Pre-compiled binary packages provide a convenient way of efficiently distributing software that has been adopted by most Linux package management systems. However, the heterogeneity of the Linux ecosystem, combined with the growing number of R extensions available, poses a scalability problem. As a result, efforts to bring binary R packages to Linux have been scattered, and lack a proper mechanism to fully integrate them with R's package manager. This work reviews past and present of binary distribution for Linux, and presents a path forward by showcasing the `cran2copr' project, an RPM-based proof-of-concept implementation of an automated scalable binary distribution system with the capability of building, maintaining and distributing thousands of packages, while providing a portable and extensible bridge to the system package manager.
The increasing availability of cloud computing and scientific super computers brings great potential for making R accessible through public or shared resources. This allows us to efficiently run code requiring lots of cycles and memory, or embed R functionality into, e.g., systems and web services. However some important security concerns need to be addressed before this can be put in production. The prime use case in the design of R has always been a single statistician running R on the local machine through the interactive console. Therefore the execution environment of R is entirely unrestr…
Data depth concept offers a variety of powerful and user friendly tools for robust exploration and inference for multivariate socio-economic phenomena. The offered techniques may be successfully used in cases of lack of our knowledge on parametric models generating data due to their nonparametric nature. This paper presents the R package DepthProc, which is available under GPL-2 licence on CRAN and R-forge servers for Windows, Linux and OS X platform. The package consist of among others successful implementations of several data depth techniques involving multivariate quantile-quantile plots, …
University of Southern California（南加州大学）；University of California, Berkeley（加州大学伯克利分校）
A network embedding consists of a vector representation for each node in the network. Its usefulness has been shown in many real-world application domains, such as social networks and web networks. Directed networks with text associated with each node, such as software package dependency networks, are commonplace. However, to the best of our knowledge, their embeddings have hitherto not been specifically studied. In this paper, we propose PCTADW-1 and PCTADW-2, two algorithms based on neural networks that learn embeddings of directed networks with text associated with each node. We create two …
Ecological processes may exhibit memory to past disturbances affecting the resilience of ecosystems to future disturbance. Understanding the role of ecological memory in shaping ecosystem responses to disturbance under global change is a critical step toward developing effective adaptive management strategies to maintain ecosystem function and biodiversity. We developed EcoMem, an R package for quantifying ecological memory functions using common environmental time series data (continuous, count, proportional) applying a Bayesian hierarchical framework. The package estimates memory functions f…
This report presents the open-source package which implements the series of our boosting works in the past years. In particular, the package includes mainly three lines of techniques, among which the following two are already the standard implementations in popular boosted tree platforms: (i) The histogram-based (feature-binning) approach makes the tree implementation convenient and efficient. In Li et al (2007), a simple fixed-length adaptive binning algorithm was developed. In this report, we demonstrate that such a simple algorithm is still surprisingly effective compared to more sophistica…
We describe the vote package in R, which implements the plurality (or first-past-the-post), two-round runoff, score, approval and single transferable vote (STV) electoral systems, as well as methods for selecting the Condorcet winner and loser. We emphasize the STV system, which we have found to work well in practice for multi-winner elections with small electorates, such as committee and council elections, and the selection of multiple job candidates. For single-winner elections, the STV is also called instant runoff voting (IRV), ranked choice voting (RCV), or the alternative vote (AV) syste…
The use of naturalistic driving studies (NDSs) for driver behavior research has skyrocketed over the past two decades. Intersections are a key target for traffic safety, with up to 25-percent of fatalities and 50-percent injuries from traffic crashes in the United States occurring at intersections. NDSs are increasingly being used to assess driver behavior at intersections and devise strategies to improve intersection safety. A common challenge in NDS intersection research is the need for to combine spatial locations of driver-visited intersections with concurrent video clips of driver traject…
University of Vienna（维也纳大学）；Austrian Research Institute for Artificial Intelligence (OFAI)（奥地利人工智能研究所（OFAI））
This paper introduces scikit-hubness, a Python package for efficient nearest neighbor search in high-dimensional spaces. Hubness is an aspect of the curse of dimensionality, and is known to impair various learning tasks, including classification, clustering, and visualization. scikit-hubness provides algorithms for hubness analysis ("Is my data affected by hubness?"), hubness reduction ("How can we improve neighbor retrieval in high dimensions?"), and approximate neighbor search ("Does it work for large data sets?"). It is integrated into the scikit-learn environment, enabling rapid adoption b…
Researchers are often interested in using longitudinal data to estimate the causal effects of hypothetical time-varying treatment interventions on the mean or risk of a future outcome. Standard regression/conditioning methods for confounding control generally fail to recover causal effects when time-varying confounders are themselves affected by past treatment. In such settings, estimators derived from Robins's g-formula may recover time-varying treatment effects provided sufficient covariates are measured to control confounding by unmeasured risk factors. The package gfoRmula implements in R …
CMHSU: An R Statistical Software Package to Detect Mental Health Status, Substance Use Status, and their Concurrent Status in the North American Healthcare Administrative Databases
This paper discusses about an R package that implements the Pattern Sequence based Forecasting (PSF) algorithm, which was developed for univariate time series forecasting. This algorithm has been successfully applied to many different fields. The PSF algorithm consists of two major parts: clustering and prediction. The clustering part includes selection of the optimum number of clusters. It labels time series data with reference to such clusters. The prediction part includes functions like optimum window size selection for specific patterns and prediction of future values with reference to pas…
It is well known in the literature that the problem of learning the structure of Bayesian networks is very hard to tackle: its computational complexity is super-exponential in the number of nodes in the worst case and polynomial in most real-world scenarios. Efficient implementations of score-based structure learning benefit from past and current research in optimisation theory, which can be adapted to the task by using the network score as the objective function to maximise. This is not true for approaches based on conditional independence tests, called constraint-based learning algorithms. T…
BEND: An R Package for the Bayesian Estimation of Nonlinear Longitudinal Data
Human Resources Research Organization (HumRRO)（人力资源研究组织）；Bloomington Public Schools（布卢明顿公立学校）；Center for Research and Teaching in Economics（经济研究与教学中心）；University of Minnesota（明尼苏达大学）
The CAST package for training and assessment of spatial prediction models in R
Institute of Landscape Ecology（景观生态学研究所）；University of Münster（明斯特大学）；ISGlobal, Barcelona Institute for Global Health（ISGlobal巴塞罗那全球健康研究所）；Universitat Pompeu Fabra（庞培法布拉大学）
University of Tübingen（图宾根大学）；Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）
Because the choice and tuning of the optimizer affects the speed, and ultimately the performance of deep learning, there is significant past and recent research in this area. Yet, perhaps surprisingly, there is no generally agreed-upon protocol for the quantitative and reproducible evaluation of optimization strategies for deep learning. We suggest routines and benchmarks for stochastic optimization, with special focus on the unique aspects of deep learning, such as stochasticity, tunability and generalization. As the primary contribution, we present DeepOBS, a Python package of deep learning …
Latent Gaussian models are an extremely popular, flexible class of models. Bayesian inference for these models is, however, tricky and time consuming. Recently, Rue, Martino and Chopin introduced the Integrated Nested Laplace Approximation (INLA) method for deterministic fast approximate inference. In this paper, we outline the INLA approximation and its related R package. We will discuss the newer components of the r-INLA program as well as some possible extensions.
