example.con.txt

# This file demonstrates the format of age constraints used by the script snapp_prep.rb:
# 
# - All lines beginning with # are ignored by snapp_prep.rb, as are empty lines.
# - Lines beginning with "normal", "lognormal", "uniform", "exponential, "or "cladeage"
#   are assumed to specify age constraints. The clades used for these constraints are
#   always also constrained to be monophyletic. Clades can also be constrained to be
#   monophyletic without additional age constraints. These monophyly constraints can be
#   specified with lines starting with "monophyletic".
# - The format for these age constraints consists of three character strings separated
#   by white space (tabs or spaces).
# - The first of these three character strings specifies the prior distribution, where
#   the type of the distribution ("normal", "lognormal", "uniform", "exponential", or
#   "cladeage") is followed by the parameters of the distribution, given in parentheses
#   and separated by commas.
#      For a normal distribution, these parameters are (in this order)
#        (1.)   offset
#        (2.)   mean
#        (3.)   standard deviation
#      For a lognormal distribution, these parameters are
#        (1.)   offset
#        (2.)   mean in real space
#        (3.)   standard deviation (of log-transformed distribution)
#      For a uniform distribution, these parameters are
#        (1.)   lower boundary
#        (2.)   upper boundary
#      For an exponential distribution, these parameters are
#        (1.)   offset
#        (2.)   mean
#      For a cladeage distribution, these parameters are
#        (1.)   minimum estimate of fossil age
#        (2.)   maximum estimate of fossil age
#        (3.)   minimum estimate of net diversification
#        (4.)   maximum estimate of net diversification
#        (5.)   minimum estimate of turnover
#        (6.)   maximum estimate of turnover
#        (7.)   minimum estimate of sampling rate
#        (8.)   maximum estimate of sampling rate
#        See Matschiner et al. (2017; https://doi.org/10.1093/sysbio/syw076) for more
#        information on cladeage constraints.
#   The exception to this are pure monophyly constraints, in which case the first of the
#   three character strings is simply "monophyletic".
# - The second of the three character strings should be either "crown", "stem" or "NA"
#   and specifies whether the age constraint should apply to the crown or stem age of the
#   clade. Note that cladeage constraints always apply to the stem age of a clade. For
#   pure monophyly constraints, only "NA" (not applicable) should be specified as the
#   second character string.
# - The third of the three character strings should be a comma-separated list of all
#   sampled species included the constrained clade.
#
# Examples:
# - normal(10,5,1)	crown	speciesA,speciesB,speciesC
# - lognormal(10,5,1)	stem	speciesA,speciesB,speciesC
# - uniform(10,15)	crown	speciesA,speciesB,speciesC
# - exponential(10,5)	crown speciesA,speciesB,speciesC
# - cladeage(10,11,0.01,0.02,0.2,0.5,0.001,0.01)	stem	speciesA,speciesB,speciesC
# - monophyletic	NA	speciesA,speciesB,speciesC

lognormal(0,7.66172,0.1)	stem	s17,s0
monophyletic	NA	s1,s6,s11,s12,s3