into R:
-- + @@ -20,8 +14,6 @@ - - - ++# we assume outputdir contains the path to the directory with processed profiles my_vpfiles <- list.files(outputdir, full.names = TRUE, pattern="KHGX") # print them @@ -652,7 +646,7 @@Processing multiple polar volumesmy_vplist <- read_vpfiles(my_vpfiles)
You can now continue with visualizing and post-processing as we did earlier:
-+@@ -753,17 +745,17 @@# make a time series of profiles: my_vpts <- bind_into_vpts(my_vplist) # plot them between 0 - 3 km altitude: @@ -673,7 +667,7 @@Parallel processing
+process_file <- function(file_in){ # construct output filename from input filename file_out <- paste(outputdir, "/", basename(file_in), "_vp.h5", sep = "") @@ -692,7 +686,7 @@Parallel processingprocess_file(my_pvolfiles[1])
Next, we use
-mclapply()to do the parallel processing for all files:Further analysis outside bioRad -
Site built with pkgdown 2.0.9.
+Site built with pkgdown 2.1.0.
- + @@ -105,7 +97,7 @@@@ -120,9 +112,9 @@Adriaan M. Dokter
- Source:vignettes/range_correction.Rmd+ Source:vignettes/range_correction.Rmdrange_correction.Rmd1 Preparationsoptions("sp_evolution_status" = 2L) library(bioRad)
-## Welcome to bioRad version 0.7.3.9000-## Attempting to load MistNet from: /home/runner/work/_temp/Library/vol2birdR/lib -## MistNet successfully initialized.+## using vol2birdR version 1.0.2 (MistNet installed)+## Attempting to load MistNet from:/home/runner/work/_temp/Library/vol2birdR/lib+## MistNet successfully initialized.## using vol2birdR version 1.0.3 (MistNet installed)- +2 Beam propagation @@ -141,14 +133,14 @@
2 Beam propagation
+# define a range grid from 0 to 200 km: my_range <- seq(0, 200000, 1000) # plot the beam height for each range, for a 0.5 degree elevation beam: plot(my_range, beam_height(my_range, elev = .5), xlab = "range [m]", ylab = "beam height [m]")
The beam width also broadens with range:
-- ++# plot the beam width, for a beam opening angle of 1 degree (typical for most weather radars): plot(my_range, beam_width(my_range, beam_angle = 1), xlab = "range [m]", ylab = "beam width [m]")@@ -157,17 +149,17 @@
2 Beam propagation
+# plot the beam profile, for a 0.5 degree elevation beam at 50 km distance from the radar: plot(beam_profile(height = 0:4000, 50000, 0.5), 0:4000, xlab = "normalized radiated energy", ylab = "height [m]", main = "beam elevation: 0.5 deg, distance=50km")-
- ++# plot the beam profile, for a 2 degree elevation beam at 50 km distance from the radar: plot(beam_profile(height = 0:4000, 50000, 2), 0:4000, xlab = "normalized radiated energy", ylab = "height [m]", main = "beam elevation: 2 deg, distance=50km")
We can also calculate the normalized radiation profile for the two beams combined:
-- ++# plot the combined beam profile for a 0.5 and 2.0 degree elevation beam at 50 km distance from the radar: plot(beam_profile(height = 0:4000, 50000, c(0.5, 2)), 0:4000, xlab = "normalized radiated energy", ylab = "height [m]", main = "beam elevations: 0.5,2 deg, distance=50km")@@ -177,7 +169,7 @@
3 Vertical profiles and polar volum
Let us now assume we have calculated a vertical profile (of birds) for a certain polar volume file. Let’s load an example
-- ++- +# let's load an example polar volume: pvolfile <- system.file("extdata", "volume.h5", package = "bioRad") example_pvol <- read_pvolfile(file = pvolfile) @@ -193,13 +185,13 @@3 Vertical profiles and polar volum ## generated by: vol2bird 0.3.17
Let’s plot the vertical profile, for the quantity eta (the linear reflectivity):
-+plot(example_vp, quantity = "eta")
Note that eta is directly related to reflectivity factor (DBZH), i.e. a reflectivity factor of 5 dBZ amounts to the following eta at a radar wavelength of 5.3 cm:
-@@ -224,19 +216,25 @@+dbz_to_eta(5, wavelength = 5.3)## [1] 1140.5884 Spatial estima
calculate for each ground surface pixel the vertical radiation profile at that pixel for that particular scan, following above paragraph 2. -calculate the reflectivity we expect at that pixel (\(eta_{expected}\)), given the vertical -profile (of birds) and the part of the profile radiated by the beam. -This \(eta_{expected}\) is simply the -average of (linear) eta in the profile (as plotted in paragraph 3 -above), weighted by the vertical radiation profile (as plotted in -paragraph 2). +calculate the reflectivity we expect at that pixel +(), +given the vertical profile (of birds) and the part of the profile +radiated by the beam. This + +is simply the average of (linear) eta in the profile (as plotted in +paragraph 3 above), weighted by the vertical radiation profile (as +plotted in paragraph 2). we also calculated the observed eta at this pixel, which is simply given by -dbz_to_eta(DBZH)(see paragraph 3), with DBZH the reflectivity factor measured at the pixel’s distance from the radar.For each pixel on the ground, we thus end up with a set of \(eta_{expected}\) and a set of \(eta_{observed}\). From those we can -calculate a correction factor at that pixel, as \(R=\sum{eta_{observed}}/\sum{eta_{expected}}\), +
For each pixel on the ground, we thus end up with a set of + +and a set of +. +From those we can calculate a correction factor at that pixel, as +, with the sum running over scans.
To arrive at the final PPI image:
@@ -255,7 +253,7 @@
4 Spatial estima
5 Example: estimating a VID image
Let’s first make a PPI plot of the lowest uncorrected scan:
-- ++# extract the first scan from the polar volume: my_scan <- example_pvol$scans[[1]] # project it as a PPI on the ground: @@ -264,7 +262,7 @@5 Example: estimating a VID imageplot(my_ppi)
Now let’s calculate the range-corrected PPI
-- ++@@ -274,16 +272,16 @@# let's use a 500 metre spatial grid (res), and restrict to 100x100 km area my_corrected_ppi <- integrate_to_ppi(example_pvol, example_vp, res = 500, xlim = c(-100000, 100000), ylim = c(-100000, 100000)) my_corrected_ppi5 Example: estimating a VID image## dims: 400 x 400 pixels
The range corrected PPI has four parameters: VIR, VID, R, overlap. Let’s plot the adjustment factor R:
-@@ -95,7 +89,7 @@+# plot the adjustment factor R: plot(my_corrected_ppi, param = "R")
Let’s also plot the vertically integrated reflectivity:
-- + @@ -29,7 +23,7 @@ - ++plot(my_corrected_ppi, param = "VIR")
Or plot the vertically integrated density on a map:
-- ++bm <- "osm" map(my_corrected_ppi, map=bm, param = "VIR", alpha = .5)## Warning in CPL_crs_from_input(x): GDAL Message 1: +init=epsg:XXXX syntax is @@ -308,7 +306,7 @@6 Overlap between ra
We can calculate overlap between emitted radiation and the biological profile as follows:
-- ++@@ -363,17 +359,17 @@# calculate overlap between vertical profile of birds # and the vertical radiation profile emitted by the radar: bpo <- beam_profile_overlap(example_vp, get_elevation_angles(example_pvol), seq(0, 100000, 1000), quantity = "eta") @@ -328,7 +326,7 @@6 Overlap between ra
The range-corrected PPI also contains a field
-overlap, which contains the same metric but then calculated on the grid of the PPI:+plot(my_corrected_ppi, param = "overlap")
The overlap metric might be used in the future to show only certain @@ -348,9 +346,7 @@
7 To do +
7 To do
Authors and Citation • bioRad - +@@ -68,7 +68,7 @@- +Authors and Citation
Adriaan M. Dokter. Author, maintainer.
@@ -110,7 +110,7 @@Authors and Citation
- -
Jurriaan Spaaks. Contributor. +
Jurriaan Spaaks. Contributor.
- @@ -118,7 +118,7 @@
Authors and Citation
- -
Lourens Veen. Contributor. +
Lourens Veen. Contributor.
- @@ -129,7 +129,7 @@
Authors and Citation
@@ -156,16 +156,16 @@Citation
- + - +- +Changelog • bioRad - +Mathematical and arithmetic operations on param's, scan's and pvol's — Math.scan • bioRad - +Mathematical and arithmetic operations on param's, scan's and pvol's
- Source:R/operators.R+ Source:R/operators.ROps.RdMathematical and arithmetic operations on param's, scan's and pvol's
-- +# S3 method for scan +# S3 method for class 'scan' Math(x, ...) -# S3 method for pvol +# S3 method for class 'pvol' Math(x, ...) -# S3 method for param +# S3 method for class 'param' Ops(e1, e2) -# S3 method for scan +# S3 method for class 'scan' Ops(e1, e2) -# S3 method for pvol +# S3 method for class 'pvol' Ops(e1, e2)Arguments
-Value
- - -an object of the input class
+an object of the input class
Details
@@ -161,16 +161,16 @@Examples
Adds expected eta to a scan — add_expected_eta_to_scan • bioRad - +Adds expected eta to a scan
- Source:R/integrate_to_ppi.R+ Source:R/integrate_to_ppi.Radd_expected_eta_to_scan.RdAdds expected eta to a scan
Arguments
-
- scan
+ + +
- scan
- -
a scan (sweep) of class scan
- vp
+- vp
- -
A
vpobject- quantity
+- quantity
- -
Character. Profile quantity on which to base range corrections, either
etaordens.- param
+- param
- -
reflectivity Character. Scan parameter on which to base range corrections. Typically the same parameter from which animal densities are estimated in
vp. EitherDBZH,DBZV,DBZ,TH, orTV.- lat
+- lat
- -
Latitude of the radar, in degrees. If missing taken from
pvol.- lon
+- lon
- -
Latitude of the radar, in degrees. If missing taken from
pvol.- antenna
+- antenna
- -
Numeric. Radar antenna height, in m. Default to antenna height in
vp.- beam_angle
+- beam_angle
- -
Numeric. Beam opening angle in degrees, typically the angle between the half-power (-3 dB) points of the main lobe.
- k
+- k
- -
Numeric. Standard refraction coefficient.
- re
+- re
- -
Numeric. Earth equatorial radius, in km.
- rp
+- rp
Numeric. Earth polar radius, in km.
Value
- - -A
+scanobject.A
scanobject.Value
Apply MistNet segmentation to a polar volume — apply_mistnet • bioRad - +Apply MistNet segmentation to a polar volume
- Source:R/apply_mistnet.R+ Source:R/apply_mistnet.Rapply_mistnet.RdApply MistNet segmentation to a polar volume
Arguments
-
- file
+ + +
- file
- -
Character. Path to a polar volume (
pvol) file.- pvolfile_out
+- pvolfile_out
- -
Character. (optional) File name. When provided, writes a polar volume (
pvol) file to disk that includes the Mistnet segmentation results.- verbose
+- verbose
- -
Logical. When
TRUE, vol2birdstdoutis piped to the R console.- mount
+- mount
- -
Character. Directory path of the mount point for the Docker container (deprecated).
- load
+- load
- -
Logical. When
TRUE, returns apvolobject.- mistnet_elevations
+- mistnet_elevations
- -
Numeric vector of length 5. Elevation angles to feed to the MistNet segmentation model, which expects exactly 5 elevation scans at 0.5, 1.5, 2.5, 3.5 and 4.5 degrees. Specifying different elevation angles may compromise segmentation results.
- local_install
+- local_install
- -
Character. Path to local vol2bird installation (e.g.
your/vol2bird_install_directory/vol2bird/bin/vol2bird) to use instead of the Docker container.- local_mistnet
+- local_mistnet
- @@ -135,9 +137,7 @@
Character. Path to local MistNet segmentation model in PyTorch format (e.g.
/your/path/mistnet_nexrad.pt) to use instead of the Docker container.Arguments
Value
- - -When
loadisTRUE, a polar volume (pvol) object with the +When
loadisTRUE, a polar volume (pvol) object with the Mistnet segmentation results. WhenloadisFALSE,TRUEon success.@@ -199,6 +199,15 @@Examples
vol2birdR::install_mistnet() vol2birdR::install_mistnet_model() } +#> Starting installation of MistNet... +#> Checking write permissions... +#> Installing MistNet libraries... +#> Initializing MistNet... +#> Attempting to load MistNet from:/home/runner/work/_temp/Library/vol2birdR/lib +#> MistNet successfully initialized. +#> MistNet initialized successfully. +#> MistNet installation complete. +#> [1] TRUE # start a temporary file to store polar volume tempfile=tempfile("KBGM_example") # Download a NEXRAD file and save as KBGM_example @@ -209,9 +218,7 @@Examples
# Calculate MistNet segmentation mistnet_pvol <- apply_mistnet(tempfile) -#> Checking file before processing: /tmp/RtmpD92Z4P/KBGM_example1a462b91d882 -#> File size: 3950079 bytes -#> Filename = /tmp/RtmpD92Z4P/KBGM_example1a462b91d882, callid = KBGM +#> Filename = /tmp/RtmpZJt3Jx/KBGM_example5ec24ee824c8, callid = KBGM #> Reading RSL polar volume with nominal time 20191001-000542, source: RAD:KBGM,PLC:BINGHAMTON,state:NY,radar_name:KBGM #> Running vol2birdSetUp #> Warning: radial velocities will be dealiased... @@ -273,16 +280,16 @@Examples
Convert a vertical profile (vp) or time series of vertical profiles (vpts) to a data frame — as.data.frame.vp • bioRad - +Convert a vertical profile (
- Source:vp) or time series of vertical profiles (vpts) to a data frameR/as.data.frame.R+ Source:R/as.data.frame.Ras.data.frame.vp.RdConvert a vertical profile (
vp) or time series of vertical prof-- +- +# S3 method for vp +- +# S3 method for class 'vp' as.data.frame( x, row.names = NULL, @@ -93,7 +93,7 @@Convert a vertical profile (
vp) or time series of vertical prof ... ) -# S3 method for vpts +# S3 method for class 'vpts' as.data.frame( x, row.names = NULL, @@ -109,55 +109,55 @@Convert a vertical profile (
vp) or time series of vertical profArguments
-
- x
+ + +
- x
- -
A
vporvptsobject.- row.names
+- row.names
- -
NULLor a character vector giving the row names for the data frame. Missing values are not allowed. Seebase::as.data.frame().- optional
+- optional
- -
Logical. If
FALSEthen the names of the variables in the data frame are checked to ensure that they are syntactically valid variable names and are not duplicated. Seebase::as.data.frame().- geo
+- geo
- -
Logical. When
TRUE, adds latitude (lat), longitude (lon) and antenna height of the radar (height_antenna) to each row.- suntime
+- suntime
- -
Logical. When
TRUE, adds whether it is daytime (day) and the datetime ofsunriseandsunsetto each row.- lat
+- lat
- -
Numeric. Radar latitude in decimal degrees. When set, overrides the latitude stored in
xforsunrise()/sunset()calculations.- lon
+- lon
- -
Numeric. Radar longitude in decimal degrees. When set, overrides the longitude stored in
xforsunrise()/sunset()calculations.- elev
+- elev
- -
Numeric. Sun elevation in degrees, used for
sunrise()/sunset()calculations.- ...
+- ...
Additional arguments to be passed to or from methods.
Value
- - -A
data.frameobject, containing radar, datetime and height as rows +A
@@ -368,16 +368,16 @@data.frameobject, containing radar, datetime and height as rows and all profile quantities as columns, complemented with some oft-used additional information (columnslat,lon,height_antenna,day,sunrise,sunset).Examples
Convert a dataframe into a vpts object — as.vpts • bioRad - +Convert a dataframe into a vpts object
Value
- - -a bioRad vpts object
+a bioRad vpts object
@@ -116,16 +116,16 @@Examples
Extract a volume coverage pattern table with all attributes — attribute_table • bioRad - +Extract a volume coverage pattern table with all attributes
- Source:R/attribute_table.R+ Source:R/attribute_table.Rattribute_table.RdExtract a volume coverage pattern table with all attributes
Arguments
-
- x
+ + +
- x
- -
Either a pvol or scan for which the table should be created.
- select
+- select
- -
A character vector which the column names that should be returned when NULL all attributes are to be returned
- ...
+- ...
Currently not used
This function tabulates the attributes of one scan or all scans of a pvol. Attributes that have a length longer then one are presented as a list column. @@ -103,9 +105,7 @@
Arguments
Value
- - -A data.frame with the attributes of the scan(s)
+A data.frame with the attributes of the scan(s)
@@ -142,16 +142,16 @@Examples
Calculate radar beam distance — beam_distance • bioRad - +Calculate radar beam distance
Arguments
-
- range
+ + +
- range
- -
Numeric. Slant range, i.e. the length of the skywave path between target and the radar antenna, in m.
- elev
+- elev
- -
Numeric. Beam elevation, in degrees.
- k
+- k
- -
Numeric. Standard refraction coefficient.
- lat
+- lat
- -
Numeric. Geodetic latitude of the radar, in degrees.
- re
+- re
- -
Numeric. Earth equatorial radius, in km.
- rp
+- rp
Numeric. Earth polar radius, in km.
Value
- - -Beam distance (down range), in m.
+Beam distance (down range), in m.
- +Details
@@ -120,7 +120,7 @@Details
See also
Other beam_functions: +
Other beam_functions:
beam_height(),beam_profile_overlap(),beam_profile(), @@ -148,16 +148,16 @@Examples
Calculate radar beam height — beam_height • bioRad - +Calculate radar beam height
Arguments
-
- range
+ + +
- range
- -
Numeric. Slant range, i.e. the length of the skywave path between target and the radar antenna, in m.
- elev
+- elev
- -
Numeric. Beam elevation, in degrees.
- k
+- k
- -
Numeric. Standard refraction coefficient.
- lat
+- lat
- -
Numeric. Geodetic latitude of the radar, in degrees.
- re
+- re
- -
Numeric. Earth equatorial radius, in km.
- rp
+- rp
Numeric. Earth polar radius, in km.
Value
- - -numeric. Beam height in m.
+numeric. Beam height in m.
- +Details
@@ -127,7 +127,7 @@Details
See also
Other beam_functions: +
Other beam_functions:
beam_distance(),beam_profile_overlap(),beam_profile(), @@ -166,16 +166,16 @@Examples
Calculate vertical radiation profile — beam_profile • bioRad - +Calculate vertical radiation profile
Arguments
-
- height
+ + +
- height
- -
Numeric. Height in m.
- distance
+- distance
- -
Numeric. Distance from the radar as measured along sea level (down range), in m.
- elev
+- elev
- -
Numeric vector. Beam elevation(s), in degrees.
- antenna
+- antenna
- -
Numeric. Height of the centre of the radar antenna, in m.
- beam_angle
+- beam_angle
- -
Numeric. Beam opening angle in degrees, typically the angle between the half-power (-3 dB) points of the main lobe.
- k
+- k
- -
Numeric. Standard refraction coefficient.
- lat
+- lat
- -
Numeric. Geodetic latitude of the radar, in degrees.
- re
+- re
- -
Numeric. Earth equatorial radius, in km.
- rp
+- rp
Numeric. Earth polar radius, in km.
Value
- - -Numeric vector. Normalized radiated energy at each of the specified +
Numeric vector. Normalized radiated energy at each of the specified heights.
@@ -151,7 +151,7 @@Details
- +See also
-- +Other beam_functions: +
Other beam_functions:
beam_distance(),beam_height(),beam_profile_overlap(), @@ -199,16 +199,16 @@Examples
Calculate overlap between a vertical profile ('vp') and the vertical radiation profile emitted by the radar — beam_profile_overlap • bioRad - +Calculate overlap between a vertical profile ('vp') and the vertical radiation profile emitted by the radar
- Source:R/beam.R+ Source:R/beam.Rbeam_profile_overlap.RdCalculate overlap between a vertical profile ('vp') and the vertical radiati
Arguments
-
- vp
+ + +
- vp
- -
A
vpobject.- elev
+- elev
- -
Numeric vector. Beam elevation(s), in degrees.
- distance
+- distance
- -
Numeric. The distance(s) from the radar along sea level (down range) for which to calculate the overlap, in m.
- antenna
+- antenna
- -
Numeric. Radar antenna height, in m. Default to antenna height in
vp.- zlim
+- zlim
- -
Numeric vector of length two. Altitude range, in m
- noise_floor
+- noise_floor
- -
Numeric. The system noise floor in dBZ. The total system noise expressed as the reflectivity factor it would represent at a distance
noise_floor_ref_rangefrom the radar. NOT YET IMPLEMENTED- noise_floor_ref_range
+- noise_floor_ref_range
- -
Numeric. The reference distance from the radar at which
noise_flooris expressed. NOT YET IMPLEMENTED.- steps
+- steps
- -
Numeric. Number of integration steps over altitude range
zlim, defining altitude grid size used for numeric integration.- quantity
+- quantity
- -
Character. Profile quantity (
densoreta) to use for the altitude distribution.- normalize
+- normalize
- -
Logical. If
TRUE, normalize the radiation coverage pattern over the altitude range specified byzlim.- beam_angle
+- beam_angle
- -
Numeric. Beam opening angle in degrees, typically the angle between the half-power (-3 dB) points of the main lobe.
- k
+- k
- -
Numeric. Standard refraction coefficient.
- lat
+- lat
- -
Numeric. Radar latitude. Defaults to latitude in
vp.- re
+- re
- -
Numeric. Earth equatorial radius, in km.
- rp
+- rp
Numeric. Earth polar radius, in km.
Value
- - -A data.frame with columns
+distanceandoverlap.A data.frame with columns
distanceandoverlap.Details
@@ -206,7 +206,7 @@See also
Other beam_functions: +
Other beam_functions:
beam_distance(),beam_height(),beam_profile(), @@ -257,16 +257,16 @@Examples
Calculate radar beam range — beam_range • bioRad - +Calculate radar beam range
Arguments
-
- distance
+ + +
- distance
- -
Numeric. Distance from the radar as measured along sea level (down range), in m.
- elev
+- elev
- -
Numeric. Beam elevation, in degrees.
- k
+- k
- -
Numeric. Standard refraction coefficient.
- lat
+- lat
- -
Numeric. Geodetic latitude of the radar, in degrees.
- re
+- re
- -
Numeric. Earth equatorial radius, in km.
- rp
+- rp
Numeric. Earth polar radius, in km.
Value
- - -Beam range (slant range), in m.
+Beam range (slant range), in m.
Details
@@ -118,7 +118,7 @@Details
- +See also
-- +Other beam_functions: +
Other beam_functions:
beam_distance(),beam_height(),beam_profile_overlap(), @@ -146,16 +146,16 @@Examples
Calculate radar beam width — beam_width • bioRad - +Calculate radar beam width
Arguments
-Value
- - -numeric. Beam width in m, typically the full width at half maximum (FWHM).
+numeric. Beam width in m, typically the full width at half maximum (FWHM).
- +See also
-- +Other beam_functions: +
Other beam_functions:
beam_distance(),beam_height(),beam_profile_overlap(), @@ -131,16 +131,16 @@Examples
Bind vertical profiles (vp) into time series (vpts) — bind_into_vpts • bioRad - +Bind vertical profiles (
- Source:vp) into time series (vpts)R/bind_into_vpts.R+ Source:R/bind_into_vpts.Rbind_into_vpts.RdBind vertical profiles (
vp) into time series (vptsbind_into_vpts(x, ...) -# S3 method for vp +# S3 method for class 'vp' bind_into_vpts(...) -# S3 method for list +# S3 method for class 'list' bind_into_vpts(x, ...) -# S3 method for vpts +# S3 method for class 'vpts' bind_into_vpts(..., attributes_from = 1)Arguments
-Value
- - -A
vptsfor a single radar or a list ofvptsfor multiple radars. +A
vptsfor a single radar or a list ofvptsfor multiple radars. Inputvpare sorted on datetime in the outputvpts.@@ -120,7 +120,7 @@Details
Methods (by class)
- +
- @@ -198,16 +198,16 @@
bind_into_vpts(vp): Bind multiplevpinto avpts. Ifvpfor multiple radars are provided, a list is returned containing avptsfor each radar.Examples
Deprecated bioRad functions and data — bioRad-deprecated • bioRad - +Deprecated bioRad functions and data
- Source:R/bioRad-deprecated.R+ Source:R/bioRad-deprecated.RbioRad-deprecated.RdDeprecated bioRad functions and data
Value
- - -- - - +
TRUE
TRUENo return value, called for warning message side effect only
- -an object of class numeric_version
- - -No return value, called for warning message side effect only
check_docker
- +This function has been removed and always returns TRUE
update_docker
- +This function has been deprecated
vol2bird_version
- +This function has been moved to package vol2birdR
download_basemap
- +This function has been deprecated ggmap has been replaced by ggspatial which no longer requires a pre-downloaded raster basemap
@@ -142,16 +132,16 @@download_basemap
bioRad: Biological Analysis and Visualization of Weather Radar Data
- Source:R/bioRad.R+ Source:R/bioRad.RbioRad-package.RdAuthor
Concatenate vertical profiles (vp) into a list of vertical profiles — c.vp • bioRad - +Concatenate vertical profiles (
- Source:vp) into a list of vertical profilesR/vp.R+ Source:R/vp.Rc.vp.RdConcatenate vertical profiles (
vp) into a list of vertical prof-- +# S3 method for vp +# S3 method for class 'vp' c(...)Value
- - -A list of
+vpobjects.A list of
vpobjects.See also
@@ -132,16 +132,16 @@Examples
Calculate a new scan parameter — calculate_param • bioRad - +Calculate a new scan parameter
- Source:R/calculate_param.R+ Source:R/calculate_param.Rcalculate_param.RdCalculate a new scan parameter
calculate_param(x, ...) -# S3 method for pvol +# S3 method for class 'pvol' calculate_param(x, ...) -# S3 method for ppi +# S3 method for class 'ppi' calculate_param(x, ...) -# S3 method for scan +# S3 method for class 'scan' calculate_param(x, ...)Arguments
-Value
- - -An object of the same class as
+x, either apvolorscan.An object of the same class as
x, either apvolorscan.Details
@@ -115,7 +115,7 @@Details
Methods (by class)
- +
calculate_param(pvol): Calculate a new parameter (param) for all scans in a polar volume (pvol).
calculate_param(ppi): Calculate a new parameter (param) for a plan @@ -125,7 +125,7 @@Methods (by class)
References
- +
Kilambi A, Fabry F, Meunier V (2018) A simple and effective method for separating meteorological from nonmeteorological targets using dual-polarization data. Journal of Atmospheric and Oceanic Technology 35, pp. @@ -189,16 +189,16 @@
Examples
Calculate a vertical profile (vp) from a polar volume (pvol) file — calculate_vp • bioRad - +Calculate a vertical profile (
- Source:vp) from a polar volume (pvol) fileR/calculate_vp.R+ Source:R/calculate_vp.Rcalculate_vp.RdCalculate a vertical profile (
vp) from a polar volume (pvArguments
-
- file
+ + +
- file
- -
Character (vector). Either a path to a single radar polar volume (
pvol) file containing multiple scans/sweeps, or multiple paths to scan files containing a single scan/sweep. Or a singlepvolobject. The file data format should be either 1) @@ -126,147 +128,145 @@Arguments
IRIS (IRIS RAW) format.- vpfile
+- vpfile
- -
Character. File name. When provided, writes a vertical profile file (
vpfile) either in the VPTS CSV or ODIM HDF5 format to disk.- pvolfile_out
+- pvolfile_out
- -
Character. File name. When provided, writes a polar volume (
pvol) file in the ODIM HDF5 format to disk. Useful for converting RSL formats to ODIM.- autoconf
+- autoconf
- -
Logical. When
TRUE, default optimal configuration settings are selected automatically and other user settings are ignored.- verbose
+- verbose
- -
Logical. When
TRUE, vol2birdstdoutis piped to the R console.- warnings
+- warnings
- -
Logical. When
TRUE, vol2bird warnings are piped to the R console.- mount
+- mount
- -
Character. Directory path of the mount point for the Docker container (deprecated).
- sd_vvp_threshold
+- sd_vvp_threshold
- -
Numeric. Lower threshold for the radial velocity standard deviation (profile quantity
sd_vvp) in m/s. Biological signals withsd_vvp < sd_vvp_thresholdare set to zero. Defaults to 2 m/s for C-band radars and 1 m/s for S-band radars.- rcs
+- rcs
- -
Numeric. Radar cross section per bird to use, in cm^2.
- dual_pol
+- dual_pol
- -
Logical. When
TRUE, uses dual-pol mode, in which meteorological echoes are filtered using the correlation coefficient thresholdrho_hv.- rho_hv
+- rho_hv
- -
Numeric. Lower threshold in correlation coefficient to use for filtering meteorological scattering.
- single_pol
+- single_pol
- -
Logical. When
TRUE, uses precipitation filtering in single polarization mode based on reflectivity and radial velocity quantities.- elev_min
+- elev_min
- -
Numeric. Minimum elevation angle to include, in degrees.
- elev_max
+- elev_max
- -
Numeric. Maximum elevation angle to include, in degrees.
- azim_min
+- azim_min
- -
Numeric. Minimum azimuth to include, in degrees clockwise from north.
- azim_max
+- azim_max
- -
Numeric. Maximum azimuth to include, in degrees clockwise from north.
- range_min
+- range_min
- -
Numeric. Minimum range to include, in m.
- range_max
+- range_max
- -
Numeric. Maximum range to include, in m.
- n_layer
+- n_layer
- -
Numeric. Number of altitude layers to use in generated profile.
- h_layer
+- h_layer
- -
Numeric. Width of altitude layers to use in generated profile, in m.
- dealias
+- dealias
- -
Logical. Whether to dealias radial velocities. This should typically be done when the scans in the polar volume have low Nyquist velocities (below 25 m/s).
- nyquist_min
+- nyquist_min
- -
Numeric. Minimum Nyquist velocity of scans to include, in m/s.
- dbz_quantity
+- dbz_quantity
- -
Name of the available reflectivity factor to use if not
DBZH(e.g.DBZV,TH,TV).- mistnet
+- mistnet
- -
Logical. Whether to use the MistNet segmentation model.
- mistnet_elevations
+- mistnet_elevations
- -
Numeric vector of length 5. Elevation angles to feed to the MistNet segmentation model, which expects exactly 5 elevation scans at 0.5, 1.5, 2.5, 3.5 and 4.5 degrees. Specifying different elevation angles may compromise segmentation results.
- local_install
+- local_install
- -
Character. Path to local vol2bird installation (e.g.
your/vol2bird_install_directory/vol2bird/bin/vol2bird.sh). (deprecated)- local_mistnet
+- local_mistnet
Character. Path to local MistNet segmentation model in PyTorch format (e.g.
/your/path/mistnet_nexrad.pt).Value
- - -A vertical profile object of class
vp. When defined, output files +A vertical profile object of class
vp. When defined, output filesvpfileandpvolfile_outare saved to disk.- +Details
- +Typical use
@@ -394,14 +394,15 @@See also
@@ -431,16 +432,16 @@Examples
# Locate and read the polar volume example file -pvolfile <- system.file("extdata", "volume.h5", package = "bioRad") +pvolfile_source <- system.file("extdata", "volume.h5", package = "bioRad") # Copy the file to a home directory with read/write permissions -file.copy(pvolfile, "~/volume.h5") +pvolfile <- paste0(tempdir(),"/volume.h5") +file.copy(pvolfile_source, pvolfile) #> [1] TRUE # Calculate the profile -vp <- calculate_vp("~/volume.h5") +vp <- calculate_vp(pvolfile) #> Running vol2birdSetUp #> Warning: radial velocities will be dealiased... @@ -415,7 +416,7 @@Examples
#> generated by: vol2bird 0.6.0.9201 # Clean up -file.remove("~/volume.h5") +file.remove(pvolfile) #> [1] TRUEExamples
Check if character date is in specific format — check_date_format • bioRad - +Check if character date is in specific format
- Source:R/utils.R+ Source:R/utils.Rcheck_date_format.RdCheck if character date is in specific format
Arguments
-@@ -109,16 +109,16 @@Value
- - -NULL. Will stop and show error message if date does not have correct +
NULL. Will stop and show error message if date does not have correct date format.
Value
Check if it is night at a given time and place — check_night • bioRad - +Check if it is night at a given time and place
- Source:R/check_night.R+ Source:R/check_night.Rcheck_night.RdCheck if it is night at a given time and place
check_night(x, ..., elev = -0.268, offset = 0) -# S3 method for default +# Default S3 method check_night(x, lon, lat, ..., tz = "UTC", elev = -0.268, offset = 0) -# S3 method for vp +# S3 method for class 'vp' check_night(x, ..., elev = -0.268, offset = 0) -# S3 method for list +# S3 method for class 'list' check_night(x, ..., elev = -0.268, offset = 0) -# S3 method for vpts +# S3 method for class 'vpts' check_night(x, ..., elev = -0.268, offset = 0) -# S3 method for vpi +# S3 method for class 'vpi' check_night(x, ..., elev = -0.268, offset = 0) -# S3 method for pvol +# S3 method for class 'pvol' check_night(x, ..., elev = -0.268, offset = 0)Arguments
-
- x
+ + +
- x
- -
A
pvol,vp,vpts,vpiobject, a POSIXct date or a string interpretable bybase::as.POSIXct().- ...
+- ...
- -
Optional lat, lon arguments.
- elev
+- elev
- -
Numeric (vector). Sun elevation in degrees defining nighttime. May also be a numeric vector of length two, with first element giving sunset elevation, and second element sunrise elevation.
- offset
+- offset
- -
Numeric (vector). Time duration in seconds by which to shift the start and end of nighttime. May also be a numeric vector of length two, with first element added to moment of sunset and second element added to moment of sunrise.
- lon
+- lon
- -
Numeric. Longitude, in decimal degrees.
- lat
+- lat
- -
Numeric. Latitude, in decimal degrees.
- tz
+- tz
Character. Time zone. Ignored when
datealready has an associated time zone.@@ -360,16 +360,16 @@Value
- - -
TRUEwhen night,FALSEwhen day,NAif unknown +
TRUEwhen night,FALSEwhen day,NAif unknown (either datetime or geographic location missing). Forvptsa vector ofTRUE/FALSEvalues is returned.Examples
Check if radar codes are exactly 5 characters — check_radar_codes • bioRad - +Check if radar codes are exactly 5 characters
- Source:R/utils.R+ Source:R/utils.Rcheck_radar_codes.RdCheck if radar codes are exactly 5 characters
@@ -103,16 +103,16 @@Value
- - -NULL. Will stop and show error message if at least one of the +
NULL. Will stop and show error message if at least one of the provided radar codes is not exactly 5 characters.
Value
Create a composite of multiple plan position indicators (ppi) — composite_ppi • bioRad - +Create a composite of multiple plan position indicators (
- Source:ppi)R/composite_ppi.R+ Source:R/composite_ppi.Rcomposite_ppi.RdCreate a composite of multiple plan position indicators (
ppi)Arguments
-
- x
+ + +
- x
- -
A list of
ppiobjects.- param
+- param
- -
Character (vector). One or more parameter name(s) to composite. To composite all available scan parameters use
all(default).- nx
+- nx
- -
number of raster pixels in the x (longitude) dimension
- ny
+- ny
- -
number of raster pixels in the y (latitude) dimension
- xlim
+- xlim
- -
x (longitude) range
- ylim
+- ylim
- -
y (latitude) range
- res
+- res
- -
numeric vector of length 1 or 2 to set the resolution of the raster (see res). If this argument is used, arguments
nxandnyare ignored. Unit is identical toxlimandylim.- crs
+- crs
- -
character or object of class CRS. PROJ.4 type description of a Coordinate Reference System (map projection). When 'NA' (default), an azimuthal equidistant projection with origin at the radar location is used. To use a WSG84 (lat,lon) projection, use crs="+proj=longlat +datum=WGS84"
- raster
+- raster
- -
(optional) RasterLayer with a CRS. When specified this raster topology is used for the output, and nx, ny, res arguments are ignored.
- method
+- method
- -
Character (vector). Compositing method(s), either
mean,min,maxoridw. To apply different methods for each of the parameters, provide a vector with the same length asparam.- idp
+- idp
- -
Numeric. Inverse distance weighting power.
- idw_max_distance
+- idw_max_distance
- -
Numeric. Maximum distance from the radar to consider in inverse distance weighting. Measurements beyond this distance will have a weighting factor of zero.
- coverage
+- coverage
- @@ -162,9 +164,7 @@
Logical. When
TRUE, adds an additionalcoverageparameter to theppiindicating the number ofppis covering a single composite pixel.Arguments
Value
- - -A
+ppiobject.A
ppiobject.Details
@@ -236,16 +236,16 @@Examples
Convert legacy bioRad objects — convert_legacy • bioRad - +Convert legacy bioRad objects
- Source:R/convert_legacy.R+ Source:R/convert_legacy.Rconvert_legacy.RdConvert legacy bioRad objects
convert_legacy(x) -# S3 method for vp +# S3 method for class 'vp' convert_legacy(x) -# S3 method for vpts +# S3 method for class 'vpts' convert_legacy(x)Value
- - -An updated object of the same class as the input.
+An updated object of the same class as the input.
See also
@@ -126,16 +126,16 @@Examples
Convert reflectivity factor (dBZ) to reflectivity (eta) — dbz_to_eta • bioRad - +Convert reflectivity factor (dBZ) to reflectivity (eta)
- Source:R/dbz_eta.R+ Source:R/dbz_eta.Rdbz_to_eta.RdConvert reflectivity factor (dBZ) to reflectivity (eta)
Arguments
-Value
- - -Reflectivity, in cm^2/km^3.
+Reflectivity, in cm^2/km^3.
See also
@@ -134,16 +134,16 @@Examples
-- - - + + + + + + + diff --git a/dev/reference/download_pvolfiles.html b/dev/reference/download_pvolfiles.html index 9d9c27a9..4699d9d6 100644 --- a/dev/reference/download_pvolfiles.html +++ b/dev/reference/download_pvolfiles.html @@ -1,10 +1,10 @@ -- - - - -- - -- - -- --- -Downloads a basemap for
-map.ppi()from Stamen Maps or Google Maps using -ggmap::get_map(). To use Google Maps assource, you will have to register -with Google, enable billing and provide an API key to ggmap. See the ggmap README for details.-- --download_basemap( - x, - verbose = TRUE, - zoom, - alpha = 1, - source = "stamen", - maptype = "terrain", - ... -)--Arguments
-
- x
-- - - -
A
ppiobject.- verbose
-- - - -
Logical. When
TRUE, prints information to console.- zoom
-- - - -
Integer. Optional zoom level from 3 (continent) to 21 (building), -see
ggmap::get_map(). When undefined, the zoom level will be the one -matching theppiextent.- alpha
-- - - -
Numeric. Transparency of the basemap, value between 0 and 1.
- source
-- - - -
Character. Map service to be used:
stamenor- maptype
-- - - -
Character. Type of basemap to plot. For Stamen Maps: -
terrain,terrain-background,terrain-labels,terrain-lines, -toner,toner-2010,toner-2011,toner-background,toner-hybrid, -toner-labels,toner-lines,toner-liteorwatercolor. For Google -Maps:terrain,satellite,roadmaporhybrid.- ...
-- - -
Arguments to pass to
ggmap::get_map().--Value
- - -A ggmap object for
- - -map(ppi)-- -See also
-----Examples
--# Project a scan as a ppi -ppi <- project_as_ppi(example_scan) -# \donttest{ -# Create a basemap that matches the extent of the ppi -basemap <- download_basemap(ppi) -#> Downloading zoom = 9 ... -#> ℹ Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL. - -# Map the radial velocity of the ppi onto the basemap -map(ppi, map = basemap, param = "VRADH") -- -# Increase the transparency of the basemap -basemap <- download_basemap(ppi, alpha = 0.3) -#> Downloading zoom = 9 ... -#> ℹ Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL. -map(ppi, map = basemap, param = "VRADH") -
- -# Download a different type of basemap, e.g. a gray-scale image. -# See get_map() in ggmap library for full documentation of the options. -basemap <- download_basemap(ppi, maptype = "toner-lite") -#> Downloading zoom = 9 ... -#> ℹ Map tiles by Stamen Design, under CC BY 3.0. Data by OpenStreetMap, under ODbL. -map(ppi, map = basemap, param = "VRADH") -
-# } -
Download polar volume (pvol) files from the NEXRAD archive — download_pvolfiles • bioRad Download polar volume (pvol) files from the NEXRAD archive — download_pvolfiles • bioRad - +Download polar volume (
- Source:pvol) files from the NEXRAD archiveR/download_pvolfiles.R+ Source:R/download_pvolfiles.Rdownload_pvolfiles.RdDownload polar volume (
pvol) files from the NEXRAD archiveArguments
-
- date_min
+ + +
- date_min
- -
POSIXct. Start date of file selection. If no timezone are provided, it will be assumed to be UTC.
- date_max
+- date_max
- -
POSIXct. End date of file selection.If no timezone are provided, it will be assumed to be UTC.
- radar
+- radar
- -
character (vector). 4-letter radar code(s) (e.g. "KAMA")
- directory
+- directory
- -
character. Path to local directory where files should be downloaded
- overwrite
+- overwrite
- -
logical. TRUE for re-downloading and overwriting previously downloaded files of the same names.
- bucket
+- bucket
character. Bucket name to use.
@@ -157,16 +157,16 @@Value
- - -
NULL. The function's primary effect is to download selected polar volume +
NULL. The function's primary effect is to download selected polar volume files from the NEXRAD Level II archive to a specified local directory, and to provide a message and a progress bar in the console indicating the download status.Examples
Download vertical profile (vp) files from the ENRAM data repository — download_vpfiles • bioRad - +Download vertical profile (
- Source:vp) files from the ENRAM data repositoryR/download_vpfiles.R+ Source:R/download_vpfiles.Rdownload_vpfiles.RdDownload vertical profile (
vp) files from the ENRAM data reposiArguments
-
- date_min
+ + +
- date_min
- -
Character. Start date of file selection, in
YYYY-MM-DDformat. Days will be ignored.- date_max
+- date_max
- -
Character. End date of file selection, in
YYYY-MM-DDformat. Days will be ignored.- radars
+- radars
- -
Character (vector). 5-letter country/radar code(s) to include in file selection.
- directory
+- directory
- -
Character. Path to local directory where files should be downloaded and unzipped.
- overwrite
+- overwrite
Logical. When
TRUE, re-download and overwrite previously downloaded files of the same names.Value
- - -
NULL. The function's primary effect is to download selected vertical profiles +@@ -160,16 +160,16 @@
NULL. The function's primary effect is to download selected vertical profiles files from ENRAM data repository to a specified local directory, and to provide a message and a progress bar in the console indicating the download status. Message will show a 404 error for files that are not available.Examples
Look up day of year (doy) or night of year (noy) — doy_noy • bioRad - +Look up day of year (doy) or night of year (noy)
- Source:R/doy_noy.R+ Source:R/doy_noy.Rdoy_noy.RdLook up day of year (doy) or night of year (noy)
noy(x, ..., method = "fast") -# S3 method for default +# Default S3 method doy(x, lon, lat, ..., method = "fast") -# S3 method for default +# Default S3 method noy(x, lon, lat, ..., method = "fast") -# S3 method for vp +# S3 method for class 'vp' doy(x, ..., method = "fast") -# S3 method for vp +# S3 method for class 'vp' noy(x, ..., method = "fast") -# S3 method for vpts +# S3 method for class 'vpts' doy(x, ..., method = "fast") -# S3 method for vpts +# S3 method for class 'vpts' noy(x, ..., method = "fast") -# S3 method for vpi +# S3 method for class 'vpi' doy(x, ..., method = "fast") -# S3 method for vpi +# S3 method for class 'vpi' noy(x, ..., method = "fast") -# S3 method for pvol +# S3 method for class 'pvol' doy(x, ..., method = "fast") -# S3 method for pvol +# S3 method for class 'pvol' noy(x, ..., method = "fast")Arguments
-
- x
+ + +
- x
- -
A
pvol,vp,vpts, orvpiobject, or a base::as.POSIXct datetime.- ...
+- ...
- -
Optional lat, lon arguments.
- method
+- method
- -
Method by which to do the time zone lookup. Either
fast(default) oraccurate. See lutz::tz_lookup_coords].- lon
+- lon
- -
Numeric. Longitude in decimal degrees.
- lat
+- lat
Numeric. Latitude in decimal degrees.
Value
- - -integer representing the ordinal day of year or night of year.
+integer representing the ordinal day of year or night of year.
@@ -282,16 +282,16 @@Examples
Convert reflectivity (eta) to reflectivity factor (dBZ) — eta_to_dbz • bioRad - +Convert reflectivity (eta) to reflectivity factor (dBZ)
- Source:R/dbz_eta.R+ Source:R/dbz_eta.Reta_to_dbz.RdConvert reflectivity (eta) to reflectivity factor (dBZ)
Arguments
-Value
- - -Reflectivity factor, in dBZ.
+Reflectivity factor, in dBZ.
@@ -128,16 +128,16 @@Examples
Scan (scan) example — example_scan • bioRad - +Value
- - -An example object of type
+scanwhich represents a single scan from a weather radar.An example object of type
scanwhich represents a single scan from a weather radar.See also
@@ -120,16 +118,16 @@Examples
Vertical profile (vp) example — example_vp • bioRad - +Format
Value
- - -An example object of type
+vpwhich represents a vertical profile.An example object of type
vpwhich represents a vertical profile.See also
@@ -121,16 +119,16 @@Examples
Time series of vertical profiles (vpts) example — example_vpts • bioRad - +Time series of vertical profiles (
- Source:vpts) exampleR/data.R+ Source:R/data.Rexample_vpts.RdFormat
Value
- - -An example object of type
+vptswhich represents a time series of vertical profiles.An example object of type
vptswhich represents a time series of vertical profiles.See also
@@ -121,16 +119,16 @@Examples
extract strings from a vector using regex, analog to stringr::str_extract — extract_string • bioRad - +extract strings from a vector using regex, analog to stringr::str_extract
- Source:R/utils.R+ Source:R/utils.Rextract_string.Rdextract strings from a vector using regex, analog to stringr::str_extract
Arguments
-
- string
+ + +
- string
- -
Input vector. A character vector.
- pattern
+- pattern
- -
Regex pattern to look for
- ...
+- ...
passed on to
regexpr()Value
- - -A character vector with matches only, possibly of different length as +
A character vector with matches only, possibly of different length as
- -stringValue
Filter a time series of vertical profiles ('vpts') by a start and end time. Use argument night = TRUE to select only time stamps between sunset and sunrise, or night = FALSE to select daytime (sunrise to sunset). Selection for night and day uses check_night(). — filter_vpts • bioRad - +Filter a time series of vertical profiles ('vpts') by a start and end time. Use argument night = TRUE to select only time stamps between sunset and sunrise, or night = FALSE to select daytime (sunrise to sunset). Selection for night and day uses
- Source:check_night().R/filter_vpts.R+ Source:R/filter_vpts.Rfilter_vpts.RdFilter a time series of vertical profiles ('vpts') by a start and end time.
Arguments
-
- x
+ + +
- x
- -
A
vptsobject.- min
+- min
- -
POSIXct date or character. Minimum datetime to be included.
- max
+- max
- -
POSIXct date or character. Datetime up to this maximum included.
- nearest
+- nearest
- -
POSIXct date or character. If specified,
minandmaxare ignored and the profile (vp) nearest to the specified datetime is returned that matches the day/night selection criteria.- night
+- night
- -
When
TRUEselects only nighttime profiles, whenFALSEselects only daytime profiles, as classified bycheck_night().- elev
+- elev
- -
Numeric (vector). Sun elevation in degrees defining nighttime. May also be a numeric vector of length two, with first element giving sunset elevation, and second element sunrise elevation.
- offset
+- offset
Numeric (vector). Time duration in seconds by which to shift the start and end of nighttime. May also be a numeric vector of length two, with first element added to moment of sunset and second element added to @@ -123,9 +125,7 @@
Arguments
Value
- - -A
+vptsobject, or avpobject whennearestis specified.A
vptsobject, or avpobject whennearestis specified.Details
@@ -204,16 +204,16 @@Examples
Gaussian beam profile as a function of height — gaussian_beam_profile • bioRad - +Gaussian beam profile as a function of height
- Source:R/beam.R+ Source:R/beam.Rgaussian_beam_profile.RdGaussian beam profile as a function of height
Arguments
-
- height
+ + +
- height
- -
Numeric. Height in m.
- range
+- range
- -
Numeric. Slant range, i.e. the length of the skywave path between target and the radar antenna, in m.
- elev
+- elev
- -
Numeric. Beam elevation, in degrees.
- antenna
+- antenna
- -
Numeric. Height of the centre of the radar antenna, in m.
- beam_angle
+- beam_angle
- -
Numeric. Beam opening angle in degrees, typically the angle between the half-power (-3 dB) points of the main lobe.
- k
+- k
- -
Numeric. Standard refraction coefficient.
- lat
+- lat
- -
Numeric. Geodetic latitude of the radar, in degrees.
- re
+- re
- -
Numeric. Earth equatorial radius, in km.
- rp
+- rp
Numeric. Earth polar radius, in km.
Value
- - -numeric.
+numeric.
Details
@@ -144,7 +144,7 @@Details
- +See also
-- +Other beam_functions: +
Other beam_functions:
beam_distance(),beam_height(),beam_profile_overlap(), @@ -165,16 +165,16 @@See also
Get elevation angles of a polar volume (pvol), scan (scan) or parameter (param) — get_elevation_angles • bioRad - +Get elevation angles of a polar volume (
- Source:pvol), scan (scan) or parameter (param)R/get_elevation_angles.R+ Source:R/get_elevation_angles.Rget_elevation_angles.RdGet elevation angles of a polar volume (
pvol), scan (scanget_elevation_angles(x) -# S3 method for pvol +# S3 method for class 'pvol' get_elevation_angles(x) -# S3 method for scan +# S3 method for class 'scan' get_elevation_angles(x) -# S3 method for param +# S3 method for class 'param' get_elevation_angles(x)Value
- - -The elevation angle(s) in degrees.
+The elevation angle(s) in degrees.
See also
@@ -139,16 +139,16 @@Examples
Check the task type of an IRIS RAW file — get_iris_raw_task • bioRad - +Check the
tasktype of an IRIS RAW fileArguments
-@@ -117,16 +117,16 @@Value
- - -Specified
tasknames found in the header orNAif none of the +Specified
tasknames found in the header orNAif none of the task names were found.Value
Check the data type of an ODIM HDF5 file — get_odim_object_type • bioRad - +Check the
- Source:datatype of an ODIM HDF5 fileR/pvolfile.R+ Source:R/pvolfile.Rget_odim_object_type.RdCheck the
datatype of an ODIM HDF5 fileValue
- - -Character.
PVOLfor polar volume,VPfor vertical profile, +Character.
PVOLfor polar volume,VPfor vertical profile, otherwiseNA.@@ -124,16 +124,16 @@Examples
Get a parameter (param) from a scan (scan) — get_param • bioRad - +Get a parameter (
- Source:param) from a scan (scan)R/get_param.R+ Source:R/get_param.Rget_param.RdGet a parameter (
param) from a scan (scan)Arguments
-
- x
+ + +
- x
- -
A
scanobject.- param
+- param
Character. A scan parameter, such as
DBZHorVRADH. Seesummary.param()for commonly available parameters.Value
- - -A
+paramobject.A
paramobject.See also
@@ -134,16 +134,16 @@Examples
Get a quantity from a vertical profile (vp) or time series of vertical profiles (vpts) — get_quantity • bioRad - +Get a quantity from a vertical profile (
- Source:vp) or time series of vertical profiles (vpts)R/get_quantity.R+ Source:R/get_quantity.Rget_quantity.RdGet a quantity from a vertical profile (
vp) or time series of vget_quantity(x, quantity) -# S3 method for vp +# S3 method for class 'vp' get_quantity(x, quantity = "dens") -# S3 method for list +# S3 method for class 'list' get_quantity(x, quantity = "dens") -# S3 method for vpts +# S3 method for class 'vpts' get_quantity(x, quantity = "dens")Arguments
-@@ -211,16 +205,16 @@Value
- - -the value of a specific profile quantity specified in
- - +quantity.the value of a specific profile quantity specified in
quantity.For a
- -vpobject: a named (height bin) vector with values for the selected quantity.For a
- -listobject: a list of named (height bin) vectors with values for the selected quantity.For a
vptsobject: a (height bin * datetime) matrix with values for the selected quantity.Examples
Get a scan (scan) from a polar volume (pvol) — get_scan • bioRad - +Get a scan (
- Source:scan) from a polar volume (pvol)R/get_scan.R+ Source:R/get_scan.Rget_scan.RdGet a scan (
scan) from a polar volume (pvol)Arguments
-Value
- - -A
- - +scanobject whenallequalsFALSE(default), or a list ofscanobjects ifallequalsTRUEA
scanobject whenallequalsFALSE(default), or a list ofscanobjects ifallequalsTRUEDetails
@@ -161,16 +159,16 @@Examples
Package index • bioRad - +Other functions -
Site built with pkgdown 2.0.9.
+Site built with pkgdown 2.1.0.
Vertically integrate profiles (vp or vpts) into an integrated profile (vpi) — integrate_profile • bioRad - +Vertically integrate profiles (
- Source:vporvpts) into an integrated profile (vpi)R/integrate_profile.R+ Source:R/integrate_profile.Rintegrate_profile.RdVertically integrate profiles (
vporvpts) into an height_quantile = NA ) -# S3 method for vp +# S3 method for class 'vp' integrate_profile( x, alt_min = 0, @@ -99,7 +99,7 @@Vertically integrate profiles (
vporvpts) into an height_quantile = NA ) -# S3 method for list +# S3 method for class 'list' integrate_profile( x, alt_min = 0, @@ -110,7 +110,7 @@Vertically integrate profiles (
vporvpts) into an height_quantile = NA ) -# S3 method for vpts +# S3 method for class 'vpts' integrate_profile( x, alt_min = 0, @@ -124,36 +124,38 @@Vertically integrate profiles (
vporvpts) into anArguments
-
- x
+ + +
- x
- -
A
vporvptsobject.- alt_min
+- alt_min
- -
Minimum altitude in m.
"antenna"can be used to set the minimum altitude to the height of the antenna.- alt_max
+- alt_max
- -
Maximum altitude in m.
- alpha
+- alpha
- -
Migratory direction in clockwise degrees from north.
- interval_max
+- interval_max
- -
Maximum time interval belonging to a single profile in seconds. Traffic rates are set to zero at times
tfor which no profiles can be found within the periodt-interval_max/2tot+interval_max/2. Ignored for single profiles of classvp.- interval_replace
+- interval_replace
- -
Time interval to use for any interval > interval_max. By default the mean of all intervals <= interval_max
- height_quantile
+- height_quantile
- @@ -161,14 +163,12 @@
For default
NAthe calculated height equals the mean flight altitude. Otherwise a number between 0 and 1 specifying a quantile of the height distribution.Arguments
Value
- - -an object of class
vpi, a data frame with vertically +an object of class
vpi, a data frame with vertically integrated profile quantities- +Details
- +Available quantities
The function generates a specially classed data frame with the following @@ -272,7 +272,7 @@
Ground speed (ff) and
Methods (by class)
- +
integrate_profile(vp): Vertically integrate a vertical profile (vp).- @@ -6139,16 +6139,16 @@
integrate_profile(list): Vertically integrate a list of vertical profiles (vp).Examples
Calculate a plan position indicator (ppi) of vertically integrated density adjusted for range effects — integrate_to_ppi • bioRad - +Calculate a plan position indicator (
- Source:ppi) of vertically integrated density adjusted for range effectsR/integrate_to_ppi.R+ Source:R/integrate_to_ppi.Rintegrate_to_ppi.RdCalculate a plan position indicator (
ppi) of vertically integraArguments
-
- pvol
+ + +
- pvol
- -
A
pvolobject.- vp
+- vp
- -
A
vpobject- nx
+- nx
- -
number of raster pixels in the x (longitude) dimension
- ny
+- ny
- -
number of raster pixels in the y (latitude) dimension
- xlim
+- xlim
- -
x (longitude) range
- ylim
+- ylim
- -
y (latitude) range
- zlim
+- zlim
- -
Numeric vector of length two. Altitude range, in m
- res
+- res
- -
numeric vector of length 1 or 2 to set the resolution of the raster (see res). If this argument is used, arguments
nxandnyare ignored. Unit is identical toxlimandylim.- quantity
+- quantity
- -
Character. Profile quantity on which to base range corrections, either
etaordens.- param
+- param
- -
reflectivity Character. Scan parameter on which to base range corrections. Typically the same parameter from which animal densities are estimated in
vp. EitherDBZH,DBZV,DBZ,TH, orTV.- raster
+- raster
- -
(optional) RasterLayer with a CRS. When specified this raster topology is used for the output, and nx, ny, res arguments are ignored.
- lat
+- lat
- -
Latitude of the radar, in degrees. If missing taken from
pvol.- lon
+- lon
- -
Latitude of the radar, in degrees. If missing taken from
pvol.- antenna
+- antenna
- -
Numeric. Radar antenna height, in m. Default to antenna height in
vp.- beam_angle
+- beam_angle
- -
Numeric. Beam opening angle in degrees, typically the angle between the half-power (-3 dB) points of the main lobe.
- crs
+- crs
- -
character or object of class CRS. PROJ.4 type description of a Coordinate Reference System (map projection). When 'NA' (default), an azimuthal equidistant projection with origin at the radar location is used. To use a WSG84 (lat,lon) projection, use crs="+proj=longlat +datum=WGS84"
- param_ppi
+- param_ppi
- -
Character (vector). One or multiple of
VIR,VID,R,overlap,eta_sumoreta_sum_expected.- k
+- k
- -
Numeric. Standard refraction coefficient.
- re
+- re
- -
Numeric. Earth equatorial radius, in km.
- rp
+- rp
Numeric. Earth polar radius, in km.
Value
- - -A
+ppiobject.A
ppiobject.Details
@@ -256,7 +256,7 @@Details
References
- +
Kranstauber B, Bouten W, Leijnse H, Wijers B, Verlinden L, Shamoun-Baranes J, Dokter AM (2020) High-Resolution Spatial Distribution of Bird Movements Estimated from a Weather Radar Network. Remote Sensing 12 (4), 635. @@ -358,16 +358,16 @@
Examples
Identify NaN in a dataframe — is.nan.data.frame • bioRad - +Identify
NaNin a dataframe-# S3 method for data.frame +# S3 method for class 'data.frame' is.nan(x)@@ -108,16 +108,16 @@Value
- - -A matrix of the same dimension as
x, withTRUE/FALSEvalues for +A matrix of the same dimension as
x, withTRUE/FALSEvalues for whether each cell in the original data frame is a number or not.Value
Check if a file is a polar volume (pvol) — is.pvolfile • bioRad - +Check if a file is a polar volume (
- Source:pvol)R/pvolfile.R+ Source:R/pvolfile.Ris.pvolfile.RdCheck if a file is a polar volume (
pvol)Value
- - -+
TRUEfor a polar volume file in readable format, otherwiseFALSE.
TRUEfor a polar volume file in readable format, otherwiseFALSE.See also
@@ -124,16 +124,16 @@Examples
Check if a file is a vertical profile (vp) — is.vpfile • bioRad - +Check if a file is a vertical profile (
vp)Value
- - -
TRUEfor a vertical profile file in readable format, otherwise +
TRUEfor a vertical profile file in readable format, otherwiseFALSE.@@ -123,16 +123,16 @@Examples
List aloft urls for time series of vertical profiles (vpts) of radar stations — list_vpts_aloft • bioRad - +List aloft urls for time series of vertical profiles (
- Source:vpts) of radar stationsR/list_vpts_aloft.R+ Source:R/list_vpts_aloft.Rlist_vpts_aloft.RdList aloft urls for time series of vertical profiles (
vpts) ofArguments
-
- date_min
+ + +
- date_min
- -
Character, the first date to return urls for. In the shape of YYYY-MM-DD.
- date_max
+- date_max
- -
Character, the last date to return urls for. In the shape of YYYY-MM-DD.
- radars
+- radars
- -
Character vector, radar stations to return urls for.
- format
+- format
- -
Character, the format of archive urls to return, either csv or hdf5. Currently only csv urls are supported.
- source
+- source
- -
Character, either
baltradorecog-04003- show_warnings
+- show_warnings
Logical, whether to print warnings for dates or radar stations for which no data was found.
Value
- - -A character vector of aloft urls
+A character vector of aloft urls
Examples
list_vpts_aloft(radars = "bejab") -#> Warning: Radar data found between 2018-10 and 2024-06 but not every date has radar data +#> Warning: Radar data found between 2018-10 and 2024-07 but not every date has radar data #> https://aloftdata.s3-eu-west-1.amazonaws.com/baltrad/monthly/bejab/2018/bejab_vpts_201810.csv.gz #> https://aloftdata.s3-eu-west-1.amazonaws.com/baltrad/monthly/bejab/2018/bejab_vpts_201811.csv.gz #> https://aloftdata.s3-eu-west-1.amazonaws.com/baltrad/monthly/bejab/2018/bejab_vpts_201812.csv.gz @@ -148,6 +148,7 @@Examples
#> https://aloftdata.s3-eu-west-1.amazonaws.com/baltrad/monthly/bejab/2024/bejab_vpts_202404.csv.gz #> https://aloftdata.s3-eu-west-1.amazonaws.com/baltrad/monthly/bejab/2024/bejab_vpts_202405.csv.gz #> https://aloftdata.s3-eu-west-1.amazonaws.com/baltrad/monthly/bejab/2024/bejab_vpts_202406.csv.gz +#> https://aloftdata.s3-eu-west-1.amazonaws.com/baltrad/monthly/bejab/2024/bejab_vpts_202407.csv.gzExamples
Map a plan position indicator (ppi) on a map — map • bioRad - +Map a plan position indicator (
ppi) on a map- +- +map(x, ...) -# S3 method for ppi +# S3 method for class 'ppi' map( x, map = "cartolight", @@ -96,69 +96,69 @@Map a plan position indicator (
ppi) on a mapArguments
-
- x
+ + +
- x
- -
A
ppiobject.- ...
+- ...
- -
Arguments passed to
ggplot2::ggplot().- map
+- map
- -
Basemap to use, one of
rosm::osm.types()- param
+- param
- -
Character. Scan parameter to plot, e.g.
DBZHorVRADH. Seesummary.param()for commonly available parameters.- alpha
+- alpha
- -
Numeric. Transparency of the data, value between 0 and 1.
- xlim
+- xlim
- -
Numeric vector of length 2. Range of x values (degrees longitude) to plot.
- ylim
+- ylim
- -
Numeric vector of length 2. Range of y values (degrees latitude) to plot.
- zlim
+- zlim
- -
Numeric vector of length 2. The range of values to plot.
- ratio
+- ratio
- -
Numeric. Aspect ratio between x and y scale, by default \(1/cos(latitude radar * pi/180)\).
- radar_size
+- radar_size
- -
Numeric. Size of the symbol indicating the radar position.
- radar_color
+- radar_color
- -
Character. Color of the symbol indicating the radar position.
- n_color
+- n_color
- -
Numeric. Number of colors (>=1) to use in the palette.
- palette
+- palette
Character vector. Hexadecimal color values defining the plot color scale, e.g. output from
viridisLite::viridis().Value
- - -A ggplot object
+A ggplot object
Details
@@ -177,7 +177,7 @@Details
Methods (by class)
- +
map(ppi): Plot appiobject on a map.@@ -247,16 +247,16 @@Examples
Match a set of regular expressions to a list of files — match_filenames • bioRad - +Match a set of regular expressions to a list of files
- Source:R/utils.R+ Source:R/utils.Rmatch_filenames.RdMatch a set of regular expressions to a list of files
Arguments
-@@ -114,16 +114,16 @@Value
- - -character vector. Subset of filenames from the file_list that comply +
character vector. Subset of filenames from the file_list that comply to the provided regular expressions in regex_list.
Value
Convert a NEXRAD polar volume file to an ODIM polar volume file — nexrad_to_odim • bioRad - +Convert a NEXRAD polar volume file to an ODIM polar volume file
- Source:R/nexrad_odim.R+ Source:R/nexrad_odim.Rnexrad_to_odim.RdConvert a NEXRAD polar volume file to an ODIM polar volume file
Arguments
-
- pvolfile_nexrad
+ + +
- pvolfile_nexrad
- -
Character (vector). Either a path to a single radar polar volume (
pvol) file containing multiple scans/sweeps, or multiple paths to scan files containing a single scan/sweep. Or a singlepvolobject. The file data format should be either 1) @@ -90,21 +92,19 @@Arguments
IRIS (IRIS RAW) format.- pvolfile_odim
+- pvolfile_odim
- -
Filename for the polar volume in ODIM HDF5 format to be generated.
- verbose
+- verbose
Logical. When
TRUE, vol2birdstdoutis piped to the R console.Value
- - -+
TRUEon success
TRUEon success@@ -121,9 +121,7 @@Examples
new_path = file.path(tempdir(), "KBGM_example.h5") nexrad_to_odim(path, new_path) -#> Checking file before processing: /tmp/RtmpD92Z4P/KBGM_example -#> File size: 3950079 bytes -#> Filename = /tmp/RtmpD92Z4P/KBGM_example, callid = KBGM +#> Filename = /tmp/RtmpZJt3Jx/KBGM_example, callid = KBGM #> Reading RSL polar volume with nominal time 20191001-000542, source: RAD:KBGM,PLC:BINGHAMTON,state:NY,radar_name:KBGM # verify that we have generated a polar volume in ODIM HDF5 format @@ -148,16 +146,16 @@Examples
Calculate Nyquist velocity for a given pulse repetition frequency (PRF) — nyquist_velocity • bioRad - +Calculate Nyquist velocity for a given pulse repetition frequency (PRF)
- Source:R/nyquist_velocity.R+ Source:R/nyquist_velocity.Rnyquist_velocity.RdCalculate Nyquist velocity for a given pulse repetition frequency (PRF)
Arguments
-Value
- - -Nyquist velocity, in m/s.
+Nyquist velocity, in m/s.
@@ -125,16 +125,16 @@Examples
Plot a plan position indicator (ppi) — plot.ppi • bioRad - +Plot a plan position indicator (
ppi)-- +- +# S3 method for ppi +- +# S3 method for class 'ppi' plot( x, param, @@ -91,44 +91,44 @@Plot a plan position indicator (
ppi)Arguments
-
- x
+ + +
- x
- -
An object of class
ppi.- param
+- param
- -
The scan parameter to plot, see details below.
- xlim
+- xlim
- -
Range of x values to plot.
- ylim
+- ylim
- -
Range of y values to plot.
- zlim
+- zlim
- -
The range of parameter values to plot. Defaults to parameter specific limits for plotting, not full range of data.
- ratio
+- ratio
- -
Aspect ratio between x and y scale.
- na.value
+- na.value
- -
ggplot argument setting the plot color of NA values
- ...
+- ...
Arguments passed to low level ggplot function.
Value
- - -No return value, side effect is a plot.
+No return value, side effect is a plot.
Details
@@ -195,16 +195,16 @@Examples
Plot a scan (scan) in polar coordinates — plot.scan • bioRad - +Plot a scan (
- Source:scan) in polar coordinatesR/plot.scan.R+ Source:R/plot.scan.Rplot.scan.RdPlot a scan (
scan) in polar coordinates-- +- +# S3 method for scan +- +# S3 method for class 'scan' plot( x, param, @@ -90,43 +90,43 @@Plot a scan (
scan) in polar coordinatesArguments
-
- x
+ + +
- x
- -
A
scanobject.- param
+- param
- -
Character. Scan parameter to plot, e.g.
DBZHorVRADH. Seesummary.param()for commonly available parameters.- xlim
+- xlim
- -
Numeric vector of length 2. Range of x values (range, distance to radar) to plot.
- ylim
+- ylim
- -
Numeric vector of length 2. Range of y values (azimuth) to plot.
- zlim
+- zlim
- -
Numeric vector of length 2. The range of parameter values to plot. Defaults to parameter specific limits for plotting, not full range of data.
- na.value
+- na.value
- -
Character.
ggplot2::ggplot()parameter to set the color ofNAvalues.- ...
+- ...
Arguments passed to
ggplot2::ggplot().Value
- - -No return value, side effect is a plot.
+No return value, side effect is a plot.
Details
@@ -176,16 +176,16 @@Examples
Plot a vertical profile (vp) — plot.vp • bioRad - +Plot a vertical profile (
vp)-- +- +# S3 method for vp +- +# S3 method for class 'vp' plot( x, quantity = "dens", @@ -90,11 +90,13 @@Plot a vertical profile (
vp)Arguments
-
- x
+ + +
- x
- -
A
vpclass object.- quantity
+- quantity
- -
Character string with the quantity to plot. See vp for list of available quantities.
Aerial density related :
dens,eta,dbz,DBZHfor density, reflectivity, reflectivity factor and total reflectivity factor, @@ -104,40 +106,38 @@Arguments
- xlab
+- xlab
- -
A title for the x axis.
- ylab
+- ylab
- -
A title for the y axis.
- line_col
+- line_col
- -
Color of the plotted curve.
- line_lwd
+- line_lwd
- -
Line width of the plotted curve.
- line.col
+- line.col
- -
Deprecated argument, use line_col instead.
- line.lwd
+- line.lwd
- -
Deprecated argument, use line_lwd instead.
- ...
+- ...
Additional arguments to be passed to the low level plot plotting function.
Value
- - -No return value, side effect is a plot.
+No return value, side effect is a plot.
@@ -175,16 +175,16 @@Examples
Plot an integrated profile (vpi) — plot.vpi • bioRad - +Plot an integrated profile (
vpi)-- +- +# S3 method for vpi +- +# S3 method for class 'vpi' plot( x, quantity = "mtr", @@ -93,12 +93,14 @@Plot an integrated profile (
vpi)Arguments
-
- x
+ + +
- x
- -
1 class object inheriting from class
vpi, typically a call to integrate_profile.- quantity
+- quantity
- -
Character string with the quantity to plot, one of
vid(vertically integrated density),
vir(vertically integrated reflectivity),- @@ -112,55 +114,53 @@
mtr(migration traffic rate),Arguments
- xlab
+- xlab
- -
A title for the x-axis.
- ylab
+- ylab
- -
A title for the y-axis.
- main
+- main
- -
A title for the plot.
- night_shade
+- night_shade
- -
Logical, whether to plot night time shading.
- elev
+- elev
- -
Numeric, sun elevation to use for day/night transition, see sunrise.
- lat
+- lat
- -
(optional) Latitude in decimal degrees. Overrides the lat attribute of
x.- lon
+- lon
- -
(optional) Longitude in decimal degrees. Overrides the lon attribute of
x.- ylim
+- ylim
- -
y-axis plot range, numeric atomic vector of length 2.
- nightshade
+- nightshade
- -
Deprecated argument, use night_shade instead.
- ...
+- ...
Additional arguments to be passed to the low level plot plotting function.
Value
- - -No return value, side effect is a plot.
+No return value, side effect is a plot.
Details
@@ -211,16 +211,16 @@Examples
Plot a time series of vertical profiles (vpts) — plot.vpts • bioRad - +Plot a time series of vertical profiles (
- Source:vpts)R/plot.vpts.R+ Source:R/plot.vpts.Rplot.vpts.RdPlot a time series of vertical profiles (
vpts)-- +- +# S3 method for vpts +- +# S3 method for class 'vpts' plot( x, xlab = "time", @@ -102,104 +102,104 @@Plot a time series of vertical profiles (
vpts)Arguments
-
- x
+ + +
- x
- -
A vp class object inheriting from class
vpts.- xlab
+- xlab
- -
A title for the x-axis.
- ylab
+- ylab
- -
A title for the y-axis.
- quantity
+- quantity
- -
Character string with the quantity to plot, one of '
dens','eta','dbz','DBZH' for density, reflectivity, reflectivity factor and total reflectivity factor, respectively.- log
+- log
- -
Logical, whether to display
quantitydata on a logarithmic scale.- barbs
+- barbs
- -
Logical, whether to overlay speed barbs.
- barbs_height
+- barbs_height
- -
Integer, number of barbs to plot in altitudinal dimension.
- barbs_time
+- barbs_time
- -
Integer, number of barbs to plot in temporal dimension.
- barbs_dens_min
+- barbs_dens_min
- -
Numeric, lower threshold in aerial density of individuals for plotting speed barbs in individuals/km^3.
- zlim
+- zlim
- -
Optional numerical atomic vector of length 2, specifying the range of
quantityvalues to plot.- legend_ticks
+- legend_ticks
- -
Numeric atomic vector specifying the ticks on the color bar.
- legend.ticks
+- legend.ticks
- -
Deprecated argument, use legend_ticks instead.
- main
+- main
- -
A title for the plot.
- barbs.h
+- barbs.h
- -
Deprecated argument, use barbs_height instead.
- barbs.t
+- barbs.t
- -
Deprecated argument, use barbs_time instead.
- barbs.dens
+- barbs.dens
- -
Deprecated argument, use barbs_dens_min instead.
- na_color
+- na_color
- -
Color to use for NA values, see class
vpts()conventions.- nan_color
+- nan_color
- -
Color to use for NaN values, see class
vpts()conventions.- n_color
+- n_color
- -
The number of colors (>=1) to be in the palette.
- palette
+- palette
- -
(Optional) character vector of hexadecimal color values defining the plot color scale, e.g. output from viridis
- ...
+- ...
Additional arguments to be passed to the low level image plotting function.
Value
- - -No return value, side effect is a plot.
+No return value, side effect is a plot.
Details
@@ -299,16 +299,16 @@Examples
A wrapper for spTransform(). Converts projected coordinates to geographic (WGS84) coordinates. — proj_to_wgs • bioRad - +A wrapper for
- Source:spTransform(). Converts projected coordinates to geographic (WGS84) coordinates.R/utils.R+ Source:R/utils.Rproj_to_wgs.RdA wrapper for
spTransform(). Converts projected coordinates toArguments
-Value
- - -An object of class
+SpatialPoints.An object of class
SpatialPoints.Value
Project a scan (scan) or parameter (param) to a plan position indicator (ppi) — project_as_ppi • bioRad - +Project a scan (
- Source:scan) or parameter (param) to a plan position indicator (ppi)R/project_as_ppi.R+ Source:R/project_as_ppi.Rproject_as_ppi.RdProject a scan (
scan) or parameter (param) to a pl rp = 6357 ) -# S3 method for param +# S3 method for class 'param' project_as_ppi( x, grid_size = 500, @@ -101,7 +101,7 @@Project a scan (
scan) or parameter (param) to a pl rp = 6357 ) -# S3 method for scan +# S3 method for class 'scan' project_as_ppi( x, grid_size = 500, @@ -118,52 +118,52 @@Project a scan (
scan) or parameter (param) to a plArguments
-
- x
+ + +
- x
- -
An object of class
paramorscan.- grid_size
+- grid_size
- -
Cartesian grid size in m.
- range_max
+- range_max
- -
Maximum range in m.
- project
+- project
- -
Whether to vertically project onto earth's surface.
- ylim
+- ylim
- -
The range of latitudes to include.
- xlim
+- xlim
- -
The range of longitudes to include.
- raster
+- raster
- -
(optional) RasterLayer with a CRS. When specified this raster topology is used for the output, and
grid_size,range_max,xlim,ylimare ignored.- k
+- k
- -
Numeric. Standard refraction coefficient.
- re
+- re
- -
Numeric. Earth equatorial radius, in km.
- rp
+- rp
Numeric. Earth polar radius, in km.
Details
@@ -171,7 +171,7 @@Details
Methods (by class)
- +
project_as_ppi(param): Project asppifor a single scan parameter.- @@ -239,16 +239,16 @@
project_as_ppi(scan): Project multipleppi's for all scan parameters in a scanExamples
Set radar cross section — rcs<- • bioRad - +Set radar cross section
Arguments
-Value
- - -The input object with updated density
+x$data$densand updated radar cross section attribute.The input object with updated density
x$data$densand updated radar cross section attribute.See also
@@ -144,16 +144,16 @@Examples
Get radar cross section — rcs • bioRad - +Get radar cross section
rcs(x) -# S3 method for vp +# S3 method for class 'vp' rcs(x) -# S3 method for list +# S3 method for class 'list' rcs(x) -# S3 method for vpts +# S3 method for class 'vpts' rcs(x) -# S3 method for vpi +# S3 method for class 'vpi' rcs(x)Value
- - -The radar cross section in cm^2.
+The radar cross section in cm^2.
See also
@@ -137,16 +137,16 @@Examples
Read a vertical profile (vp) from UMASS Cajun text file — read_cajun • bioRad - +Read a vertical profile (
- Source:vp) from UMASS Cajun text fileR/read_cajun.R+ Source:R/read_cajun.Rread_cajun.RdRead a vertical profile (
vp) from UMASS Cajun text fileArguments
-
- file
+ + +Value
- - -A
+vpobject.A
vpobject.See also
@@ -118,16 +118,16 @@See also
Read a polar volume (pvol) from file — read_pvolfile • bioRad - +Read a polar volume (
- Source:pvol) from fileR/read_pvolfile.R+ Source:R/read_pvolfile.Rread_pvolfile.RdRead a polar volume (
pvol) from fileArguments
-
- file
+ + +
- file
- -
A string containing the path to a polar volume file
- param
+- param
- -
An atomic vector of character strings, containing the names of scan parameters to read. To read all scan parameters use 'all'.
- sort
+- sort
- -
A logical value, when
TRUEsort scans ascending by elevation.- lat
+- lat
- -
Latitude in decimal degrees of the radar position. If not specified, value stored in file is used. If specified, value stored in file is overwritten.
- lon
+- lon
- -
Longitude in decimal degrees of the radar position. If not specified, value stored in file is used. If specified, value stored in file is overwritten.
- height
+- height
- -
Height of the center of the antenna in meters above sea level. If not specified, value stored in file is used. If specified, value stored in file is overwritten.
- elev_min
+- elev_min
- -
Minimum scan elevation to read in degrees.
- elev_max
+- elev_max
- -
Maximum scan elevation to read in degrees.
- verbose
+- verbose
- -
A logical value, whether to print messages (
TRUE) to console.- mount
+- mount
- -
(deprecated) A character string with the mount point (a directory path) for the Docker container.
- local_install
+- local_install
(deprecated) String with path to local vol2bird installation, to use local installation instead of Docker container
Value
- - -An object of class pvol, which is a list +
An object of class pvol, which is a list containing polar scans, i.e. objects of class
- -scanDetails
@@ -243,16 +241,16 @@Examples
Read a time series of vertical profiles (vpts) from file — read_stdout • bioRad - +Read a time series of vertical profiles (
- Source:vpts) from fileR/read_stdout.R+ Source:R/read_stdout.Rread_stdout.RdRead a time series of vertical profiles (
vpts) from fileArguments
-
- file
+ + +
- file
- -
A text file containing the standard output (stdout) generated by vol2bird (or the package function
calculate_vp).- radar
+- radar
- -
A string containing a radar identifier.
- lat
+- lat
- -
numeric. Latitude of the radar in decimal degrees.
- lon
+- lon
- -
numeric. Longitude of the radar in decimal degrees.
- height
+- height
- -
numeric. Height above sea level of the radar antenna in meters.
- wavelength
+- wavelength
- -
Radar wavelength in cm, or one of 'C' or 'S' for C-band and S-band radar, respectively, in which case C-band wavelength is assumed to be 5.3 cm and S-band wavelength 10.6 cm
- sep
+- sep
the field separator character, see utils::read.table
@@ -145,16 +145,16 @@Value
- - -An object inheriting from class
vpts, see +An object inheriting from class
vpts, seevpts()for details.Examples
Read a vertical profile (vp) from file — read_vp • bioRad - +Read a vertical profile (
- Source:vp) from fileR/read_vpfiles.R+ Source:R/read_vpfiles.Rread_vp.RdRead a vertical profile (
vp) from fileArguments
-
- file
+ + +
- file
A string containing the path to a vertical profile generated by calculate_vp.
Value
Read a vertical profile (vp) or a list of vertical profiles (vp) from files — read_vpfiles • bioRad - +Read a vertical profile (
- Source:vp) or a list of vertical profiles (vp) from filesR/read_vpfiles.R+ Source:R/read_vpfiles.Rread_vpfiles.RdRead a vertical profile (
vp) or a list of vertical profiles (Arguments
-
- files
+ + +
- files
A character vector containing the file names of vertical profiles in ODIM HDF5 format generated by calculate_vp.
Value
- - -A single
+vpobject or a list ofvpobjects.A single
vpobject or a list ofvpobjects.@@ -143,16 +143,16 @@Examples
Read time series of vertical profiles (vpts) from file(s) — read_vpts • bioRad - +Read time series of vertical profiles (
- Source:vpts) from file(s)R/read_vpts.R+ Source:R/read_vpts.Rread_vpts.RdRead time series of vertical profiles (
vpts) from file(s)Arguments
-Value
- - -+
vptsobject.
vptsobject.@@ -153,16 +153,16 @@Examples
Regularize a time series of vertical profiles (vpts) on a regular time grid — regularize_vpts • bioRad - +Regularize a time series of vertical profiles (
- Source:vpts) on a regular time gridR/regularize_vpts.R+ Source:R/regularize_vpts.Rregularize_vpts.RdRegularize a time series of vertical profiles (
vpts) on a regulArguments
-
- ts
+ + +
- ts
- -
An object inheriting from class
vpts, seevpts()for details.- interval
+- interval
- -
Time interval grid to project on. When '
auto' the median interval in the time series is used.- date_min
+- date_min
- -
Start time of the projected time series, as a POSIXct object. Taken from
tsby default'.- date_max
+- date_max
- -
End time of the projected time series, as a POSIXct object. Taken from
tsby default.- units
+- units
- -
Optional units of
intervalandfill, one of 'secs', 'mins', 'hours','days', 'weeks'. Defaults to 'mins'.- fill
+- fill
- -
Numeric or Logical. fill each regularized timestep with the closest original profile found within a time window of +/-
fill. WhenTRUE,fillmaps tointerval, filling single missing timesteps. WhenFALSE,fillmaps to 0, disabling filling.- verbose
+- verbose
- -
Logical, when
TRUEprints text to console.- keep_datetime
+- keep_datetime
Logical, when
TRUEkeep original radar acquisition timestamps.Value
- - -An object of class
+vptswith regular time steps.An object of class
vptswith regular time steps.Details
@@ -174,16 +174,16 @@Examples
convert a polar scan into a raster — scan_to_raster • bioRad - +convert a polar scan into a raster
- Source:R/scan_convert.R+ Source:R/scan_convert.Rscan_to_raster.Rdconvert a polar scan into a raster
Arguments
-
- scan
+ + +
- scan
- -
a scan (sweep) of class scan
- nx
+- nx
- -
number of raster pixels in the x (longitude) dimension
- ny
+- ny
- -
number of raster pixels in the y (latitude) dimension
- xlim
+- xlim
- -
x (longitude) range
- ylim
+- ylim
- -
y (latitude) range
- res
+- res
- -
numeric vector of length 1 or 2 to set the resolution of the raster (see res). If this argument is used, arguments
nxandnyare ignored. Unit is identical toxlimandylim.- param
+- param
- -
scan parameters to include. If
NAinclude all scan parameters. Reducing the number of scan parameters speeds up evaluation.- raster
+- raster
- -
(optional) RasterLayer with a CRS. When specified this raster topology is used for the output, and nx, ny, res arguments are ignored.
- lat
+- lat
- -
Geodetic latitude of the radar in degrees. If missing taken from
scan.- lon
+- lon
- -
Geodetic longitude of the radar in degrees. If missing taken from
scan.- crs
+- crs
- -
character or object of class CRS. PROJ.4 type description of a Coordinate Reference System (map projection). When 'NA' (default), an azimuthal equidistant projection with origin at the radar location is used. To use a WSG84 (lat,lon) projection, use crs="+proj=longlat +datum=WGS84"
- k
+- k
- -
Numeric. Standard refraction coefficient.
- re
+- re
- -
Numeric. Earth equatorial radius, in km.
- rp
+- rp
Numeric. Earth polar radius, in km.
Value
- - -a RasterBrick
+a RasterBrick
Details
@@ -224,16 +224,16 @@Examples
convert a polar scan into a spatial object. — scan_to_spatial • bioRad - +convert a polar scan into a spatial object.
- Source:R/scan_convert.R+ Source:R/scan_convert.Rscan_to_spatial.Rdconvert a polar scan into a spatial object.
Arguments
-
- scan
+ + +
- scan
- -
a scan (sweep) of class scan
- lat
+- lat
- -
Geodetic latitude of the radar in degrees. If missing taken from
scan.- lon
+- lon
- -
Geodetic longitude of the radar in degrees. If missing taken from
scan.- k
+- k
- -
Numeric. Standard refraction coefficient.
- re
+- re
- -
Numeric. Earth equatorial radius, in km.
- rp
+- rp
Numeric. Earth polar radius, in km.
Value
- - -a SpatialPointsDataFrame
+a SpatialPointsDataFrame
Details
@@ -20137,16 +20137,16 @@Examples
Set threshold of the radial velocity standard deviation — sd_vvp_threshold<- • bioRad - +Set threshold of the radial velocity standard deviation
- Source:R/sd_vvp_threshold.R+ Source:R/sd_vvp_threshold.Rsd_vvp_threshold-set.RdSet threshold of the radial velocity standard deviation
sd_vvp_threshold(x) <- value -# S3 method for vp +# S3 method for class 'vp' sd_vvp_threshold(x) <- value -# S3 method for list +# S3 method for class 'list' sd_vvp_threshold(x) <- value -# S3 method for vpts +# S3 method for class 'vpts' sd_vvp_threshold(x) <- valueArguments
-Value
- - -The input object with updated density
+x$data$densandsd_vvp_threshattribute.The input object with updated density
x$data$densandsd_vvp_threshattribute.See also
@@ -141,16 +141,16 @@Examples
Get threshold of the radial velocity standard deviation — sd_vvp_threshold • bioRad - +Get threshold of the radial velocity standard deviation
- Source:R/sd_vvp_threshold.R+ Source:R/sd_vvp_threshold.Rsd_vvp_threshold.RdGet threshold of the radial velocity standard deviation
sd_vvp_threshold(x) -# S3 method for vp +# S3 method for class 'vp' sd_vvp_threshold(x) -# S3 method for list +# S3 method for class 'list' sd_vvp_threshold(x) -# S3 method for vpts +# S3 method for class 'vpts' sd_vvp_threshold(x)Value
- - -The
+sd_vvpthreshold in m/s.The
sd_vvpthreshold in m/s.See also
@@ -134,16 +134,16 @@Examples
Select vertical profile (vp) files from computer — select_vpfiles • bioRad - +Select vertical profile (
- Source:vp) files from computerR/select_vpfiles.R+ Source:R/select_vpfiles.Rselect_vpfiles.RdSelect vertical profile (
vp) files from computerArguments
-
- date_min
+ + +
- date_min
- -
character. YYYY-MM-DD start date of file selection.
- date_max
+- date_max
- -
character. YYYY-MM-DD end date of file selection.
- radars
+- radars
- -
character (vector). 5-letter country/radar code(s) (e.g.
bejab) of radars to include in file selection.- directory
+- directory
character. Path to local directory where files should be looked for.
Value
- - -Character vector of file paths that comply to the given date and +
Character vector of file paths that comply to the given date and radar range.
@@ -143,16 +143,16 @@Examples
Skip test if no mistnet — skip_if_no_mistnet • bioRad - +Skip test if no mistnet
Value
- - -Invisibly returns TRUE if MistNet is available, otherwise skips the test with a message "No MistNet".
+Invisibly returns TRUE if MistNet is available, otherwise skips the test with a message "No MistNet".
Value
Skip test if vol2birdR not installed — skip_if_no_vol2birdR • bioRad - +Skip test if vol2birdR not installed
- Source:R/utils.R+ Source:R/utils.Rskip_if_no_vol2birdR.RdSkip test if vol2birdR not installed
@@ -101,16 +99,16 @@Value
- - -Invisibly returns TRUE if vol2birdR is installed, otherwise skips the test with +
Invisibly returns TRUE if vol2birdR is installed, otherwise skips the test with a message "Package vol2birdR not installed".
Value
Subset a plan position indicator (ppi) — [.ppi • bioRad - +Subset a plan position indicator (
ppi)-+# S3 method for ppi -[(x, i)# S3 method for class 'ppi' +x[i]Arguments
-Value
- - -A
+ppiobject containing a subset of parameters (param).A
ppiobject containing a subset of parameters (param).@@ -148,16 +148,16 @@Examples
Inspect a parameter (param) — summary.param • bioRad - +Inspect a parameter (
param)-- +- +# S3 method for param +@@ -82,23 +82,23 @@# S3 method for class 'param' summary(object, ...) is.param(x)Inspect a parameter (
param)Arguments
-Value
- - -For
is.param():TRUEfor an object of classparam, otherwise +For
is.param():TRUEfor an object of classparam, otherwiseFALSE.@@ -152,16 +152,16 @@Examples
Inspect a plan position indicator (ppi) — summary.ppi • bioRad - +Inspect a plan position indicator (
ppi)-# S3 method for ppi +Arguments
-@@ -171,16 +169,16 @@Value
- - -For
is.ppi():TRUEfor an object of classppi, otherwise +For
- -is.ppi():TRUEfor an object of classppi, otherwiseFALSE.For
dim.ppi(): number of parameters (param), x and y pixels in a plan position indicator (ppi).Examples
Inspect a polar volume (pvol) — summary.pvol • bioRad - +Inspect a polar volume (
pvol)-# S3 method for pvol +Arguments
-@@ -192,16 +190,16 @@Value
- - -For
is.pvol():TRUEfor an object of classpvol, otherwise +For
- -is.pvol():TRUEfor an object of classpvol, otherwiseFALSE.For
dim.pvol(): number of scans (scan) in a polar volume (pvol).Examples
Inspect a scan (scan) — summary.scan • bioRad - +Inspect a scan (
scan)-# S3 method for scan +Arguments
-@@ -206,16 +202,16 @@Value
- - -For
- - +summary.scan(): prints a summary of thescanobjectFor
summary.scan(): prints a summary of thescanobjectFor
- -is.scan():TRUEfor an object of classscan, otherwiseFALSE.For
dim.scan(): number of parameters (param), bins and rays in a scan (scan).Examples
Inspect a vertical profile (vp) — summary.vp • bioRad - +Inspect a vertical profile (
vp)-# S3 method for vp +Arguments
-@@ -147,7 +143,7 @@Value
- - -For
- - +summary.vp(): prints summary of thevpobject.For
summary.vp(): prints summary of thevpobject.For
- -is.vp():TRUEfor an object of classvp, otherwiseFALSE.For
dim.vp(): number of heights and quantities in a vertical profile (vp).Details
Conventions
- +
- @@ -207,16 +203,16 @@
NA: Maps tonodatain the ODIM convention: value to denote areas void of data (never radiated).Examples
Inspect an integrated profile (vpi) — summary.vpi • bioRad - +Inspect an integrated profile (
vpi)-- +# S3 method for vpi +@@ -84,25 +84,23 @@# S3 method for class 'vpi' summary(object, ...) is.vpi(x)Inspect an integrated profile (
vpi)Arguments
-@@ -165,16 +163,16 @@Value
- - -For
- - +summary.vpi(): prints summary of thevpiobject.For
summary.vpi(): prints summary of thevpiobject.For
is.vpi():TRUEfor an object of classvpi, otherwiseFALSE.Examples
Inspect a time series of vertical profiles (vpts) — summary.vpts • bioRad - +Inspect a time series of vertical profiles (
- Source:vpts)R/vpts.R+ Source:R/vpts.Rsummary.vpts.RdInspect a time series of vertical profiles (
vpts)-+# S3 method for vpts -summary(object, ...) - -# S3 method for vpts -print(x, digits = max(3L, getOption("digits") - 3L), ...) - -is.vpts(x) - -# S3 method for vpts -dim(x) - -# S3 method for vpts -[(x, i)Arguments
-
- object
+ + +
- object
- -
A
vptsobject.- ...
+- ...
- -
Additional arguments affecting the summary produced.
- x
+- x
- -
A
vptsobject.- digits
+- digits
- -
The number of significant digits to use when printing. Defaults to
max(3L, getOption("digits") - 3L).- i
+- i
Integer. Index/indices specifying which range of vertical profiles to extract.
@@ -163,7 +155,7 @@Value
- - -For
- - +summary.vpts(): prints the summary of thevptsobject.For
summary.vpts(): prints the summary of thevptsobject.For
- -print.vpts(): prints the summary of thevptsobject.For
- -is.vpts():TRUEfor an object of classvpts, otherwiseFALSE.For
- -dim.vpts(): number of datetimes, heights and quantities in a time series of vertical profiles (vpts).For
[.vpts: Avptsobject containing a subset of vertical profiles (vp) or avpobject when subsetting a single vertical profile (vp).Details
Conventions
- +
- @@ -250,16 +242,16 @@
NA: Maps tonodatain the ODIM convention: value to denote areas void of data (never radiated).Examples
Calculate sunrise or sunset for a time and place — sunrise_sunset • bioRad - +Calculate sunrise or sunset for a time and place
- Source:R/sunrise_sunset.R+ Source:R/sunrise_sunset.Rsunrise_sunset.RdCalculate sunrise or sunset for a time and place
Arguments
-
- date
+ + +
- date
- -
POSIXct. Date interpretable by
base::as.Date().- lon
+- lon
- -
Numeric. Longitude in decimal degrees.
- lat
+- lat
- -
Numeric. Latitude in decimal degrees.
- elev
+- elev
- -
Numeric. Sun elevation in degrees.
- tz
+- tz
- -
Character. Time zone of
date, ignored ifdatealready has an associated time zone.- force_tz
+- force_tz
Logical. If
TRUE, the output is converted to the timezone set bytz.Value
- - -The moment of sunrise or sunset for the date set by
dateand time zone as specified +The moment of sunrise or sunset for the date set by
dateand time zone as specified (bydateandtz) or in UTC if not specified.@@ -248,16 +248,16 @@Examples
Bind vertical profiles (vp) into time series (vpts) — vplist_to_vpts • bioRad - +Bind vertical profiles (
- Source:vp) into time series (vpts)R/bind_into_vpts.R+ Source:R/bind_into_vpts.Rvplist_to_vpts.RdBind vertical profiles (
vp) into time series (vptsArguments
-
- x
+ + +
- x
- -
A list of
vpobjects, usually a result of a call to read_vpfiles.- radar
+- radar
optional string containing the radar identifier to generate time series for.
@@ -123,16 +121,16 @@Value
- - -an object of class vpts when
- - -listcontains profiles of a single radar. A list of objects of class +
an object of class vpts when
list+contains profiles of a single radar. A list of objects of class vpts in case whenlistcontains profiles of multiple radars, containing vpts objects for each radar.Examples
A wrapper for spTransform(). Converts geographic (WGS84) coordinates to a specified projection — wgs_to_proj • bioRad - +A wrapper for
- Source:spTransform(). Converts geographic (WGS84) coordinates to a specified projectionR/utils.R+ Source:R/utils.Rwgs_to_proj.RdA wrapper for
spTransform(). Converts geographic (WGS84) coordiArguments
-Value
- - -An object of class
+SpatialPoints.An object of class
SpatialPoints.Value
Write a polar volume (pvol) object to ODIM HDF5 file — write_pvolfile • bioRad - +Write a polar volume (
- Source:pvol) object to ODIM HDF5 fileR/write_pvolfile.R+ Source:R/write_pvolfile.Rwrite_pvolfile.RdWrite a polar volume (
pvol) object to ODIM HDF5 fileArguments
-
- pvol
+ + +
- pvol
- -
An object of class
pvol.- file
+- file
- -
string. A filepath to write the
pvolobject to.- overwrite
+- overwrite
- -
logical. Overwrites existing file when TRUE.
- infer_dtype
+- infer_dtype
- @@ -99,9 +101,7 @@
logical. By default (infer_dtype = FALSE) writes 'params' back into ODIM HDF5 files with data stored in original data types. When TRUE infers data type from the R object data type, at the cost of (heavily) inflated file sizes.
Arguments
Value
- - -0 on success. A
+pvolobject will be written to file in ODIM H5 format.0 on success. A
pvolobject will be written to file in ODIM H5 format.@@ -133,16 +133,16 @@Examples
