Chapter 2 Installing the software you need
You need R (>=3.6) and we strongly recommend RStudio as an IDE.
If you’re not sure which version of R you’re running, try
R.version## _
## platform x86_64-apple-darwin17.0
## arch x86_64
## os darwin17.0
## system x86_64, darwin17.0
## status
## major 4
## minor 1.0
## year 2021
## month 05
## day 18
## svn rev 80317
## language R
## version.string R version 4.1.0 (2021-05-18)
## nickname Camp PontanezenIf that gives you an error, you likely have an older version, but this should work.
sessionInfo()## R version 4.1.0 (2021-05-18)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 11.4
##
## Matrix products: default
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] astrochron_1.0 ggthemes_4.2.4 readr_2.0.1 purrr_0.3.4 egg_0.4.5 gridExtra_2.3 magrittr_2.0.1
## [8] ggplot2_3.3.5 dplyr_1.0.7 geoChronR_1.1.0 lipdR_0.3.0 bookdown_0.22
##
## loaded via a namespace (and not attached):
## [1] backports_1.2.1 spam_2.7-0 Hmisc_4.5-0 plyr_1.8.6 sp_1.4-5
## [6] splines_4.1.0 dplR_1.7.2 digest_0.6.27 arsenal_3.6.3 foreach_1.5.1
## [11] htmltools_0.5.1.1 viridis_0.6.1 fansi_0.5.0 checkmate_2.0.0 tensor_1.5
## [16] cluster_2.1.2 doParallel_1.0.16 tzdb_0.1.2 remotes_2.4.2 matrixStats_0.59.0
## [21] vroom_1.5.4 R.utils_2.10.1 lomb_2.0 spatstat.sparse_2.0-0 prettyunits_1.1.1
## [26] jpeg_0.1-8.1 colorspace_2.0-2 signal_0.7-7 xfun_0.24 callr_3.7.0
## [31] crayon_1.4.1 jsonlite_1.7.2 spatstat.data_2.1-0 survival_3.2-11 iterators_1.0.13
## [36] glue_1.4.2 polyclip_1.10-0 gtable_0.3.0 pkgbuild_1.2.0 IDPmisc_1.1.20
## [41] BiocGenerics_0.38.0 maps_3.3.0 abind_1.4-5 scales_1.1.1 DBI_1.1.1
## [46] Rcpp_1.0.7 viridisLite_0.4.0 multitaper_1.0-15 htmlTable_2.2.1 spatstat.core_2.2-0
## [51] bit_4.0.4 foreign_0.8-81 mapproj_1.2.7 dotCall64_1.0-1 Formula_1.2-4
## [56] htmlwidgets_1.5.3 httr_1.4.2 RColorBrewer_1.1-2 ellipsis_0.3.2 pkgconfig_2.0.3
## [61] XML_3.99-0.6 R.methodsS3_1.8.1 farver_2.1.0 nnet_7.3-16 sass_0.4.0
## [66] deldir_0.2-10 utf8_1.2.1 tidyselect_1.1.1 labeling_0.4.2 rlang_0.4.11
## [71] reshape2_1.4.4 munsell_0.5.0 tools_4.1.0 cli_3.0.0 generics_0.1.0
## [76] ggmap_3.0.0.903 ggridges_0.5.3 evaluate_0.14 stringr_1.4.0 yaml_2.2.1
## [81] goftest_1.2-2 bit64_4.0.5 processx_3.5.2 knitr_1.33 IntCal_0.2.0
## [86] RgoogleMaps_1.4.5.3 pbapply_1.4-3 nlme_3.1-152 R.oo_1.24.0 compiler_4.1.0
## [91] rstudioapi_0.13 curl_4.3.2 png_0.1-7 rbacon_2.5.6 spatstat.utils_2.2-0
## [96] tibble_3.1.2 tweenr_1.0.2 bslib_0.2.5.1 stringi_1.6.2 highr_0.9
## [101] ps_1.6.0 fields_12.5 lattice_0.20-44 Matrix_1.4-0 vctrs_0.3.8
## [106] rEDM_1.9.0 pillar_1.6.1 lifecycle_1.0.0 BiocManager_1.30.16 spatstat.geom_2.2-2
## [111] jquerylib_0.1.4 data.table_1.14.0 bitops_1.0-7 R6_2.5.0 latticeExtra_0.6-29
## [116] pcaMethods_1.84.0 codetools_0.2-18 MASS_7.3-54 assertthat_0.2.1 Bchron_4.7.6
## [121] withr_2.4.2 mgcv_1.8-35 parallel_4.1.0 hms_1.1.0 grid_4.1.0
## [126] rpart_4.1-15 tidyr_1.1.3 coda_0.19-4 rmarkdown_2.9 nuspectral_1.0
## [131] ggforce_0.3.3 Biobase_2.52.0 oxcAAR_1.1.1 base64enc_0.1-32.1 Installing lipdR
The lipdR package is your gateway to working with LiPD data. To install lipdR, you’ll need the remotes package if you don’t already have it.
install.packages("remotes")
remotes::install_github("nickmckay/lipdR")2.2 Installing geoChronR
Finally, you can install geoChronR using a similar command:
remotes::install_github("nickmckay/GeoChronR")This should also install all the dependencies you need. geoChronR is built on top of a large collection of other packages, which means it can take a while to install, but also it means that changes to those packages sometimes causes errors in geoChronR. If you get an error during installation, please report it here, and we’ll fix it as soon as possible.