| Type: | Package |
| Title: | Read some less Popular Formats Used in Meteorology |
| Version: | 1.7.1 |
| Date: | 2024-03-01 |
| Author: | Clemens Druee, Universitaet Trier |
| Maintainer: | Clemens Druee <druee@uni-trier.de> |
| Description: | Contains tools for reading and writing data from or to files in the formats: akterm, dmna, Scintec Format-1, and Campbell Scientific TOA5. |
| License: | GPL-3 |
| NeedsCompilation: | no |
| Packaged: | 2024-03-01 11:06:51 UTC; druee |
| Repository: | CRAN |
| Date/Publication: | 2024-03-01 14:30:02 UTC |
Read some less Popular Formats Used in Meteorology
Description
Contains tools for reading and writing data from or to files in dmna, Scintec Format-1, Campbell Scientific TOA5 formats.
Details
| Package: | readmet |
| Type: | Package |
| Version: | 1.6.9 |
| Date: | 2023-02-11 |
| License: | GPL-3 |
Currently supported:
| DMNA | Self describing gridded ASCII by Ing.Buero Janicke/Umweltbundesamt |
| format descrition in e.g. AUSTAL dispersion model description https://www.umweltbundesamt.de/sites/default/files/medien/2338/dokumente/austal_de.pdf (available only in German) | |
| Scintec Format-1 | Format used to store atmospheric data from wind profilers, SODAR, RASS and Scintillometer devices by Scintec AG, Rottenburg, Germany |
| format descrition in the device manuals, available to customers upon registration from https://www.scintec.com | |
| TOA5 | Table oriented ACSII format #5 by Campbell Scientific |
| format descrition in the device manuals, e.g. CR3000 data logger https://s.campbellsci.com/documents/us/manuals/cr3000.pdf) | |
Available functions:
| Function | Format |
| read.akterm | function to read contents of a file in AKTERM-format |
| read.dmna | function to read contents of a file in DMNA-format |
| dmna.axes | read grid positions from a file in DMNA-format |
| dmna.header | read header information from a file in DMNA-format |
| dmna.grid | read (horizontal) grid definition from a file in DMNA-format |
| write.dmna | function to write data to a file in DMNA-format |
| write.arcgrid | function to write data (read from DMNA file) into an ESRI ArcInfo gridded ASCII file |
| read.toa5 | function to read contents of a file in TOA5-format |
| read.scintec1 | function to read the contents of a file in Scintec Format-1 |
| scintec1.comments | read the comment fields of a file in Scintec Format-1 format |
| scintec1.header | read the header of a file in Scintec Format-1 format |
| scintec1.nonprofiles | read the single-level data from a file in Scintec Format-1 format |
| scintec1.profile | read the multi-level (profile) variables from a Scintec Format-1 file |
| scintec1.variables | read the variable descriptions from a file in Scintec Format-1 format |
Author(s)
Clemens Druee, Umweltmeteorologie, Universitaet Trier, Germany <druee@uni-trier.de>
read grid positions from a file in DMNA-format
Description
Files in DMNA format contain gridded data. The header provides information on how the data are organized. This routine expands the positions of the grid planes along each dimension used in the file. The values are put out in columns x, y, z for each respective axis.
Usage
dmna.axes(file, debug = FALSE)
Arguments
file |
name (and path if necessary) of the file to read |
debug |
if TRUE shwon debugging information |
Value
returns a data.frame with the following columns:
x |
grid positions along the x axis |
y |
grid positions along the y axis |
z |
grid level heights |
Note
Prior to version 1.2.4, this function did not arrays with more than two dimensions, or multiple variables in files of more than one dimension. The number of dimensions is currently limited to three.
Author(s)
Clemens Druee
References
AUSTAL 3.1 model reference (by Ingenieurbuero Janicke)
Examples
ax <- dmna.axes(system.file("extdata", "example-grid.dmna", package="readmet"))
ax$x
read (horizontal) grid definition from a file in DMNA-format
Description
Files in DMNA format contain gridded data. The header provides information on the grid definition. This function extracts the horizontal grid definition ans provides a list that may be supplied directly to function write.arcgrid. DMNA is used for example by the German national dispersion model AUSTAL.
Usage
dmna.grid(file)
Arguments
file |
name (and path if necessary) of the file to read |
Value
returns a list of character. List entries are:
xlen |
number of cells in x direction |
ylen |
number of cells in y direction |
xll |
easting of the lower left (i.e. southwest) corner |
yll |
northing of the lower left (i.e. southwest) corner |
delta |
grid node spacing |
Note
This function was added in version 1.3.0.
Author(s)
Clemens Druee
References
AUSTAL 3.1 model reference (by Ingenieurbuero Janicke)
Examples
dmna.grid(system.file("extdata", "example-grid.dmna", package="readmet"))
read header information from a file in DMNA-format
Description
Files in DMNA format contain gridded data. The header provides information on how the data are organized and other user-specified meta data. DMNA is used for example by the German national dispersion model AUSTAL2000.
Usage
dmna.header(file)
Arguments
file |
name (and path if necessary) of the file to read |
Value
list(character)
Author(s)
Clemens Druee
References
AUSTAL2000 model reference (by Ingenieurbuero Janicke)
Examples
hdr <- dmna.header(system.file("extdata", "example-grid.dmna", package="readmet"))
hdr$idnt
function to read contents of a file in AKTERM-format
Description
reads weather data time series from a AKTERM format file that is used for example by the German national dispersion model AUSTAL
Usage
read.akterm(file)
Arguments
file |
name (and path if necessary) of the file to read |
Value
returns a data.frame with the following columns:
"Time" is the time of obeservation as POSIXct.
"STA" is the WMO number of the observing statin
"QDD" is the quality byte for DD
"QFF" is the quality byte for FF
"DD" is the wind direction clockwise in degrees from north
"FF" is the wind speed in m/s
"QQ1" is the quality byte for KM
"KM" is the Klug/Manier stability class
"QQ2" is the quality byte for HM
"HM" is unsused
"QQ3" is the overall quality byte.
Note that DD and FF are always in degrees and m/s, indepenent from the value of the quality byte. Values where the quality byte is 9 are always NA. I.e. the quality byte is given for informational purposes only.
Note
Prior to version 1.2.4, this function did not arrays with more than two dimensions, or multiple variables in files of more than one dimension. Prior to version 1.5.0 timeseries were not implemented.
Author(s)
Clemens Druee
References
AUSTAL 3.1 model reference (by Ingenieurbuero Janicke)
Examples
series <- read.akterm(system.file("extdata", "example-series.akterm", package="readmet"))
plot(series$Time, series$FF, type="l")
function to read contents of a file in DMNA-format
Description
reads gridded one to two dimensional data from a DMNA format that used for example by the German national dispersion model AUSTAL
Usage
read.dmna(file, val=1, debug=FALSE)
Arguments
file |
name (and path if necessary) of the file to read |
val |
name (number of name of the variable to be extracted. Only needed in case the file contains gridded data and more than one variable) |
debug |
if TRUE shwon debugging information |
Value
returns an object whos type depends on the data containt in the file.
If the file contains a timeseries, a data.frame is returned that contains each variable in the file as a column. Column names are taken from the format description embedded in the file. If a column for time (name "te") is present, times are returned as POSIXct.
If the file contains gridded data an array of numeric is returned. The number of dimensions of the array is the lowest needed to hold the data. If the file contains mor than one variable, the function will return only one variable with each call. Choose the varibale by providing paramter val (name or number of variable).
Note
Prior to version 1.2.4, this function did not arrays with more than two dimensions, or multiple variables in files of more than one dimension. Prior to version 1.5.0 timeseries were not implemented.
Author(s)
Clemens Druee
References
AUSTAL 3.1 model reference (by Ingenieurbuero Janicke)
Examples
so2 <- read.dmna(system.file("extdata", "example-grid.dmna", package="readmet"))
ax <- dmna.axes(system.file("extdata", "example-grid.dmna", package="readmet"))
filled.contour(ax$x, ax$y, so2)
monitor <- read.dmna(system.file("extdata", "example-monitor.dmna", package="readmet"))
plot(monitor$te, monitor$X2, type="l")
series <- read.dmna(system.file("extdata", "example-series.dmna", package="readmet"))
plot(series$te, series$ua, type="l")
function to read the contents of a file in Scintec Format-1
Description
reads output data (extension ".mnd") from Scintec atmospheric measurement systems into a list that contains the variable names as names and the values as either matrix or vector.
Usage
read.scintec1(files)
Arguments
files |
array containing names (and path if necessary) of the files to read |
Value
list(different types)
vector |
lenght = n (number of times contained in the file) |
matrix |
dim(n,m) where n is number of times contained in the file and m is
the number of levels |
Author(s)
Clemens Druee
References
Scintec APRun software manual
Examples
mnd <- read.scintec1(system.file("extdata", "example.mnd", package="readmet"))
mnd$CT2
function to read contents of a file in TOA5-format
Description
reads the contents of a Campbell Scientific table-orientad ASCII format 5 (TOA5) into a data frame, columns are named after the TOA5 vribale names
Usage
read.toa5(file)
Arguments
file |
name (and path if necessary) of the file to read |
Value
data.frame
Author(s)
Clemens Druee
References
Campbell Scientific CR3000 data logger manual
Examples
dat <- read.toa5(system.file("extdata", "example.dat", package="readmet"))
dat$time <- as.POSIXct(dat$TIMESTAMP)
plot (dat$time, dat$AirTC_Avg)
read the comment fields of a file in Scintec Format-1 format
Description
get comment entries from a a Scintec atmospheric profiler data format "Format-1" (extension ".mnd")
Usage
scintec1.comments(file, header = list())
Arguments
file |
name (and path if necessary) of the file to read |
header |
optionally, instead of reading the header from the file again,
the output of a previous call to |
Value
named list |
each entry corresponds to one comment field |
Author(s)
Clemens Druee
References
Scintec APRun software manual
Examples
hdr <- read.scintec1(system.file("extdata", "example.mnd", package="readmet"))
hdr$`Serial Number`
read the header of a file in Scintec Format-1 format
Description
get timeseries of non-profile variables from a a Scintec atmospheric profiler data format "Format-1" (extension ".mnd")
Usage
scintec1.header(file)
Arguments
file |
name (and path if necessary) of the file to read |
Value
named list; each entry corresponds to one header field:
starttime |
starting time of the measurement as POSIXct object |
filecount |
running number of files produced during the current measurement |
instrument |
model type of the device |
commentlines |
lines of text containing the coment list |
variables |
lines of text containing the list of the variables in encoded form |
heightlevels |
number of height of levels where data are produced |
Author(s)
Clemens Druee
References
Scintec APRun software manual
Examples
hdr <- read.scintec1(system.file("extdata", "example.mnd", package="readmet"))
hdr$instrument
read the single-level variables from a file in Scintec Format-1 format
Description
get timeseries of non-profile variables from a a Scintec atmospheric profiler data format "Format-1" (extension ".mnd")
Usage
scintec1.nonprofile(file, header = list(), vars = list())
Arguments
file |
name (and path if necessary) of the file to read |
header |
optionally, instead of reading the header from the file again,
the output of a previous call to |
vars |
optionally, instead of reading the header from the file again,
the output of a previous call to |
Value
list(vector); length(vector) = n (number of times contained in the file)
each vevtor contains a non-profile variable (see variable list)
special varaible name "time" contains the times as POSIXct
Author(s)
Clemens Druee
References
Scintec APRun software manual
Examples
dat <- scintec1.nonprofile(system.file("extdata", "example.mnd", package="readmet"))
head(dat)
read the multi-level (profile) variables from a Scintec Format-1 file
Description
get profile variables from a Scintec atmospheric profiler data format "Format-1" (extension ".mnd")
Usage
scintec1.profile(file, header = list(), vars = list())
Arguments
file |
name (and path if necessary) of the file to read |
header |
optionally, instead of reading the header from the file again,
the output of a previous call to |
vars |
optionally, instead of reading the header from the file again,
the output of a previous call to |
Value
list(matrix); dim(matrix)=c(n,m)
where n is number of times contained in the file and m is
the number of levels
i.e. rows represents timeseries of at a fixed level,
columns represent profiles at a fixed time
Author(s)
Clemens Druee
References
Scintec APRun software manual
Examples
dat <- scintec1.profile(system.file("extdata", "example.mnd", package="readmet"))
dat
read the variable descriptions from a file in Scintec Format-1 format
Description
get timeseries of non-profile variables from a a Scintec atmospheric profiler data format "Format-1" (extension ".mnd")
Usage
scintec1.variables(file, header = list())
Arguments
file |
name (and path if necessary) of the file to read |
header |
optionally, instead of reading the header from the file again,
the output of a previous call to |
Value
data.frame; each entry corresponds to one variable. The columns are:
label |
Name of variable |
symbol |
short name; corresponds to list name in scintec1.profile,scintec1.nonprofile, and read.scintec1 |
unit |
physical unit |
type |
code describing for example averaging, profile/nonprofile, measured, derived or assimilated. See Scintec Software Manual |
error.mask |
See Scintec Software Manual |
gap.value |
value in files representing missing values of this variable |
Author(s)
Clemens Druee
References
Scintec APRun software manual
Examples
vars <- scintec1.variables(system.file("extdata", "example.mnd", package="readmet"))
head(vars)
function to write data (read from DMNA file) into an ESRI ArcInfo gridded ASCII file
Description
This function writes a 2D matrix into an ESRI ArcInfo gridded ASCII file that can be easily imported into most geographic information systems (GIS)
Usage
write.arcgrid(z,file,xlen,ylen,xll,yll,delta,grid,naval=-9999)
Arguments
z |
2D matrix containing tha data |
file |
name (incuding path, if needed) of the file to write to |
xlen, ylen |
number of data alon x and y axis, resp. |
xll, yll |
position of the lower left (i.e. southwest) corner |
delta |
grid spacing |
grid |
a list containing grid parameters.
Instead of providing xlen,ylen,xll,yll, and delta individually,
containing these values way be provided. For example, such a list is returned
when calling |
naval |
value written to file instead of NA and +/-Inf |
Details
The standard plotting functions for R plot columns along the x axis and
rows along the y axis. Hence the matrix is rotated 90 degrees left (compared to
write.table or write.csv) to yield the same
orientation of the data when plotted in R and in GIS.
Value
nothing.
Note
This function was added in version 1.3.0.
Author(s)
Clemens Druee
References
Wikipedia entry on Esri grid : https://en.wikipedia.org/wiki/Esri_grid
See Also
Examples
# read data and grid info
infile <- system.file("extdata", "example-grid.dmna", package="readmet")
so2 <- read.dmna(infile)
grid <- dmna.grid(infile)
# write file
write.arcgrid(so2, file = "myfile.grid", grid = grid)
# show head of file
writeLines(readLines("myfile.grid", n=7))
# delete file
file.remove("myfile.grid")
function to write data to a file in DMNA-format
Description
writes gridded on-e, two or three-dimensional data or timeseries to a DMNA format that is used for example by the German national dispersion model AUSTAL
Usage
write.dmna(filename, values, axes=NULL, name=NULL, types=NULL, vldf="V", debug=FALSE)
Arguments
filename |
name (and path if necessary) of the file to write |
values |
matrix or list(matrix) or data.frame. Matrix or list(matrix) implies writing gridded data. list(matrix) must be named using the variable names. data.frame implies writing a timeseries and must contain a column named "te" containing time as POXIXct. |
axes |
data.frame. Required for gridded data. Must contain columns "x" and column "y" if values are two-dimensional and additionally "sk" (or "z") if data are three-dimensional. The spacing of all values in "x" and "y" must be identical. |
name |
character string. Variable name. Required if values is of class matrix. Is ignored else. |
types |
named list. Variable type for each variable. If 'values' is a list, names in 'types' must match names in in 'values'. If 'values' is a matrix, a name in 'types' must match 'name'. Types are:
|
vldf |
character string. specifies, where values are located in the model grid. "V" denotes volume average, "P" volumne center point values, or "" volume edge values. |
debug |
boolean. ignored. Is kept for compatibility |
Value
returns nothing
Note
Introduced in version 1.6.0.
Author(s)
Clemens Druee
References
AUSTAL 3.1 model reference (by Ingenieurbuero Janicke)
Examples
#create data and write file
len <- 25
val <- list(random = matrix(runif(len * len),nrow = len))
ax <- list(x = 1:len,
y = 1:len)
write.dmna("myfile.dmna", val, ax)
# show first lines
writeLines(readLines('myfile.dmna', n=12))
# delete file
unlink("myfile.dmna")