# Arni Magnusson

#### 19 packages on CRAN

Interface between the GMT map-making software and R, enabling the user to manipulate geographic data within R and call GMT commands to draw and annotate maps in postscript format. The 'gmt' package is about interactive data analysis, rapidly visualizing subsets and summaries of geographic data, while performing statistical analysis in the R console.

Import, plot, and diagnose results from statistical catch-at-age models, used in fisheries stock assessment.

Functions to support the ICES Transparent Assessment Framework <http://taf.ices.dk> to organize data, methods, and results used in ICES assessments. ICES is an organization facilitating international collaboration in marine science.

Markov chain Monte Carlo diagnostic plots. The purpose of the package is to combine existing tools from the 'coda' and 'lattice' packages, and make it easy to adjust graphical details.

Plot stacked areas and confidence bands as filled polygons, or add polygons to existing plots. A variety of input formats are supported, including vectors, matrices, data frames, formulas, etc.

Easy-to-use functions to explore Oracle databases and import data into R. User interface for the ROracle package.

Various R programming tools for data manipulation, including: - medical unit conversions ('ConvertMedUnits', 'MedUnits'), - combining objects ('bindData', 'cbindX', 'combine', 'interleave'), - character vector operations ('centerText', 'startsWith', 'trim'), - factor manipulation ('levels', 'reorder.factor', 'mapLevels'), - obtaining information about R objects ('object.size', 'elem', 'env', 'humanReadable', 'is.what', 'll', 'keep', 'ls.funs', 'Args','nPairs', 'nobs'), - manipulating MS-Excel formatted files ('read.xls', 'installXLSXsupport', 'sheetCount', 'xlsFormats'), - generating fixed-width format files ('write.fwf'), - extricating components of date & time objects ('getYear', 'getMonth', 'getDay', 'getHour', 'getMin', 'getSec'), - operations on columns of data frames ('matchcols', 'rename.vars'), - matrix operations ('unmatrix', 'upperTriangle', 'lowerTriangle'), - operations on vectors ('case', 'unknownToNA', 'duplicated2', 'trimSum'), - operations on data frames ('frameApply', 'wideByFactor'), - value of last evaluated expression ('ans'), and - wrapper for 'sample' that ensures consistent behavior for both scalar and vector arguments ('resample').

Provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.

Various R programming tools for plotting data, including: - calculating and plotting locally smoothed summary function as ('bandplot', 'wapply'), - enhanced versions of standard plots ('barplot2', 'boxplot2', 'heatmap.2', 'smartlegend'), - manipulating colors ('col2hex', 'colorpanel', 'redgreen', 'greenred', 'bluered', 'redblue', 'rich.colors'), - calculating and plotting two-dimensional data summaries ('ci2d', 'hist2d'), - enhanced regression diagnostic plots ('lmplot2', 'residplot'), - formula-enabled interface to 'stats::lowess' function ('lowess'), - displaying textual data in plots ('textplot', 'sinkplot'), - plotting a matrix where each cell contains a dot whose size reflects the relative magnitude of the elements ('balloonplot'), - plotting "Venn" diagrams ('venn'), - displaying Open-Office style plots ('ooplot'), - plotting multiple data on same region, with separate axes ('overplot'), - plotting means and confidence intervals ('plotCI', 'plotmeans'), - spacing points in an x-y plot so they don't overlap ('space').

A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.

With this tool, a user should be able to quickly implement complex random effect models through simple C++ templates. The package combines 'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain an efficient implementation of the applied Laplace approximation with exact derivatives. Key features are: Automatic sparseness detection, parallelism through 'BLAS' and parallel user templates.

Fit linear and generalized linear mixed models with various extensions, including zero-inflation. The models are fitted using maximum likelihood estimation via 'TMB' (Template Model Builder). Random effects are assumed to be Gaussian on the scale of the linear predictor and are integrated out using the Laplace approximation. Gradients are calculated using automatic differentiation.

This package provides generic functions to analyze the distribution of two continuous variables: 'conf2d' to calculate a smooth empirical confidence region, and 'freq2d' to calculate a frequency distribution.

R interface to access the web services of the ICES (International Council for the Exploration of the Sea) DATRAS trawl survey database <https://datras.ices.dk/WebServices/Webservices.aspx>.

R interface to access the RECO POX web services of the ICES (International Council for the Exploration of the Sea) Vocabularies database <http://vocab.ices.dk/services/POX.aspx>.

R interface to access the web services of the ICES Stock Assessment Graphs database <http://sg.ices.dk>.

Used by Hafro staff to draw maps showing the distribution of fishing intensity and catches, and of survey data for Icelandic fish stocks. Potentially useful for others.