Convert an FBD posterior parameter table from wide to long format
FBD_reshape.RdConverts FBD posterior parameter table, such as those imported using combine_log, from wide to long format.
Usage
FBD_reshape(posterior, variables = NULL, log.type = c("MrBayes", "BEAST2"))Arguments
- posterior
Single posterior parameter sample dataset with skyline FBD parameters produced with
combine_log.- variables
Names of FBD rate variables in the log. If NULL (default), will attempt to auto-detect the names and log type.
- log.type
Name of the software which produced the log (currently supported: MrBayes or BEAST2). Has to be set if
variablesis not NULL.
Details
The posterior parameters log files produced by Bayesian evolutionary analyses using skyline birth-death tree models, including the skyline FBD model, result into two or more estimates for each FBD parameter, one for each time bin. This function will convert a table of parameters with skyline FBD parameters from wide to long format, with one row per generation per time bin and a new column "Time_bin" containing the respective time bins as a factor. The long format is necessary for downstream analyses using FBD_summary, FBD_dens_plot, FBD_normality_plot, FBD_tests1, or FBD_tests2, as similarly done by clock_reshape for clock rate tables.
The format of the log files can either be specified using the variables and log.type or auto-detected by the function.
The "posterior" data frame can be obtained by reading in a log file directly (e.g. using the read.table function) or by combining several output log files from Mr. Bayes using combine_log.
Value
A data frame of posterior parameter estimates containing a single "Time_bin" column and one column for each FBD parameter value.
See also
vignette("fbd-params") for the use of this function as part of an analysis pipeline.
Examples
# See vignette("fbd-params") for how to use this
# function as part of an analysis pipeline
data("posterior3p")
head(posterior3p)
#> Gen LnL LnPr TH.all. TL.all. prop_ancfossil.all. sigma.1.
#> 1 8750000 -1449.425 -143.1907 5.271118 11.969460 0 0.07660715
#> 2 8761000 -1458.367 -174.9627 4.775064 11.070210 0 0.05850396
#> 3 8771000 -1449.445 -163.9216 5.927716 12.628460 0 0.05182430
#> 4 8782000 -1453.218 -153.2030 4.451376 9.931809 0 0.14644520
#> 5 8792000 -1461.906 -132.1172 5.095504 11.083810 0 0.14143120
#> 6 8803000 -1452.809 -129.3066 4.715021 10.481830 0 0.10207230
#> sigma.2. sigma.3. m.1. m.2. m.3. net_speciation_1.all.
#> 1 1.33351500 0.8523453 0.3695799 1.544579 1.362332 0.04987983
#> 2 0.06463618 0.1380557 0.5083868 1.495777 1.108471 0.04675159
#> 3 0.67980130 0.7776142 0.4275609 1.569911 1.144364 0.01064803
#> 4 0.65005980 0.2999867 0.6445027 1.329942 1.148377 0.07373453
#> 5 0.52745340 1.3928490 0.4993570 1.368074 1.445410 0.04990040
#> 6 1.31535200 0.7405540 0.4835195 1.359665 1.508596 0.03950198
#> net_speciation_2.all. net_speciation_3.all. net_speciation_4.all.
#> 1 0.030036060 0.009395822 0.02637372
#> 2 0.013372350 0.021293800 0.02126325
#> 3 0.010895640 0.017047410 0.04032594
#> 4 0.007208267 0.021414940 0.03326603
#> 5 0.006333419 0.019637100 0.01893420
#> 6 0.005410397 0.026179850 0.02002429
#> relative_extinction_1.all. relative_extinction_2.all.
#> 1 0.6785586 0.9373640
#> 2 0.9174022 0.9838011
#> 3 0.9677827 0.9857446
#> 4 0.8976315 0.9883790
#> 5 0.7887825 0.9883790
#> 6 0.8675209 0.9851012
#> relative_extinction_3.all. relative_extinction_4.all.
#> 1 0.9555714 0.002227504
#> 2 0.5125231 0.028959450
#> 3 0.9032853 0.012431660
#> 4 0.9464226 0.011271430
#> 5 0.9658652 0.008529459
#> 6 0.9268501 0.026359290
#> relative_fossilization_1.all. relative_fossilization_2.all.
#> 1 0.055629950 0.03741083
#> 2 0.006523517 0.02198622
#> 3 0.010535440 0.02155796
#> 4 0.001264865 0.02106140
#> 5 0.036796000 0.03160199
#> 6 0.006094768 0.04703950
#> relative_fossilization_3.all. relative_fossilization_4.all. tk02var.1.
#> 1 0.020690570 0.0253022700 0.3197728
#> 2 0.034472140 0.0004126629 0.2710006
#> 3 0.073427910 0.0004126629 0.2853423
#> 4 0.014086210 0.0004126629 0.4670378
#> 5 0.006486824 0.0409175900 0.2115789
#> 6 0.008285265 0.0016655860 0.2020097
#> tk02var.2. tk02var.3. clockrate.all.
#> 1 0.3848931 0.2075079 0.01192715
#> 2 0.3609312 0.3622265 0.01086355
#> 3 0.1831945 0.6146289 0.01349259
#> 4 0.3483061 0.4949015 0.01016002
#> 5 0.2723863 0.3463915 0.01160514
#> 6 0.2846277 0.4073166 0.01075419
## Reshape FBD table to long format
posterior3p_long <- FBD_reshape(posterior3p)
head(posterior3p_long)
#> Gen LnL LnPr TH.all. TL.all. prop_ancfossil.all. sigma.1.
#> 1 8750000 -1449.425 -143.1907 5.271118 11.969460 0 0.07660715
#> 2 8761000 -1458.367 -174.9627 4.775064 11.070210 0 0.05850396
#> 3 8771000 -1449.445 -163.9216 5.927716 12.628460 0 0.05182430
#> 4 8782000 -1453.218 -153.2030 4.451376 9.931809 0 0.14644520
#> 5 8792000 -1461.906 -132.1172 5.095504 11.083810 0 0.14143120
#> 6 8803000 -1452.809 -129.3066 4.715021 10.481830 0 0.10207230
#> sigma.2. sigma.3. m.1. m.2. m.3. tk02var.1. tk02var.2.
#> 1 1.33351500 0.8523453 0.3695799 1.544579 1.362332 0.3197728 0.3848931
#> 2 0.06463618 0.1380557 0.5083868 1.495777 1.108471 0.2710006 0.3609312
#> 3 0.67980130 0.7776142 0.4275609 1.569911 1.144364 0.2853423 0.1831945
#> 4 0.65005980 0.2999867 0.6445027 1.329942 1.148377 0.4670378 0.3483061
#> 5 0.52745340 1.3928490 0.4993570 1.368074 1.445410 0.2115789 0.2723863
#> 6 1.31535200 0.7405540 0.4835195 1.359665 1.508596 0.2020097 0.2846277
#> tk02var.3. clockrate.all. Time_bin net_speciation relative_extinction
#> 1 0.2075079 0.01192715 1 0.04987983 0.6785586
#> 2 0.3622265 0.01086355 1 0.04675159 0.9174022
#> 3 0.6146289 0.01349259 1 0.01064803 0.9677827
#> 4 0.4949015 0.01016002 1 0.07373453 0.8976315
#> 5 0.3463915 0.01160514 1 0.04990040 0.7887825
#> 6 0.4073166 0.01075419 1 0.03950198 0.8675209
#> relative_fossilization
#> 1 0.055629950
#> 2 0.006523517
#> 3 0.010535440
#> 4 0.001264865
#> 5 0.036796000
#> 6 0.006094768