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Register a new userrstap: An R Package for Spatial Temporal Aggregated Predictor Models
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Added by
Adam Peterson
Publication date
2018
fields
Mathematical Statistics
and research's language is
English
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The rstap package implements Bayesian spatial temporal aggregated predictor models in R using the probabilistic programming language Stan. A variety of distributions and link functions are supported, allowing users to fit this extension to the generalized linear model with both independent and correlated outcomes.
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We propose the spatial-temporal aggregated predictor (STAP) modeling framework to address measurement and estimation issues that arise when assessing the relationship between built environment features (BEF) and health outcomes. Many BEFs can be mapped as point locations and thus traditional exposure metrics are based on the number of features within a pre-specified spatial unit. The size of the spatial unit--or spatial scale--that is most appropriate for a particular health outcome is unknown and its choice inextricably impacts the estimated health effect. A related issue is the lack of knowledge of the temporal scale--or the length of exposure time that is necessary for the BEF to render its full effect on the health outcome. The proposed STAP model enables investigators to estimate both the spatial and temporal scales for a given BEF in a data-driven fashion, thereby providing a flexible solution for measuring the relationship between outcomes and spatial proximity to point-referenced exposures. Simulation studies verify the validity of our method for estimating the scales as well as the association between availability of BEFs and health outcomes. We apply this method to estimate the spatial-temporal association between supermarkets and BMI using data from the Multi-Ethnic Atherosclerosis Study, demonstrating the methods applicability in cohort studies.
FRK is an R software package for spatial/spatio-temporal modelling and prediction with large datasets. It facilitates optimal spatial prediction (kriging) on the most commonly used manifolds (in Euclidean space and on the surface of the sphere), for both spatial and spatio-temporal fields. It differs from many of the packages for spatial modelling and prediction by avoiding stationary and isotropic covariance and variogram models, instead constructing a spatial random effects (SRE) model on a fine-resolution discretised spatial domain. The discrete element is known as a basic areal unit (BAU), whose introduction in the software leads to several practical advantages. The software can be used to (i) integrate multiple observations with different supports with relative ease; (ii) obtain exact predictions at millions of prediction locations (without conditional simulation); and (iii) distinguish between measurement error and fine-scale variation at the resolution of the BAU, thereby allowing for reliable uncertainty quantification. The temporal component is included by adding another dimension. A key component of the SRE model is the specification of spatial or spatio-temporal basis functions; in the package, they can be generated automatically or by the user. The package also offers automatic BAU construction, an expectation-maximisation (EM) algorithm for parameter estimation, and functionality for prediction over any user-specified polygons or BAUs. Use of the package is illustrated on several spatial and spatio-temporal datasets, and its predictions and the model it implements are extensively compared to others commonly used for spatial prediction and modelling.
R package krippendorffsalpha provides tools for measuring agreement using Krippendorffs Alpha coefficient, a well-known nonparametric measure of agreement (also called inter-rater reliability and various other names). This article first develops Krippendorffs Alpha in a natural way, and situates Alpha among statistical procedures. Then the usage of package krippendorffsalpha is illustrated via analyses of two datasets, the latter of which was collected during an imaging study of hip cartilage. The package permits users to apply the Alpha methodology using built-in distance functions for the nominal, ordinal, interval, or ratio levels of measurement. User-defined distance functions are also supported. The fitting function can accommodate any number of units, any number of coders, and missingness. Bootstrap inference is supported, and the bootstrap computation can be carried out in parallel.
The multivariate Bayesian structural time series (MBSTS) model citep{qiu2018multivariate,Jammalamadaka2019Predicting} as a generalized version of many structural time series models, deals with inference and prediction for multiple correlated time series, where one also has the choice of using a different candidate pool of contemporaneous predictors for each target series. The MBSTS model has wide applications and is ideal for feature selection, time series forecasting, nowcasting, inferring causal impact, and others. This paper demonstrates how to use the R package pkg{mbsts} for MBSTS modeling, establishing a bridge between user-friendly and developer-friendly functions in package and the corresponding methodology. A simulated dataset and object-oriented functions in the pkg{mbsts} package are explained in the way that enables users to flexibly add or deduct some components, as well as to simplify or complicate some settings.
Vector Auto-Regressive (VAR) models capture lead-lag temporal dynamics of multivariate time series data. They have been widely used in macroeconomics, financial econometrics, neuroscience and functional genomics. In many applications, the data exhibit structural changes in their autoregressive dynamics, which correspond to changes in the transition matrices of the VAR model that specify such dynamics. We present the R package VARDetect that implements two classes of algorithms to detect multiple change points in piecewise stationary VAR models. The first exhibits sublinear computational complexity in the number of time points and is best suited for structured sparse models, while the second exhibits linear time complexity and is designed for models whose transition matrices are assumed to have a low rank plus sparse decomposition. The package also has functions to generate data from the various variants of VAR models discussed, which is useful in simulation studies, as well as to visualize the results through network layouts.
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