Calculates the Effective Sample Sizes of the traces of multiple estimated variables.
Source:R/calc_summary_stats.R
calc_summary_stats_traces.RdCalculates the Effective Sample Sizes of the traces of multiple estimated variables.
Arguments
- traces
a data frame with traces of estimated parameters. Assumes the burn-ins are removed.
- sample_interval
the interval in timesteps between samples
See also
Use remove_burn_ins to remove the burn-ins
of all traces
Examples
estimates_all <- parse_beast_tracelog_file(
get_tracerer_path("beast2_example_output.log")
)
estimates <- remove_burn_ins(estimates_all, burn_in_fraction = 0.1)
calc_summary_stats_traces(
estimates,
sample_interval = 1000
)
#> mean stderr_mean stdev variance median
#> posterior -70.5839432 0.50448873 1.6816291 2.82787643 -69.8797613
#> likelihood -60.1725009 0.39642076 1.3214025 1.74610467 -60.0504225
#> prior -10.4114423 0.54245052 1.8081684 3.26947291 -10.5950270
#> treeLikelihood -60.1725009 0.39642076 1.3214025 1.74610467 -60.0504225
#> TreeHeight 0.9744748 0.14399367 0.3916244 0.15336965 0.8755907
#> BirthDeath -3.5036870 0.54245052 1.8081684 3.26947291 -3.6872718
#> birthRate2 1.4470488 0.21344112 0.6713951 0.45077144 1.4118781
#> relativeDeathRate2 0.4937568 0.06502354 0.1709096 0.02921009 0.4480670
#> mode geom_mean hpd_interval_low hpd_interval_high
#> posterior n/a n/a -74.1526820 -68.6852294
#> likelihood n/a n/a -62.4090389 -58.7371284
#> prior n/a n/a -14.1703653 -7.2820933
#> treeLikelihood n/a n/a -62.4090389 -58.7371284
#> TreeHeight n/a 0.91041547166058 0.4529637 1.8159958
#> BirthDeath n/a n/a -7.2626100 -0.3743380
#> birthRate2 n/a 1.28823302868404 0.3909076 2.8041208
#> relativeDeathRate2 n/a 0.466468860930895 0.2496224 0.7107459
#> act ess
#> posterior 1000.000 10.000000
#> likelihood 1000.000 10.000000
#> prior 1000.000 10.000000
#> treeLikelihood 1000.000 10.000000
#> TreeHeight 1502.121 6.657254
#> BirthDeath 1000.000 10.000000
#> birthRate2 1122.942 8.905181
#> relativeDeathRate2 1608.296 6.217762