Description Usage Arguments Details Value References Examples
This function takes epd.entity-class
or
epd.entity.df-class
objects, as those returned by
get_entity
or entity_to_matrices
,
extracts datation information and reshapes it to complies with
CLAM or BACON format.
1 2 3 4 5 6 7 8 9 | export_entity(format, x, chronology = NULL, incl_chron_not_in_c14 = NULL,
incl_c14_not_in_chron = NULL, use_c14_conf_age = NULL,
use_c14_conf_depth = NULL, include_depths = TRUE, incl_events = NULL)
## S4 method for signature 'character,epd.entity'
export_entity(format, x, chronology = NULL,
incl_chron_not_in_c14 = NULL, incl_c14_not_in_chron = NULL,
use_c14_conf_age = NULL, use_c14_conf_depth = NULL,
include_depths = TRUE, incl_events = NULL)
|
format |
character Character string indicating whether to export to "clam" or to "bacon" format. |
x |
epd.entity |
chronology |
numeric Number indicating the chronology from which to extract the agebasis for the "clam" or "bacon" file. If unspecified, the function use the default chronology according to the EPD for that particular entity. |
incl_chron_not_in_c14 |
logical Logical value indicating whether the function should include in the result agebasis present in the specified (or the default) chronology (TRUE) but not in the C14 table, or should not include them (FALSE). |
incl_c14_not_in_chron |
logical Logical value indicating whether the function should include in the result agebasis present in the C14 data but not present in the specified (or default) chronology (TRUE), or should not include them (FALSE). |
use_c14_conf_age |
logical Logical value indicating whether the function should use data from C14 table when there are conflicting ages between the C14 table or the chronology (TRUE), or it should take data from the chronology instead (FALSE). |
use_c14_conf_depth |
logical Logical value indicating whether the function should use data from C14 table when there are conflicting depths between the C14 table or the chronology (TRUE), or it should take data from the chronology instead (FALSE). |
include_depths |
logical Logical value indicating whether depths of pollen samples should be exported too. The default value is TRUE. This is helpful because running CLAM or BACON with depths calculate the calibrated ages for those samples in the same step. |
incl_events |
logical Logical value indicating whether events information should be included (TRUE), or not (FALSE). |
The function has an interactive implementation. If some of the parameters
incl_chron_not_in_c14
, incl_c14_not_in_chron
,
use_c14_conf_age
, and/or use_c14_conf_depth
are not
specified, the function will check the data and ask the user how
it should proceed regarding some conflicts in the data between C14 data
and agebasis tables.
Data frame with specific format for "CLAM" or "BACON" age-depth
modelling softwares. CLAM format has 7 columns: $ID
,
$C14_age
, $cal_age
, $error
, $reservoir
,
$depth
, and $thickness
. $ID
is the code
of the radiocarbon (C14) samples. $C14_age
is the radiocarbon (C14)
dates. $error
is the error estimated in the radiocarbon (C14)
datation of the samples. $reservoir
is to specify if the
samples have marine reservoir effects. $depth
is the depth in
cm of the radiocarbon samples. $thickness
is the tickness of
the radiocarbon samples. BACON format has 4 columns: $labID
,
$age
, $error
, and $depth
. $labID
is the
code of the radiocarbon (C14) samples. $age
is the radiocarbon
(C14) date. $error
is the error estimated in the radiocarbon
(C14) datation for the samples. $depth
is the depth in cm of
the radiocarbon samples. The function also produce the files required
by CLAM or BACON in the working directory according to this folder
structure: ~/{format}/Cores/{entity_number}/
The function creates a file .csv
({entity_number}.csv
) with
the radiocarbon data and two .txt
({entity_number}_depths.txt
and {entity_number}_depthsID.txt
). The last one is not used by
CLAM or BACON but it might be useful to follow track of samples depths.
http://www.chrono.qub.ac.uk/blaauw/clam.html
http://chrono.qub.ac.uk/blaauw/bacon.html
1 2 3 4 5 6 7 8 9 10 11 | ## Not run:
epd.connection <- connect_to_epd(host = "localhost", database = "epd",
user = "epdr", password = "epdrpw")
epd.400 <- get_entity(400, epd.connection)
export_entity("clam", epd.400) # Also check new folders in your working directory
export_entity("bacon", epd.400) # Also check new folders in your working directory
epd.1 <- get_entity(1, epd.connection)
export_entity("clam", epd.1)
export_entity("bacon", epd.1)
## End(Not run)
|
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