A topical approach to retrievability bias estimation

Retrievability is an independent evaluation measure that offers insights to an aspect of retrieval systems that performance and efficiency measures do not. Retrievability is often used to calculate the retrievability bias, an indication of how accessible a system makes all the documents in a collection. Generally, computing the retrievability bias of a system requires a colossal number of queries to be issued for the system to gain an accurate estimate of the bias. However, it is often the case that the accuracy of the estimate is not of importance, but the relationship between the estimate of bias and performance when tuning a systems parameters. As such, reaching a stable estimation of bias for the system is more important than getting very accurate retrievability scores for individual documents. This work explores the idea of using topical subsets of the collection for query generation and bias estimation to form a local estimate of bias which correlates with the global estimate of retrievability bias. By using topical subsets, it would be possible to reduce the volume of queries required to reach an accurate estimate of retrievability bias, reducing the time and resources required to perform a retrievability analysis. Findings suggest that this is a viable approach to estimating retrievability bias and that the number of queries required can be reduced to less than a quarter of what was previously thought necessary

Maximum clade credibility tree of NDus

This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the node dating analysis using 12 fossils (based on an uniform density prior), resulting from the beast2 analysis using the NDus.xml input-file

Data from: Fossils matter: improved estimates of divergence times in Pinus reveal older diversification

Background: The taxonomy of pines (genus Pinus) is widely accepted and a robust gene tree based on entire plastome sequences exists. However, there is a large discrepancy in estimated divergence times of major pine clades among existing studies, mainly due to differences in fossil placement and dating methods used. We currently lack a dated molecular phylogeny that makes use of the rich pine fossil record, and this study is the first to estimate the divergence dates of pines based on a large number of fossils (21) evenly distributed across all major clades, in combination with applying both node and tip dating methods. Results: We present a range of molecular phylogenetic trees of Pinus generated within a Bayesian framework. We find the origin of pines is likely up to 30 Myr older (Early Cretaceous) than inferred in most previous studies (Late Cretaceous) and propose generally older divergence times for major clades within Pinus than previously thought. Our age estimates vary significantly between the different dating approaches, but the results generally agree on older divergence times. We present a revised list of 21 fossils that are suitable to use in dating or comparative analyses of pines. Conclusions: Reliable estimates of divergence times in pines are essential if we are to link diversification processes and functional adaptation of this genus to geological events or to changing climates. In addition to older divergence times in Pinus, our results also indicate that node age estimates in pines depend on dating approaches and the specific fossil sets used, reflecting inherent differences in various dating approaches. The sets of dated phylogenetic trees of pines presented here provide a way to account for uncertainties in age estimations when applying comparative phylogenetic methods

Input file for FBDs analysis

This is the XML file which configures all parameters for the BEAST program for the Bayesian MCMC analysis using the fossilized birth-death dating approach including 14 fossils (FBDs). The file was generated in BEAUti 2.3.1

Subsample of trees from FBDl analysis

This is a set of 1401 subsampled random trees from the posterior distribution of the fossilized birth-death analysis using 21 fossils (see FBDl.xml file for detailed settings of the Bayesian analysis)

Input file for NDus analysis

This is the XML file which configures all parameters for the beast2 program for the Bayesian MCMC analysis using the node dating approach including 12 fossils and an uniform calibration prior (NDus). The file was generated in BEAUti 2.3.1

Subsample of trees from FBDs analysis

This is a set of 1401 subsampled random trees from the posterior distribution of the fossilized birth-death analysis using 14 fossils (see FBDs.xml file for detailed settings of the Bayesian analysis)

Subsample of trees from NDul analysis

This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis using 15 fossils and an uniform calibration prior (see NDul.xml file for detailed settings of the Bayesian analysis)

Ambtenarenzakboekje

This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis (with narrow calibration densities) using 12 fossils (see NDns.xml file for detailed settings of the Bayesian analysis)

Maximum clade credibility tree of NDul

This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the node dating analysis using 15 fossils (based on an uniform density prior), resulting from the beast2 analysis using the NDul.xml input-file