Documentation for SLiM function createLogFile, which is a method of the
SLiM class Community.
Note that the R function is a stub, it does not do anything in R (except bring
up this documentation). It will only do
anything useful when used inside a slim_block function further
nested in a slim_script
function call, where it will be translated into valid SLiM code as part of a
full SLiM script.
createLogFile(
filePath,
initialContents,
append,
compress,
sep,
logInterval,
flushInterval
)An object of type string. Must be of length 1 (a singleton). See details for description.
An object of type null or string. The default value is
NULL. See details for description.
An object of type logical. Must be of length 1 (a singleton). The
default value is F. See details for description.
An object of type logical. Must be of length 1 (a singleton).
The default value is F. See details for description.
An object of type string. Must be of length 1 (a singleton). The
default value is ",". See details for description.
An object of type null or integer. Must be of length 1 (a
singleton). The default value is NULL. See details for description.
An object of type null or integer. Must be of length 1 (a
singleton). The default value is NULL. See details for description.
An object of type LogFile object. Return will be of length 1 (a singleton)
Documentation for this function can be found in the official SLiM manual: page 665.
Creates and returns a new LogFile object that logs data from the simulation (see the documentation for the LogFile class for details). Logged data will be written to the file at filePath, overwriting any existing file at that path by default, or appending to it instead if append is T (successive rows of the log table will always be appended to the previously written content, of course). Before the header line for the log is written out, any string elements in initialContents will be written first, separated by newlines, allowing for a user-defined file header. If compress is T, the contents will be compressed with zlib as they are written, and the standard .gz extension for gzip-compressed files will be appended to the filename in filePath if it is not already present. The sep parameter specifies the separator between data values within a row. The default of "," will generate a "comma-separated value" (CSV) file, while passing sep="\t" will use a tab separator instead to generate a "tab-separated value" (TSV) file. Other values for sep may also be used, but are less standard. LogFile supports periodic automatic logging of a new row of data, enabled by supplying a non-NULL value for logInterval. In this case, a new row will be logged (as if logRow() were called on the LogFile) at the end of every logInterval ticks (just before the tick counter increments, in both WF and nonWF models), starting at the end of the tick in which the LogFile was created. A logInterval of 1 will cause automatic logging at the end of every tick, whereas a logInterval of NULL disables automatic logging. Automatic logging can always be disabled or reconfigured later with the LogFile method setLogInterval(), or logging can be triggered manually by calling logRow(). When compression is enabled, LogFile flushes new data lazily by default, for performance reasons, buffering data for multiple rows before writing to disk. Passing a non-NULL value for flushInterval requests a flush every flushInterval rows (with a value of 1 providing unbuffered operation). Note that flushing very frequently will likely result in both lower performance and a larger final file size (in one simple test, 48943 bytes instead of 4280 bytes, or more than a 10× increase in size). Alternatively, passing a very large value for flushInterval will effectively disable automatic flushing, except at the end of the simulation (but be aware that this may use a large amount of memory for large log files). In any case, the log file will be created immediately, with its requested initial contents; the initial write is not buffered. When compression is not enabled, the flushInterval setting is ignored. The LogFile documentation discusses how to configure and use LogFile to write out the data you are interested in from your simulation; see section 25.10.
This is documentation for a function in the SLiM software, and has been reproduced from the official manual, which can be found here: http://benhaller.com/slim/SLiM_Manual.pdf. This documentation is Copyright © 2016-2020 Philipp Messer. All rights reserved. More information about SLiM can be found on the official website: https://messerlab.org/slim/
Other Community:
Co,
deregisterScriptBlock(),
genomicElementTypesWithIDs(),
interactionTypesWithIDs(),
mutationTypesWithIDs(),
outputUsage(),
registerEarlyEvent(),
registerFirstEvent(),
registerInteractionCallback(),
registerLateEvent(),
rescheduleScriptBlock(),
scriptBlocksWithIDs(),
simulationFinished(),
speciesWithIDs(),
subpopulationsWithIDs(),
usage()