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

0.1.1 Installing R and RStudio

Please download both R and RStudio, links below will direct you to the download page, just selesct the appropriate download for your operating system and follow the instructions given!

0.2 Other places to learn R/RStudio/tidyverse

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/.