List of R packages
This book would of course not have been possible without the free availability of R (R Core Team, 2018) and some excellent packages. The book itself was compiled using knitr v1.20 (Xie, 2015) while running R v3.4.4. All other R packages that were at some point used throughout the book, together with a brief description of how they were used, are listed below.
| Package | Reference | How used |
|---|---|---|
| animation v2.5 | Xie (2013) | spatio-temporal visualizations |
| ape v5.1 | Paradis et al. (2004) | Moran’s \(I\) tests in space and space-time using Moran.I |
| broom v0.5.0 | Robinson & Hayes (2018) | casting the summary outputs of tests into data frames using tidy |
| CCA v1.2 | González & Déjean (2012) | canonical correlation analysis of spatio-temporal data using cancor |
| devtools v1.13.6 | Wickham & Chang (2017) | installing STRbook |
| dplyr v0.7.6 | Wickham et al. (2017) | data-wrangling spatio-temporal data - in particular filtering, sorting, selecting variables and creating new variables |
| EFDR v0.1.1 | Zammit-Mangion & Huang (2015) | carrying out field significance tests with EFDR |
| expm v0.999-2 | Goulet et al. (2017) | raising matrices to a power using %^% |
| fields v9.6 | Nychka et al. (2015) | computing distances using rdist and plotting using image.show |
| FRK v0.2.2 | Zammit-Mangion (2018a) | modeling spatio-temporal data with spatio-temporal basis functions |
| ggplot2 v3.0.0 | Wickham (2016) | visualizing data by plotting facets of line, contour, or raster plots |
| ggmap v2.6.1 | Kahle & Wickham (2013) | plotting of regional maps |
| ggquiver v0.1.0 | O’Hara-Wild (2017) | visualizing directional data with quivers |
| gridExtra v2.3 | Auguie (2016) | arranging ggplot2 plots into a grid using grid.arrange or arrangeGrob |
| gstat v1.1-6 | Gräler et al. (2016) | inverse distance weighting, fitting spatio-temporal semivariograms, and spatio-temporal kriging |
| IDE v0.2.0 | Zammit-Mangion (2018b) | modeling spatio-temporal data with integro-difference-equation models |
| INLA v18.07.12 | Lindgren & Rue (2015) | modeling non-Gaussian spatio-temporal data with a separable model |
| lattice v0.20-35 | Sarkar (2008) | surface plots using wireframe |
| leaps v3.0 | Lumley (2017) | stepwise regression using regsubsets |
| lmtest v0.9-36 | Zeileis & Hothorn (2002) | Durbin–Watson tests using dwtest |
| maps v3.3.0 | Becker & Wilks (2017) | reading in state boundaries for plotting using map_data |
| maptools v0.9-3 | R. Bivand & Lewin-Koh (2017) | reading in data from shapefiles using readShapePoly |
| Matrix v1.2-14 | Bates & Maechler (2017) | handling objects of class Matrix |
| mgcv v1.8-23 | Wood (2017) | modeling non-Gaussian spatio-temporal data using generalized additive models using gamm |
| nlme v3.1-131 | Pinheiro et al. (2017) | fitting linear models with correlated error using gls |
| plyr v1.8.4 | Wickham (2011) | filling in missing columns during row binding using rbind.fill |
| purrr v0.2.5 | Henry & Wickham (2017) | carrying out tests on groups of data using map |
| RColorBrewer v1.1-2 | Neuwirth (2014) | generating a color palette using brewer.pal |
| scoringRules v0.9.5 | Jordan et al. (2017) | multivariate probabilistic validation using es_sample and vs_sample |
| sp v1.3-1 | R. S. Bivand et al. (2013) | creating and handling spatial objects such as SpatialPoints or SpatialPolygons |
| spacetime v1.2-2 | Pebesma (2012) | creating and handling spatio-temporal objects such as STIDF or STFDF |
| SpatialVx v0.6-3 | Gilleland (2018) | field-matching methods for assessing predictions |
| SpatioTemporal v1.1.7 | Lindstrom et al. (2013) | modeling spatio-temporal data with temporal basis functions |
| SpecsVerification v0.5-2 | Siegert (2017) | plotting verification rank histograms |
| stargazer v5.2.2 | Hlavac (2015) | generating ~tables from the results of standard tests |
| STRbook v0.1.0 | Zammit-Mangion (2018c) | companion package for this book, containing several data sets and helper functions. Needs to be installed using devtools through install_github("andrewzm/STRbook") |
| tidyr v0.8.1 | Wickham & Henry (2017) | data-wrangling spatio-temporal data - in particular, going from space-wide or time-wide to long formats, and nesting and unnesting data frames |
| verification v1.42 | NCAR – Research Applications Laboratory (2015) | probabilistic validation using the continuous ranked probability score with the function crps |
| xtable v1.8-2 | Dahl (2016) | generating ~tables from data frames |