CERC Atmospheric Dispersion Modelling System (ADMS) data import function(s) for openairSource:
Function(s) to import various ADMS file types into openair. Currently handles
".met", ".bgd", ".mop" and ".pst" file structures. Uses
to read in data, format for R and openair and apply some file structure
importADMS( file = file.choose(), file.type = "unknown", drop.case = TRUE, drop.input.dates = TRUE, keep.units = TRUE, simplify.names = TRUE, test.file.structure = TRUE, drop.delim = TRUE, add.prefixes = TRUE, names = NULL, all = FALSE, ... )
The ADMS file to be imported. Default,
file.choose()opens browser. Use of
utils::read.csv()also allows this to be a readable text-mode connection or url (although these options are currently not fully tested).
Type of ADMS file to be imported. With default, "unknown", the import uses the file extension to identify the file type and, where recognised, uses this to identify the file structure and import method to be applied. Where file extension is not recognised the choice may be forced by setting
file.typeto one of the known
file.typeoptions: "bgd", "met", "mop" or "pst".
Option to convert all data names to lower case. Default,
FALSE, returns data with name cases as defined in file.
Option to remove ADMS "hour", "day", and "year" data columns after generating openair "date" timeseries. Default,
FALSE, returns both "date" and the associated ADMS data columns as part of openair data frame.
Option to retain ADMS data units. Default,
TRUE, retains units (if recoverable) as character vector in data frame comment if defined in
FALSE, discards units. (NOTE: currently, only
.pstfiles assign units. So, this option is ignored when importing
Option to simplify data names in accordance with common
FALSE, returns data with names as interpreted by standard R. (NOTE: Some ADMS file data names include symbols and structures that R does not allow as part of a name, so some renaming is automatic regardless of
simplify.namessetting. For example, brackets or symbols are removed from names or replaced with ".", and names in the form "1/x" may be returned as "X1.x" or "recip.x".)
Option to test file structure before trying to import. Default,
TRUE, tests for expected file structure and halts import operation if this is not found. Alternative,
FALSE, attempts import regardless of structure.
Option to remove delim columns from the data frame. ADMS .mop files include two columns, "INPUT_DATA:" and "PROCESSED_DATA:", to separate model input and output types. Default,
TRUE, removes these. Alternative,
FALSE, retains them as part of import. (Note: Option ignored when importing
Option to add prefixes to data names. ADMS .mop files include a number of input and process data types with shared names. Prefixes can be automatically added to these so individual data can be readily identified in the R/openair environment. Default,
TRUE, adds "process." as a prefix to processed data. Other options include:
FALSEwhich uses no prefixes and leave all name rationalisation to R, and character vectors which are treated as the required prefixes. If one vector is sent, this is treated as processed data prefix. If two (or more) vectors are sent, the first and second are treated as the input and processed data prefixes, respectively. For example, the argument (
add.prefixes="out") would add the "out" prefix to processed data names, while the argument (
add.prefixes=c("in","out")) would add "in" and "out" prefixes to input and output data names, respectively. (Note: Option ignored when importing
Option applied by
simplify.namesis enabled. All names are simplified for the default setting,
For .MOP files, return all variables or not. If
all = TRUEa large number of processed variables are returned.
Arguments passed on to
a logical value indicating whether the file contains the names of the variables as its first line. If missing, the value is determined from the file format:
headeris set to
TRUEif and only if the first row contains one fewer field than the number of columns.
the field separator character. Values on each line of the file are separated by this character. If
sep = ""(the default for
read.table) the separator is ‘white space’, that is one or more spaces, tabs, newlines or carriage returns.
the set of quoting characters. To disable quoting altogether, use
quote = "". See
scanfor the behaviour on quotes embedded in quotes. Quoting is only considered for columns read as character, which is all of them unless
the character used in the file for decimal points.
TRUEthen in case the rows have unequal length, blank fields are implicitly added. See ‘Details’.
character: a character vector of length one containing a single character or an empty string. Use
""to turn off the interpretation of comments altogether.
In standard use
importADMS() returns a data frame for use in
openair. By comparison to the original file, the resulting data frame is
modified as follows:
Time and date information will combined in a single column "date",
formatted as a conventional timeseries (
drop.input.dates is enabled data series combined to generated the
new "date" data series will also be removed.
simplify.names is enabled common chemical names may be
simplified, and some other parameters may be reset to openair standards
(e.g. "ws", "wd" and "temp") according to operations defined in
simplifyNamesADMS. A summary of simplification operations can be
obtained using, e.g., the call
drop.case is enabled all upper case characters in names will be
converted to lower case.
keep.units is enabled data units information may also be retained
as part of the data frame comment if available.
.mop files, input and processed data series names may also been
modified on the basis of
importADMS function were developed to help import various ADMS
file types into openair. In most cases the parent import function should work
in default configuration, e.g.
mydata <- importADMS(). The function
currently recognises four file formats:
.pst. Where other file extensions have been set but the file
structure is known, the import call can be forced by, e.g,
importADMS(file.type="bgd"). Other options can be adjusted to provide fine
control of the data structuring and renaming.
########## #example 1 ########## #To be confirmed #all current simplify.names operations importADMS(simplify.names) #> Simplification operation summary #> [ADMS => R => OPENAIR]: #> 1/LMO => X1.LMO => RECIP.LMO #> 1/MONIN-OBUKHOV LENGTH => X1.MONIN.OBUKHOV.LENGTH => RECIP.LMO #> ALBEDO(D) => ALBEDO.D. => ALBEDO.DISP #> ALBEDO (D) => ALBEDO..D. => ALBEDO.DISP #> ALBEDO(DISP) => ALBEDO.DISP. => ALBEDO.DISP #> ALBEDO (DISP) => ALBEDO..DISP. => ALBEDO.DISP #> ALBEDO (DISPERSION AREA) => ALBEDO..DISPERSION.AREA. => ALBEDO.DISP #> ALBEDO(M) => ALBEDO.M. => ALBEDO.MET #> ALBEDO (M) => ALBEDO..M. => ALBEDO.MET #> ALBEDO(MET) => ALBEDO.MET. => ALBEDO.MET #> ALBEDO (MET) => ALBEDO..MET. => ALBEDO.MET #> ALBEDO (MET SITE) => ALBEDO..MET.SITE. => ALBEDO.MET #> ALPHA(D) => ALPHA.D. => ALPHA.DISP #> ALPHA (D) => ALPHA..D. => ALPHA.DISP #> ALPHA(DISP) => ALPHA.DISP. => ALPHA.DISP #> ALPHA (DISP) => ALPHA..DISP. => ALPHA.DISP #> ALPHA(M) => ALPHA.M. => ALPHA.MET #> ALPHA (M) => ALPHA..M. => ALPHA.MET #> ALPHA(MET) => ALPHA.MET. => ALPHA.MET #> ALPHA (MET) => ALPHA..MET. => ALPHA.MET #> BL DEPTH => BL.DEPTH => H #> BOUNDARY LAYER DEPTH => BOUNDARY.LAYER.DEPTH => H #> BUOYANCY FREQUENCY ABOVE BOUNDARY LAYER => BUOYANCY.FREQUENCY.ABOVE.BOUNDARY.LAYER => NU #> CLOUD => CLOUD => CL #> CLOUD AMOUNT (OKTAS) => CLOUD.AMOUNT..OKTAS. => CL #> Conc|ppb|NAME|SOURCES|-| RESOLUTION => Conc.ppb.NAME.SOURCES....RESOLUTION => NAME.SOURCES.RESOLUTION #> Conc|ppm|NAME|SOURCES|-| RESOLUTION => Conc.ppm.NAME.SOURCES....RESOLUTION => NAME.SOURCES.RESOLUTION #> Conc|ug/m3|NAME|SOURCES|-| RESOLUTION => Conc.ug.m3.NAME.SOURCES....RESOLUTION => NAME.SOURCES.RESOLUTION #> NAME.All.sources.1hr => NAME.All.sources.1hr => NAME #> NAME.All.sources.RESOLUTION => NAME.All.sources.RESOLUTION => NAME.RESOLUTION #> NAME.SOURCE.1hr => NAME.SOURCE.1hr => NAME.SOURCE #> D(RELATIVE HUMIDITY)/DZ ABOVE BOUNDARY LAYER (PERCENT/M) => D.RELATIVE.HUMIDITY..DZ.ABOVE.BOUNDARY.LAYER..PERCENT.M. => DRHDZU #> DELTAPHI => DELTAPHI => DELTA.WD #> DELTAT => DELTAT => DELTA.T #> DELTA T => DELTA.T => DELTA.T #> DELTATHETA => DELTATHETA => DELTA.THETA #> DELTA THETA => DELTA.THETA => DELTA.THETA #> DIRN CHANGE => DIRN.CHANGE => DELTA.WD #> DRH/DZ => DRH.DZ => DRHDZU #> GEOSTROPHIC MINUS SURFACE WIND DIRECTION (DEGREES) => GEOSTROPHIC.MINUS.SURFACE.WIND.DIRECTION..DEGREES. => DELTA.WD #> HEAT FLUX => HEAT.FLUX => FTHETA0 #> INCOMING SOLAR RADIATION => INCOMING.SOLAR.RADIATION => K #> LATENT HEAT FLUX => LATENT.HEAT.FLUX => LAMBDAE #> LAT HT FLUX => LAT.HT.FLUX => LAMBDAE #> MODIFIED PRIESTLEY-TAYLOR PARAMETER (DISPERSION AREA) => MODIFIED.PRIESTLEY.TAYLOR.PARAMETER..DISPERSION.AREA. => ALPHA.DISP #> MODIFIED PRIESTLEY-TAYLOR PARAMETER (MET SITE) => MODIFIED.PRIESTLEY.TAYLOR.PARAMETER..MET.SITE. => ALPHA.MET #> N ABOVE BL => N.ABOVE.BL => NU #> PHI => PHI => WD #> PHI0 => PHI0 => WD.0 #> PHIG => PHIG => WD.G #> PHISEC => PHISEC => WD.SEC #> PRECIP => PRECIP => P #> PRECIPITATION RATE (MM/HOUR) => PRECIPITATION.RATE..MM.HOUR. => P #> R => R => ALBEDO.MET #> RECIPLMO => RECIPLMO => RECIP.LMO #> RELATIVE HUMIDITY ABOVE BOUNDARY LAYER (PERCENT) => RELATIVE.HUMIDITY.ABOVE.BOUNDARY.LAYER..PERCENT. => RHU #> RH ABOVE BL => RH.ABOVE.BL => RHU #> RHUM => RHUM => RHU #> ROUGHNESS LENGTH (DISPERSION AREA) => ROUGHNESS.LENGTH..DISPERSION.AREA. => Z0.DISP #> ROUGHNESS LENGTH (MET SITE) => ROUGHNESS.LENGTH..MET.SITE. => Z0.MET #> S HUMIDITY => S.HUMIDITY => SHU #> SEA SURFACE TEMPERATURE (C) => SEA.SURFACE.TEMPERATURE..C. => TSEA #> SEA TEMP => SEA.TEMP => TSEA #> SENSIBLE HEAT FLUX => SENSIBLE.HEAT.FLUX => FTHETA0 #> SIGMATHETA => SIGMATHETA => SIGMA.THETA #> SIGMA THETA => SIGMA.THETA => SIGMA.THETA #> SIGMA THETA (DEGREES) => SIGMA.THETA..DEGREES. => SIGMA.THETA #> SOLAR RAD => SOLAR.RAD => K #> SPECIFIC HUMIDITY => SPECIFIC.HUMIDITY => SHU #> T0C => T0C => TEMP #> TEMPERATURE => TEMPERATURE => TEMP #> TEMPERATURE (C) => TEMPERATURE..C. => TEMP #> TEMPERATURE JUMP ACROSS BOUNDARY LAYER TOP => TEMPERATURE.JUMP.ACROSS.BOUNDARY.LAYER.TOP => DELTA.THETA #> TEMPERATURE OVER LAND MINUS SEA SURFACE TEMPERATURE => TEMPERATURE.OVER.LAND.MINUS.SEA.SURFACE.TEMPERATURE => DELTA.T #> Time(s) => Time.s. => Time #> U => U => WS #> UG => UG => WS.G #> UGSTAR => UGSTAR => WS.GSTAR #> USTAR => USTAR => WS.STAR #> WIND DIRN => WIND.DIRN => WD #> WIND DIRECTION (DEGREES) => WIND.DIRECTION..DEGREES. => WD #> WIND HEIGHT => WIND.HEIGHT => WIND.HEIGHT #> WIND MEASUREMENT HEIGHT => WIND.MEASUREMENT.HEIGHT => WIND.HEIGHT #> WIND SPEED => WIND.SPEED => WS #> X(m) => X.m. => X #> Y(m) => Y.m. => Y #> Z(m) => Z.m. => Z #> Z0(D) => Z0.D. => Z0.DISP #> Z0 (D) => Z0..D. => Z0.DISP #> Z0(DISP) => Z0.DISP. => Z0.DISP #> Z0 (DISP) => Z0..DISP. => Z0.DISP #> Z0(M) => Z0.M. => Z0.MET #> Z0 (M) => Z0..M. => Z0.MET #> Z0(MET) => Z0.MET. => Z0.MET #> Z0 (MET) => Z0..MET. => Z0.MET #to see what simplify.names does to adms data series name PHI new.name <- importADMS(simplify.names, names="PHI") new.name #>  "WD"