Function(s) to import various ADMS file types into openair. Currently
handles ".met", ".bgd", ".mop" and ".pst" file structures. Uses
read.csv (in utils) to read in data, format for R and openair
and apply some file structure testing.
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,
...
)The ADMS file to be imported. Default, file.choose()
opens browser. Use of read.csv (in utils) 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.type to one of the known file.type
options: "bgd", "met", "mop" or "pst".
Option to convert all data names to lower case. Default,
TRUE. Alternative, 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,
TRUE. Alternative, 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 file. Alternative, FALSE, discards units.
(NOTE: currently, only .bgd and .pst files assign units.
So, this option is ignored when importing .met or .mop
files.)
Option to simplify data names in accordance with
common openair practices. Default, TRUE. Alternative,
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.names setting. For example, brackets or
symbols are removed from names or repaced 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 .bgd, .met or .pst
files.)
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:
FALSE which 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 .bgd, .met or
.pst files.)
Option applied by simplifyNamesADMS when
simplify.names is enabled. All names are simplified for the
default setting, NULL.
Additional arguments, passed to read.csv as part of
import operation.
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 (as.POSIX*). If
drop.input.dates is enabled data series combined to generated the
new "date" data series will also be removed.
If 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 simplfication operations can be
obtained using, e.g., the call importADMS(simplify.names).
If drop.case is enabled all upper case characters in names will be
converted to lower case.
If keep.units is enabled data units information may also be retained
as part of the data frame comment if available.
With .mop files, input and processed data series names may also been
modified on the basis of drop.delim and add.prefixes
settings
The 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: .bgd, .met,
.mop and .pst. Where other file extensions have been set but
the file structure is known, the import call can be forced by, e.g,
mydata <- importADMS(file.type="bgd"). Other options can be adjusted
to provide fine control of the data structuring and renaming.
Generic import function import, for possible
alternative import methods. Other dedicated import functions available
for other file types, including importKCL,
importAURN, etc.
# NOT RUN {
##########
#example 1
##########
#To be confirmed
#all current simplify.names operations
importADMS(simplify.names)
#to see what simplify.names does to adms data series name PHI
new.name <- importADMS(simplify.names, names="PHI")
new.name
# }
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