R for Paleolimnology
Brent Thorne and Dewey Dunnington
2018-05-24
Introduction
This is the website for the “R for Paleolimnology” workshop given at the Quebec-Ontario Paleolimnology Symposium (PALS) 2018. Here you will find an expanded version of the given workshop where you will learn how to conduct data science in R with an emphasis on Paleolimnology. You will learn and be able to work on a wide variety of skill sets in R including: how to get your data into R, how to structure your data, how to transform your data, and most importantly, how to visualize your paleolimnological data! By the end of this book we hope that you can take your passion for Paleolimnology and make data analysis enjoyable! No really, it can be enjoyable once you develop these skillsets!
0.1 Prerequisites
R, RStudio, tidyverse
0.2 Other places to learn R/RStudio/tidyverse
- The book “R for Data Science” (Grolemund and Wickham 2017) (free online version at http://r4ds.had.co.nz/index.html)
- The Introduction to the tidyverse Data Camp course by David Robinson.
- tidyverse, visualization, and manipulation basics tutorial from Garrett Grolemund
0.3 Colophon
This course material was written using the bookdown package inside RStudio. Pages were built using Travis CI, pandoc and gitbook. The source is available on github.
These tutorials were built with:
## Session info -------------------------------------------------------------
## setting value
## version R version 3.5.0 (2017-01-27)
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## tz UTC
## date 2018-05-24
## Packages -----------------------------------------------------------------
## package * version date source
## assertthat 0.2.0 2017-04-11 cran (@0.2.0)
## backports 1.1.2 2017-12-13 cran (@1.1.2)
## base64enc 0.1-3 2015-07-28 cran (@0.1-3)
## BH 1.66.0-1 2018-02-13 cran (@1.66.0-)
## bindr 0.1.1 2018-03-13 cran (@0.1.1)
## bindrcpp 0.2.2 2018-03-29 cran (@0.2.2)
## broom 0.4.4 2018-03-29 cran (@0.4.4)
## callr 2.0.3 2018-04-11 cran (@2.0.3)
## cellranger 1.1.0 2016-07-27 cran (@1.1.0)
## cli 1.0.0 2017-11-05 cran (@1.0.0)
## colorspace 1.3-2 2016-12-14 cran (@1.3-2)
## compiler 3.5.0 2018-04-23 local
## crayon 1.3.4 2017-09-16 cran (@1.3.4)
## curl 3.2 2018-03-28 CRAN (R 3.5.0)
## DBI 0.8 2018-03-02 cran (@0.8)
## dbplyr 1.2.1 2018-02-19 cran (@1.2.1)
## debugme 1.1.0 2017-10-22 cran (@1.1.0)
## dichromat 2.0-0 2013-01-24 cran (@2.0-0)
## digest 0.6.15 2018-01-28 CRAN (R 3.5.0)
## dplyr 0.7.4 2017-09-28 cran (@0.7.4)
## evaluate 0.10.1 2017-06-24 cran (@0.10.1)
## forcats 0.3.0 2018-02-19 cran (@0.3.0)
## foreign 0.8-70 2017-11-28 CRAN (R 3.5.0)
## ggplot2 2.2.1 2016-12-30 cran (@2.2.1)
## glue 1.2.0 2017-10-29 cran (@1.2.0)
## graphics * 3.5.0 2018-04-23 local
## grDevices * 3.5.0 2018-04-23 local
## grid 3.5.0 2018-04-23 local
## gtable 0.2.0 2016-02-26 cran (@0.2.0)
## haven 1.1.1 2018-01-18 cran (@1.1.1)
## highr 0.6 2016-05-09 cran (@0.6)
## hms 0.4.2 2018-03-10 cran (@0.4.2)
## htmltools 0.3.6 2017-04-28 cran (@0.3.6)
## httr 1.3.1 2017-08-20 CRAN (R 3.5.0)
## jsonlite 1.5 2017-06-01 CRAN (R 3.5.0)
## knitr 1.20 2018-02-20 cran (@1.20)
## labeling 0.3 2014-08-23 cran (@0.3)
## lattice 0.20-35 2017-03-25 CRAN (R 3.5.0)
## lazyeval 0.2.1 2017-10-29 cran (@0.2.1)
## lubridate 1.7.4 2018-04-11 cran (@1.7.4)
## magrittr 1.5 2014-11-22 cran (@1.5)
## markdown 0.8 2017-04-20 cran (@0.8)
## MASS 7.3-49 2018-02-23 CRAN (R 3.5.0)
## methods * 3.5.0 2018-04-23 local
## mime 0.5 2016-07-07 CRAN (R 3.5.0)
## mnormt 1.5-5 2016-10-15 cran (@1.5-5)
## modelr 0.1.1 2017-07-24 cran (@0.1.1)
## munsell 0.4.3 2016-02-13 cran (@0.4.3)
## nlme 3.1-137 2018-04-07 CRAN (R 3.5.0)
## openssl 1.0.1 2018-03-03 CRAN (R 3.5.0)
## parallel 3.5.0 2018-04-23 local
## pillar 1.2.2 2018-04-26 cran (@1.2.2)
## pkgconfig 2.0.1 2017-03-21 cran (@2.0.1)
## plogr 0.2.0 2018-03-25 cran (@0.2.0)
## plyr 1.8.4 2016-06-08 cran (@1.8.4)
## praise 1.0.0 2015-08-11 cran (@1.0.0)
## psych 1.8.3.3 2018-03-30 cran (@1.8.3.3)
## purrr 0.2.4 2017-10-18 cran (@0.2.4)
## R6 2.2.2 2017-06-17 CRAN (R 3.5.0)
## RColorBrewer 1.1-2 2014-12-07 cran (@1.1-2)
## Rcpp 0.12.16 2018-03-13 cran (@0.12.16)
## readr 1.1.1 2017-05-16 cran (@1.1.1)
## readxl 1.1.0 2018-04-20 cran (@1.1.0)
## rematch 1.0.1 2016-04-21 cran (@1.0.1)
## reprex 0.1.2 2018-01-26 cran (@0.1.2)
## reshape2 1.4.3 2017-12-11 cran (@1.4.3)
## rlang 0.2.0 2018-02-20 cran (@0.2.0)
## rmarkdown 1.9 2018-03-01 cran (@1.9)
## rprojroot 1.3-2 2018-01-03 cran (@1.3-2)
## rstudioapi 0.7 2017-09-07 CRAN (R 3.5.0)
## rvest 0.3.2 2016-06-17 cran (@0.3.2)
## scales 0.5.0 2017-08-24 cran (@0.5.0)
## selectr 0.4-1 2018-04-06 cran (@0.4-1)
## stats * 3.5.0 2018-04-23 local
## stringi 1.1.7 2018-03-12 cran (@1.1.7)
## stringr 1.3.0 2018-02-19 cran (@1.3.0)
## testthat 2.0.0 2017-12-13 cran (@2.0.0)
## tibble 1.4.2 2018-01-22 cran (@1.4.2)
## tidyr 0.8.0 2018-01-29 cran (@0.8.0)
## tidyselect 0.2.4 2018-02-26 cran (@0.2.4)
## tidyverse 1.2.1 2017-11-14 cran (@1.2.1)
## tools 3.5.0 2018-04-23 local
## utf8 1.1.3 2018-01-03 cran (@1.1.3)
## utils * 3.5.0 2018-04-23 local
## viridisLite 0.3.0 2018-02-01 cran (@0.3.0)
## whisker 0.3-2 2013-04-28 CRAN (R 3.5.0)
## withr 2.1.2 2018-03-15 CRAN (R 3.5.0)
## xml2 1.2.0 2018-01-24 cran (@1.2.0)
## yaml 2.1.19 2018-05-01 cran (@2.1.19)
References
Grolemund, Garrett, and Hadley Wickham. 2017. R for Data Science. New York: O’Reily. http://r4ds.had.co.nz/.