monitor.colony: A function to monitor the intermediate results of the...

In rcolony: Tools for implementation and visualisation of Colony2 and its outputs.

Description

This function examines the intermediate outputs from the Colony2 program. These should be stored in a text file called "temp.txt" in the working directory. It plots the selected variable as a function of the iteration number thereby allowing the user to monitor progress. The function repeatedly calls a plot at an interval that can be set by the user (the default is 2 seconds). It keeps running until the Colony analysis has finished, or until the user interupts it (by pressing the Esc key).

Usage

monitor.colony(datadir=getwd(),variable="CrLogL",interv.t=2,last.few=10,n=1,showres=FALSE)

Arguments

datadir	The path to the directory that contains the Colony output files.
variable	The name of the variable that you wish to monitor. See details.
interv.t	The interval (in seconds) at which R should retrieve intermediate data.
last.few	(not yet implemented) How many datapoints should be displayed. Set to -1 to show all data. If the number is a positive integer, then the last x datapoints are shown.
n	If there are two variables with the same name, which one should be used? See details.
showres	Should R show the results obtained in a table to be displayed in the R console window? Boolean.

Details

The intermediate results available are:

Run : The replicate run number. Variable

Tmr : The number of temperature reductions so far within the run. Variable

Itr : The number of iterates (reconfigurations considered) so far within the run. Variable

NSucc : The number of successful (accepted) reconfigurations so far within the temperature. Variable

NSuccLmt : Maximum (Limit) number of successful reconfigurations allowed within the temperature. Constant

NFail1 : The number of reconfigurations since the last update of the best likelihood within the temperature. Variable

NFail1Lmt : Maximum (Limit) value of NFail1 within the temperature. Constant

NFail2 : The total number of reconfigurations since the last update of the best likelihood within the run. Variable

NFail2Lmt : Maximum (Limit) value of NFail2 within a run. Constant. The run terminates when NFail2Lmt=NFail2 and the successful rate (see below) < 0.01

SucRate% : =NSucc / Itr. Variable

SucLmt% : =NSucc / NSuccLmt. Variable

FailLmt% : =NFail1 / NFail1Lmt. Variable

IterLmt% : = (Number of iterates) / (Maximum number of iterates) within a temperature. Variable

CrLogL : The log likelihood of the current configuration. Variable

BtLogL : The best log likelihood reached with the current configuration. Variable

#F1 : Current number of paternal sib families. Variable

#F2 : Current number of maternal sib families. Variable

#F3 : Current number of sib family clusters. Variable

#FS : Current number of full sib families. Variable

HSPair : Current number of half-sib dyads. Variable

FSPair : Current number of full-sib dyads. Variable

#AssgnC1 : Current number of candidate males that are assigned parentage. Variable

#AssgnC2 : Current number of candidate females that are assigned parentage. Variable

#AssgnP1 : Current number of offspring that have assigned paternity. Variable

#AssgnP2 : Current number of offspring that have assigned maternity. Variable

F1, F2, F3, FS, HSPair, FSPair, AssgnC1, AssgnC2, AssgnP1 and AssgnP2 appear twice in the intermediate outputs of Colony2. Their first appearance is for the current status. While the second appearance is for the best status so far (i.e. the maximum value). Users wishing to plot any of these values should use the n argument to select the appropriate value (1 for the current value, 2 for best value).

Author(s)

Owen R. Jones

See Also

get.interm.data

Examples

##Not run
#monitor.colony(variable="CrLogL",interv.t=2)
##End not run

rcolony documentation built on May 2, 2019, 6:42 p.m.