The associated file is the code for the time-based version of the model, when conditioning on both the minimum and maximum number of species in the final simulated clade (MinMax variation). The model was written in R. The instructions for this model are identical to those for the Speciation-based code. However, parameter values (particularly starting rates and rate increment values, see below for explanation) will be different in time-dependent and speciation-dependent models. Parameter values must be input in the initial block of code by replacing the example numbers with numbers from the current data set. ÒminextantÓ is the minimum number of species allowed in each simulated clade and ÒmaxextantÓ is the maximum number of species; simulated clades with diversities outside these brackets will not be counted or recorded. ÒtmaxÓ is the number of time-steps over which each simulation will run; this should be proportional the the absolute age of each clade. ÒpcaxesÓ is the number of principle components axes to be simulated. ÒlambdaÓ is a vector of the eigenvalues associated with the number of axes used in Òpcaxes.Ó Òr0Ó is the starting point for the morphological change rate, and ÒpÓ is the starting value for the speciation rate. ÒqÓ should be specified as a percentage of p on the next line. ÒqpercentÓ is the ratio of q/p to allow the calculation of changing values of q as p increases. The code will increase the rates for each successive set of simulations, so these should be set based on the minimum bound of rates. NOTE: The morphological change and turnover rates increase the first time BEFORE any simulations are run, so the initial values for r and p should be the desired minimum values minus the increment of increase (described below). NOTE: By changing the value of q to 0, a Pure-Birth model variation may be examined. ÒrparameterincrementnumberÓ is the number of different values for the morphological change rate that will be explored during the set of simulations and ÒrparameterincrementÓ is the value by which the morphological change rate will increase with each successive iteration. Similarly, ÒpqparameterincrementnumberÓ is the number of different values of turnover rates to be explored and ÒpqparameterincrementÓ is the value by which origination rate will increase with each set of simulations. Finally, ÒnrepÓ is the number of simulations to be run at each combination of r, p, and q values, and Òn0Ó is the starting diversity for each simulation (typically 1). The final change that needs to be made is in the last line of the code. Type the desired name of the file in which output will be stored between the quotation marks (file = Òinsert file name hereÓ). Once all parameter values have been set, run the code in R.