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DAISIEmainland: Simulating and analysing macroevolution on islands with a dynamic mainland

A Data standards

A.1 Reasoning

There are several data types used in this package. Some of them are novel to this package and are not used elsewhere, others derive from other R packages. This document provides a standard of how the data types are formatted and which functions allow for checking the types.

To make sure the data types are correctly formatted there is a corresponding check_* function for each.

A.2 Data structure types

A.2.1 daisie_mainland_data

A list of 2 elements, $ideal_multi_daisie_data and $empirical_multi_daisie_data. Each of these elements is in the format multi_daisie_data (see below). This is the output of DAISIEmainland::sim_island_with_mainland().

Function to check if the object is daisie_mainland_data is DAISIEmainland::check_daisie_mainland_data()

A.2.2 multi_daisie_data

A list of daisie_data elements (see below). This is the data structure when the simulation is run for several replicates.

The function to check if the object is multi_daisie_data is DAISIEmainland::check_multi_daisie_data().

A.2.3 daisie_data

  • A list of n elements. The first element is a list containing the island_age with a single numeric, and the number of species not_present on the island. This first element in the daisie_data list can optionally include an stt_table. The stt_table is a matrix with five columns and a variable number of rows. Every subsequent element in the daisie_data list is data on an island clade, containing: branching_times, stac, missing_species, and optionally information on recolonisations all_colonisations. branching_times is a numeric vector containing the island age, time of island colonisation, and an subsequent branching times (all given in time before the present).

daisie_data is a single element of a multi_daisie_data list.

The function to check if the object is daisie_data is DAISIEmainland::check_daisie_data().

A.2.4 multi_mainland_clade

A list of mainland_clade objects. This data type is output from DAISIEmainland::sim_mainland().

The function to check if the object is a multi_mainland_clade is DAISIEmainland::check_multi_mainland_clade().

A.2.5 mainland_clade

A data frame of seven columns and one or more rows. The column names are: spec_id, main_anc_id, spec_type, branch_code, branch_t, spec_origin_t, spec_ex_t. A example of an mainland_clade can be created using DAISIEmainland::create_test_mainland_clade().

The function to check if the object is a mainland_clade is DAISIEmainland::check_mainland_clade()

A.2.6 island_tbl

The function to check if the object is an island_tbl is DAISIEmainland::check_island_tbl().