DOI: 10.5061/dryad.cnp5hqcgj
title: Data from: Navigating “tip fog”: Embracing uncertainty in tip measurements

description: Nature is full of messy variation, which serves as the raw material for
 evolution. Overlooking this variation not only weakens our analyses but
 also risks selecting inaccurate models, generating false precision in
 parameter estimates, and creating artificial patterns. Furthermore, the
 complexity of uncertainty extends beyond traditional “measurement error,”
 encompassing various sources of variance. To address this, we propose the
 term “tip fog” to describe the variance between the value from the overall
 modeled evolutionary process and what is recorded, without implying a
 specific mechanism. We show why accounting for tip fog remains critical by
 showing its impact on continuous comparative models and discrete
 comparative and diversification models. We rederive methods to estimate
 this variance and use simulations to assess its feasibility and importance
 in a comparative context. Our findings reveal that ignoring tip fog
 substantially affects the accuracy of rate estimates, with higher tip fog
 levels showing greater biases from the true rates, as well as affecting
 which models are chosen. The findings underscore the importance of model
 selection and the potential consequences of neglecting tip fog, providing
 insights for improving the accuracy of comparative methods in evolutionary
 biology.
description: ## Data from: Navigating “tip fog”: Embracing uncertainty in tip
 measurements "Tip fog" is our term for what used to be called
 measurement error. Take a concrete example: squid tentacle length, for
 which we want to use the average value per species. There are factors that
 lead to the given value (10.42 cm) for a species differing from the
 "truth" * Sample variation: we measured only three squids in a
 species, not every individual. * Measurement uncertainty: even if we
 measured every squid, tentacles are stretchy, so we can't know its
 true length to the micron. * Pure error: someone measured in inches not
 centimeters for one of the three measured specimens * Intraspecific
 variation: individuals differ in size In past code, we've called this
 all "measurement error" (or its less melodious name, `mserr`)
 but they're distinct factors. One could call them "noise"
 but there's often a contrast between "noise" and
 "signal" but some of these have signal for important processes
 (especially things like intraspecific variation). Thus we needed a new
 term. "tip fog" it is. ## Code: Each folder contains code used
 to conduct all analyses presented in the paper. All that is required is
 that R is installed.  ### corHMM\_sims This directory provides the code
 used to conduct and summarize our simulations and analysis of discrete
 character evolution with and without tip fog. The R packages `corHMM` ,
 `TreeSim`, `parallel`, `magittr`, `tidyverse`, and `viridis` are required
 to run these scripts. 1. sim.tree.Rsave -- provides the tree used to
 generate patterns of discrete evolution 2. CorHMMFogSim.R -- is the script
 used to run the simulations. This script will generate files with a unique
 prefix. For example, `CorHMMSim_0.15.rep1.Rsave` indicates that a tip fog
 value of 15% was used and this was the first replicate. All simulation
 files used in our paper are provided in the `simReps` directory.  3.
 simSumCorHMMFog.R -- is the script used to summarize the simulations in
 various ways. The files `CorHMM_sim.raw_results.Rsave`  and
  `CorHMM_simARD.raw_results.Rsave` were generated from this script. ###
 HiSSE\_sims This directory provides the code used to conduct and summarize
 our simulations and analysis of trait dependent diversification with and
 without tip fog. The R packages `hisse` , `diversitree`, `parallel`,
 `magittr`, `tidyverse`, and `viridis` are required to run these scripts.
 1. sim.tree2.hisse.Rsave -- the set of trees used to generate patterns of
 character dependent diversification.  2. HiSSEFogSim.R -- is the script
 used to run the simulations. This script will generate files with a unique
 prefix. For example, `HiSSESim_0.22.042.0.1.1.Rsave` indicates that a
 speciation rate of 0.22 for state 0, a speciation rate of 0.42, tip fog
 value of 10% was used, and this was the first replicate. All simulation
 files used in our paper are provided in the `simReps` directory.  3.
 simSumHiSSEFog.R -- is the script used to summarize the simulations in
 various ways. The file `HiSSE_sim.raw_results.Rsave` was generated from
 this script. ### OUwie\_sims This directory provides the code used to
 conduct and summarize our simulations and analysis of continuous trait
 evolution with and without tip fog. The R packages `OUwie`, `TreeSim`,
 `corHMM`, `parallel`, `magittr`, `tidyverse`, `dentist`, and `viridis` are
 required to run these scripts. 1. sim.tree.dat.base.Rsave -- the tree that
 contains the regime mapping used to simulation a continuous character. 2.
  sim.tree.dat.base.means.Rsave -- a pectinate trees that contains the
 regime mapping used to simulation a continuous character assuming only
 differences in the optima among regimes. 3. OUFogSim3P_take2.R -- is the
 script used to run the simulations and analyze them. This script will
 generate files with a unique prefix. For example,
 `BMS_3P_sim.0.1_1.25_1.rep1.Rsave` indicates that a Brownian motion model
 assuming different rates per regime, the three-point algorithm was used to
 estimates model parameters, a tip fog value of 10% was used, and 1.25x
 difference in rate between regime 1 and 2 was used for the first
 replicate. All simulation files used in our paper are provided in the
 `simReps` directory.  4. simSumOUwieFog.R -- is the script used to
 summarize the simulations in various ways. The
 files` BMS_sim.raw_results_updated.Rsave`,`
 OUM_sim.raw_results_updated.Rsave`, and `OUMV_sim.raw_results_updated.Rsave` were generated from this script. We also used this script to generate two likelihood surface analyses using the package `dentist`:  `OUM_f01.Rsave` and `OUM_f20.Rsave`.