cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1006469.v3
title: Peeking Inside the Black Box: Visualizing Statistical Learning With Plots of Individual Conditional Expectation

description: This article presents individual conditional expectation (ICE) plots, a tool for visualizing the model estimated by any supervised learning algorithm. Classical partial dependence plots (PDPs) help visualize the average partial relationship between the predicted response and one or more features. In the presence of substantial interaction effects, the partial response relationship can be heterogeneous. Thus, an average curve, such as the PDP, can obfuscate the complexity of the modeled relationship. Accordingly, ICE plots refine the PDP by graphing the functional relationship between the predicted response and the feature for <i>individual</i> observations. Specifically, ICE plots highlight the variation in the fitted values across the range of a covariate, suggesting where and to what extent heterogeneities might exist. In addition to providing a plotting suite for exploratory analysis, we include a visual test for additive structure in the data-generating model. Through simulated examples and real datasets, we demonstrate how ICE plots can shed light on estimated models in ways PDPs cannot. Procedures outlined are available in the R package ICEbox.
DOI: 10.6084/m9.figshare.1006469.v2
title: Peeking Inside the Black Box: Visualizing Statistical Learning With Plots of Individual Conditional Expectation

description: This article presents individual conditional expectation (ICE) plots, a tool for visualizing the model estimated by any supervised learning algorithm. Classical partial dependence plots (PDPs) help visualize the average partial relationship between the predicted response and one or more features. In the presence of substantial interaction effects, the partial response relationship can be heterogeneous. Thus, an average curve, such as the PDP, can obfuscate the complexity of the modeled relationship. Accordingly, ICE plots refine the PDP by graphing the functional relationship between the predicted response and the feature for <i>individual</i> observations. Specifically, ICE plots highlight the variation in the fitted values across the range of a covariate, suggesting where and to what extent heterogeneities might exist. In addition to providing a plotting suite for exploratory analysis, we include a visual test for additive structure in the data-generating model. Through simulated examples and real datasets, we demonstrate how ICE plots can shed light on estimated models in ways PDPs cannot. Procedures outlined are available in the R package ICEbox.
DOI: 10.6084/m9.figshare.1006465.v2
title: Objective Bayesian Model Selection in Generalized Additive Models With Penalized Splines

description: We propose an objective Bayesian approach to the selection of covariates and their penalized splines transformations in generalized additive models. The methodology is based on a combination of continuous mixtures of <i>g</i>-priors for model parameters and a multiplicity-correction prior for the models themselves. We introduce our approach in the normal model and extend it to nonnormal exponential families. A simulation study and an application with binary outcome is provided. An efficient implementation is available in the R package hypergsplines. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1006466.v1
title: Bayesian Nonparametric Instrumental Variables Regression based on Penalized Splines and Dirichlet Process Mixtures

description: We propose a Bayesian nonparametric instrumental variable approach under additive separability that allows us to correct for endogeneity bias in regression models where the covariate effects enter with unknown functional form. Bias correction relies on a simultaneous equations specification with flexible modeling of the joint error distribution implemented via a Dirichlet process mixture prior. Both the structural and instrumental variable equation are specified in terms of additive predictors comprising penalized splines for nonlinear effects of continuous covariates. Inference is fully Bayesian, employing efficient Markov Chain Monte Carlo simulation techniques. The resulting posterior samples do not only provide us with point estimates, but allow us to construct simultaneous credible bands for the nonparametric effects, including data-driven smoothing parameter selection. In addition, improved robustness properties are achieved due to the flexible error distribution specification. Both these features are challenging in the classical framework, making the Bayesian one advantageous. In simulations, we investigate small sample properties and an investigation of the effect of class size on student performance in Israel provides an illustration of the proposed approach which is implemented in an R package <i>bayesIV</i>.
DOI: 10.6084/m9.figshare.1006465.v1
title: Objective Bayesian Model Selection in Generalised Additive Models with Penalised Splines

description: We propose an objective Bayesian approach to the selection of covariates and their penalised splines transformations in generalised additive models. The methodology is based on a combination of continuous mixtures of <i>g</i>-priors for model parameters and a multiplicity-correction prior for the models themselves. We introduce our approach in the normal model and extend it to non-normal exponential families. A simulation study and an application with binary outcome is provided. An efficient implementation is available in the R-package “hypergsplines”.
DOI: 10.6084/m9.figshare.1006444
title: Chinese sentimental vocabulary by usage frequency

description: Human compiled list of Chinese sentimental vocabulary ordered by usage frequency in Google news.
DOI: 10.6084/m9.figshare.1006466.v2
title: Bayesian Nonparametric Instrumental Variables Regression Based on Penalized Splines and Dirichlet Process Mixtures

description: We propose a Bayesian nonparametric instrumental variable approach under additive separability that allows us to correct for endogeneity bias in regression models where the covariate effects enter with unknown functional form. Bias correction relies on a simultaneous equations specification with flexible modeling of the joint error distribution implemented via a Dirichlet process mixture prior. Both the structural and instrumental variable equation are specified in terms of additive predictors comprising penalized splines for nonlinear effects of continuous covariates. Inference is fully Bayesian, employing efficient Markov chain Monte Carlo simulation techniques. The resulting posterior samples do not only provide us with point estimates, but allow us to construct simultaneous credible bands for the nonparametric effects, including data-driven smoothing parameter selection. In addition, improved robustness properties are achieved due to the flexible error distribution specification. Both these features are challenging in the classical framework, making the Bayesian one advantageous. In simulations, we investigate small sample properties and an investigation of the effect of class size on student performance in Israel provides an illustration of the proposed approach which is implemented in an R package <i>bayesIV</i>. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1006427
title: Evolving topics of articles from Guokr.com

description: This dataset reflect the evolving topics of articles from Guokr.com. The graph file attached is a visulization produced by Gephi.
DOI: 10.6084/m9.figshare.1006444.v1
title: Chinese sentimental vocabularies by usage frequency

description: Human compiled list of Chinese sentimental vocabularies ordered by usage frequency in Google news.
DOI: 10.6084/m9.figshare.1005217
title: Measurement of a drowning incidence rate combining direct observation of an exposed population with mortality statistics

description: Drowning risk factors may be identified by comparing drowning incidence rates for comparable at-risk populations but precise methods are lacking. To address this knowledge gap, an ecological study extrapolated crude time-duration exposure to water for a specified at-risk sample of surf bathers to estimate the bather population for all wave-dominated beaches in Victoria, Australia, over a four-year summer season period. An incidence rate was calculated using surf bather drowning deaths frequencies matched for time and location. For the sample, 47,341 hours of surf bathing were estimated from 177,528 bathing episodes. Generalising these results to Victoria, the crude drowning deaths incidence rate in the summer season was 0.41 per 1,000,000 person-hours of surf bathing (95% CI 0.37–0.45). Further application of the method, particularly in open water settings, may be used to identify candidate drowning risk factors to advance drowning prevention strategies.
DOI: 10.6084/m9.figshare.1005217.v2
title: Measurement of a drowning incidence rate combining direct observation of an exposed population with mortality statistics

description: Drowning risk factors may be identified by comparing drowning incidence rates for comparable at-risk populations but precise methods are lacking. To address this knowledge gap, an ecological study extrapolated crude time-duration exposure to water for a specified at-risk sample of surf bathers to estimate the bather population for all wave-dominated beaches in Victoria, Australia, over a four-year summer season period. An incidence rate was calculated using surf bather drowning deaths frequencies matched for time and location. For the sample, 47,341 hours of surf bathing were estimated from 177,528 bathing episodes. Generalising these results to Victoria, the crude drowning deaths incidence rate in the summer season was 0.41 per 1,000,000 person-hours of surf bathing (95% CI 0.37–0.45). Further application of the method, particularly in open water settings, may be used to identify candidate drowning risk factors to advance drowning prevention strategies.
DOI: 10.6084/m9.figshare.1005217.v1
title: Measurement of a drowning incidence rate combining direct observation of an exposed population with mortality statistics

description: Drowning risk factors may be identified by comparing drowning incidence rates for comparable at-risk populations but precise methods are lacking. To address this knowledge gap, an ecological study extrapolated crude time-duration exposure to water for a specified at-risk sample of surf bathers to estimate the bather population for all wave-dominated beaches in Victoria, Australia, over a four-year summer season period. An incidence rate was calculated using surf bather drowning deaths frequencies matched for time and location. For the sample, 47,341 hours of surf bathing were estimated from 177,528 bathing episodes. Generalising these results to Victoria, the crude drowning deaths incidence rate in the summer season was 0.41 per 1,000,000 person-hours of surf bathing (95% CI 0.37–0.45). Further application of the method, particularly in open water settings, may be used to identify candidate drowning risk factors to advance drowning prevention strategies.
DOI: 10.6084/m9.figshare.1005159
title: Materials and Methods - Peptide-independent stabilization of MHC class I molecules breaches cellular quality control

description: Materials and Methods for the manuscript: <strong>Peptide-independent stabilization of MHC class I molecules breaches cellular quality</strong> <strong>control</strong> by Hein Z, Uchtenhagen H, Abualrous ET, Saini SK, Janßen L, Van Hateren A, Wiek C, Hanenberg H, Momburg F, Achour A, Elliott T, Springer S, Boulanger D. <em>J. Cell Sci. </em>(2014), in press.
DOI: 10.6084/m9.figshare.1005159.v1
title: Materials and Methods - Peptide-independent stabilization of MHC class I molecules breaches cellular quality control

description: Materials and Methods for the manuscript: <strong>Peptide-independent stabilization of MHC class I molecules breaches cellular quality</strong> <strong>control</strong> by Hein Z, Uchtenhagen H, Abualrous ET, Saini SK, Janßen L, Van Hateren A, Wiek C, Hanenberg H, Momburg F, Achour A, Elliott T, Springer S, Boulanger D. <em>J. Cell Sci. </em>(2014), in press.
DOI: 10.6084/m9.figshare.1005090
title: Urbanization bias I. Is it a negligible problem for global temperature estimates? - Supplementary Information

description: Supplementary information dataset for the following article: R. Connolly and M. Connolly (2014). <em>Urbanization bias I. Is it a negligible problem for global temperature estimates?</em> Open Peer Rev. J., 34 (Clim. Sci.), ver 0.1 (non peer-reviewed draft) <strong>Abstract of article</strong> Several studies have claimed that the warming bias introduced to global temperature estimates by urbanization bias is negligible. On the basis of this claim, none of the groups calculating global temperature estimates (except for NASA Goddard Institute for Space Studies) correct for urbanization bias. However, in this article, by re-evaluating these studies individually, it was found that there was no justification for this. There is considerable evidence that there has been global warming since the late 1970s. The urbanization bias problem is sometimes incorrectly framed as being a question of whether there has recently been global warming or not. However, the recent warming appears to have followed a period of global cooling from an earlier warm period which ended in the 1940s. So, resolving the urbanization bias problem is necessary to address issues such as how the recent warm period compared to the early 20th century warm period. If the earlier warm period was comparable to the recent warm period, then claims that recent global temperature trends are unprecedented or unusual will need to be re-evaluated.
DOI: 10.6084/m9.figshare.1005085
title: referances for dataset

description: referances for the dataset used in the present meta-analysis.
DOI: 10.6084/m9.figshare.1005085.v1
title: referances for dataset

description: referances for the dataset used in the present meta-analysis.
DOI: 10.6084/m9.figshare.1005076
title: r script

description: r scripts for local adaptation meta-analysis
DOI: 10.6084/m9.figshare.1005076.v1
title: r script

description: r scripts for local adaptation meta-analysis
DOI: 10.6084/m9.figshare.1005052
title: The COST model for calculation of forest operations costs

description: Since the late nineteenth century when high-cost equipment was introduced into forestry there has been a need to calculate the cost of this equipment in more detail with respect to, for example, cost of ownership, cost per hour of production, and cost per production unit. Machine cost calculations have been made using various standard economic methods, where costs have been subdivided into capital costs and operational costs. Because of differences between methods and between national regulations, mainly regarding tax rules and subsidies, international comparisons of machine costs are difficult. To address this, one of the goals of the European Cooperation in Science and Technology (COST) Action FP0902 was to establish a simple format for transparent cost calculations for machines in the forest biomass procurement chain. A working group constructed a Microsoft Excel–based spreadsheet model which is easy to understand and use. Input parameters are easy to obtain or possible to estimate by provided rules of thumb. The model gives users a simultaneous view of the input parameters and the resulting cost outputs. This technical note presents the model, explains how the calculations are made, and provides future users with a guide on how to use the model. Prospective users can view the model in the Supplementary Material linked to this article online.
DOI: 10.6084/m9.figshare.1005052.v1
title: The COST model for calculation of forest operations costs

description: Since the late nineteenth century when high-cost equipment was introduced into forestry there has been a need to calculate the cost of this equipment in more detail with respect to, for example, cost of ownership, cost per hour of production, and cost per production unit. Machine cost calculations have been made using various standard economic methods, where costs have been subdivided into capital costs and operational costs. Because of differences between methods and between national regulations, mainly regarding tax rules and subsidies, international comparisons of machine costs are difficult. To address this, one of the goals of the European Cooperation in Science and Technology (COST) Action FP0902 was to establish a simple format for transparent cost calculations for machines in the forest biomass procurement chain. A working group constructed a Microsoft Excel–based spreadsheet model which is easy to understand and use. Input parameters are easy to obtain or possible to estimate by provided rules of thumb. The model gives users a simultaneous view of the input parameters and the resulting cost outputs. This technical note presents the model, explains how the calculations are made, and provides future users with a guide on how to use the model. Prospective users can view the model in the Supplementary Material linked to this article online.
DOI: 10.6084/m9.figshare.1005041
title: dataset

description: dataset for local adaptation meta-analysis
DOI: 10.6084/m9.figshare.1005041.v1
title: dataset

description: dataset for local adaptation meta-analysis
DOI: 10.6084/m9.figshare.1005040
title: VarScan SNP calling

description: VarScan SNP calling of H. pseudoalbidus isolates, fruiting body and mixed material samples.
DOI: 10.6084/m9.figshare.1005039
title: Read number pre- and post-filtering

description: Read number pre- and post-filtering, G+C content of raw data and percentage of KW1 genome positions covered at a depth of \textgreater 10X
DOI: 10.6084/m9.figshare.1005040.v1
title: VarScan SNP calling

description: VarScan SNP calling of H. pseudoalbidus isolates, fruiting body and mixed material samples.
DOI: 10.6084/m9.figshare.1005038
title: Read Assignments

description: Reads assigned to Helotiales and Viridiplantae in normalised comparison for each sample examined. Total reads and percent of sample are shown.
DOI: 10.6084/m9.figshare.1005036
title: Sequence read and assembly datasets available in OADB.

description: Sequence read and assembly datasets available in OADB.
DOI: 10.6084/m9.figshare.1005038.v1
title: Read Assignments

description: Reads assigned to Helotiales and Viridiplantae in normalised comparison for each sample examined. Total reads and percent of sample are shown.
DOI: 10.6084/m9.figshare.1005035
title: All commits to the OADB GitHub repository

description: All commits to the OADB GitHub repository
DOI: 10.6084/m9.figshare.1005019
title: Enriched GO Terms in H.pseudoalbidus secretome

description: Enriched GO Terms in the secretome relative to the whole genome at Bonferroni corrected p less than 0.05.
DOI: 10.6084/m9.figshare.1005034
title: Assembly annotation statistics

description: Assembly annotation statistics
DOI: 10.6084/m9.figshare.1005035.v1
title: All commits to the OADB GitHub repository

description: All commits to the OADB GitHub repository
DOI: 10.6084/m9.figshare.1005016
title: Haq sea level curve

description: Digitisation of the Haq (http://www.sciencemag.org/content/235/4793/1156) sea level curve derived from the data supplied by the supplementary information in Miller et al 2005 (Science 310, 1293 DOI: 10.1126/science.1116412).
DOI: 10.6084/m9.figshare.1005034.v1
title: Assembly annotation statistics

description: Assembly annotation statistics
DOI: 10.6084/m9.figshare.1005019.v1
title: Enriched GO Terms in H.pseudoalbidus secretome

description: Enriched GO Terms in the secretome relative to the whole genome at Bonferroni corrected p less than 0.05.
DOI: 10.6084/m9.figshare.1004987
title: High frequency of character transformations is phylogenetically structured within the lichenized fungal family Graphidaceae (Ascomycota: Ostropales)

description: ABSTRACTGraphidaceae is a large family of over 2000 predominantly tropical, lichenized fungal species encompassing a remarkable range of morphological and chemical diversity. The majority of species belongs in subfamily Graphidoideae, which also exhibits the greatest amount of variation. Various phenotype characters have traditionally been used for classification at the genus and species levels, but their correlations with phylogenetic clades are poorly known. Using a multilocus approach, we reconstructed a phylogeny for 224 taxa, representing all main genera within subfamily Graphidoideae, and employed ancestral character reconstruction and character transformation analyses to understand the evolution of morphological, anatomical and chemical characters within this group. In addition, we examined the changes of habitat and photobiont types over the phylogeny. For this purpose, we focused on 10 characters, including thallus and ascoma features and chemistry. Since previous studies have shown that results may differ depending on the reconstruction method used, both Maximum-parsimony and Maximum-likelihood approaches were employed and multistate coding of characters was used. We reconstructed the ancestral states for 64 well-supported major clades in the family and found support for the ancestor of Graphidoideae being a tropical species with a trentepohlioid photobiont, apothecioid, solitary ascomata lacking both a columella and lateral paraphyses, and having non-amyloid ascospores. The frequency of transformations of morphological and chemical characters over the phylogeny of Graphidaceae was computed, resulting in a high frequency of reversible transformations for some characters, such as secondary chemistry, whereas other characters, such as photobiont, hymenial persistence or ascoma aggregation, exhibited low frequency of transformations. However, we found that even in the character with the highest number of transformations, secondary chemistry, the shifts were highly structured phylogenetically, suggesting that the evolution of the character, rather than the character state itself, can be used to predict phylogenetic relationships with certain accuracy.
DOI: 10.6084/m9.figshare.1004986
title: Global biostratigraphic comparison and correlation of an early Cisuralian palynoflora from Bolivia

description: This paper presents new data about Early Permian (Cisuralian) strata, palynostratigraphy and absolute dating from the Copacabana Formation in central Bolivia. Recent stratigraphic and palynologic data from marine and transitional rocks at Apillapampa refine the age of Cisuralian palynomorphs in South America. Twelve samples interbedded with five volcanic ashes (processed and productive) yielded 94 palynomorph species arranged in two informal palynoassemblages: the lower assemblage <i>Vittatina costabilis</i> corresponds to one sample near the base of the Copacabana Formation and the upper <i>Lueckisporites virkkiae</i> assemblage occurs in overlying marine and coal-bearing transitional intervals. Ages were also independently refined by a modern review of conodonts, fusulinids, along with those U–Pb radiometric ages (Isotope Dilution Thermal Ionization Mass Spectrometry [ID-TIMS] of zircon-bearing interbedded tuffs). These data suggest that the lower marine member of the Copacabana Formation at this location is Asselian and Sakmarian. <i>Lueckisporites virkkiae</i> is a key species of palynomorph utilised in South American and global Permian biostratigraphic reconstructions. Hence, a thorough global comparison of these palynofloras and correlations is addressed in this contribution, considering first appearances of mainly cosmopolitan diagnostic taxa. Correlations are established with many similar Permian palynofloras, some also constrained with radiometric data, in South America (Brazil, Uruguay and Argentina) and elsewhere.
DOI: 10.6084/m9.figshare.1004988
title: Gaussian Job Archive for C6H10O14P2(4-)

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.