get.interm.data: A function to collect intermediate data produced by Colony2...
In rcolony: Tools for implementation and visualisation of Colony2 and its outputs.

Description Usage Arguments Details Author(s) References See Also

While it is running, Colony2 produces output to indicate the computation progress. This function allows R to import the outputs produced. It is intended to be called from the monitor.colony function rather than being used directly by the user.

1	get.interm.data(variable="CrLogL",datadir=getwd(),n=1)

`variable`	The name of the variable that you wish to monitor. See details.
`datadir`	The path to the directory that contains the Colony output files.
`n`	If there are two variables with the same name, which one should be used? See 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).

Owen R. Jones

Wang, J. (2004) Sibship reconstruction from genetic data with typing errors. Genetics 166: 1963-1979.

monitor.colony

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