paceR is a collection of functions that make it easy to get data from the University of Calgary's PACE Database into R for further analysis.
To use the tools, you must have access to the PACE Database. If you don't know how to do this, you can ask Fernando, Urs, or John.
To use this package, you first need to install devtools with:
install.packages("devtools")Then, you can install the latest development version of paceR from github:
library(devtools)
devtools::install_github("camposfa/paceR")After you have installed the package once, you can simply load it in the future using:
library(paceR)This package makes heavy use of the data manipulation packages stringr, lubridate, tidyr, and dplyr. If not already installed, plhdbR will install these packages automatically. It also provides a convenient function to load them all into your R session, if you want to use them for other tasks:
load_pace_packages()To get data from PACE, you must create an SSH tunnel. If you have set up your SSH key, you can do it like this (but modify for your connection):
system('ssh -f [email protected] -L 3307:localhost:3306 -N')
pace_db <- src_mysql(group = "PACE", user = "camposf", dbname = "monkey", password = NULL)Now we can pull data out.
# Get the full individuals table
get_individuals(pace_db)
#> Source: local data frame [2,223 x 16]
#>
#> IndividualID ProjectName PrimateSpecies NameOf CodeName DateOfBirth
#> 1 1 Santa Rosa CCAP 2Tufts 2TUF 1988-01-01
#> 2 2 Santa Rosa CCAP A-1 A-1- NA
#> 3 3 Santa Rosa CCAP Abu ABU- 2005-04-25
#> 4 6 Santa Rosa CCAP Al AL-- 1985-01-01
#> 5 7 Santa Rosa CCAP Alfredo ALFR NA
#> 6 8 Santa Rosa CCAP Alien ALIE 1996-01-02
#> 7 9 Santa Rosa CCAP Amy AMY- 1989-01-01
#> 8 10 Santa Rosa CCAP Amy96 AM96 1996-01-01
#> 9 11 Santa Rosa CCAP Babaganouj BABA 1992-01-01
#> 10 12 Santa Rosa CCAP BabyFace BABY 1991-01-01
#> .. ... ... ... ... ... ...
#> Variables not shown: BirthdateSource (chr), Sex (chr), Mother (chr),
#> MatrilineID (int), GroupAtBirth (chr), DateOfFirstSighting (chr),
#> DayDifference (int), AgeClassAtFirstSighting (chr), GroupAtFirstSighting
#> (chr), VisionPhenotype (chr)
# Get a condensed version
get_individuals(pace_db, full = FALSE)
#> Source: local data frame [2,223 x 6]
#>
#> IndividualID NameOf ProjectName DateOfBirth Sex Mother
#> 1 1 2Tufts Santa Rosa 1988-01-01 F NA
#> 2 2 A-1 Santa Rosa NA M NA
#> 3 3 Abu Santa Rosa 2005-04-25 F Timone
#> 4 6 Al Santa Rosa 1985-01-01 M NA
#> 5 7 Alfredo Santa Rosa NA M NA
#> 6 8 Alien Santa Rosa 1996-01-02 M KathyLee
#> 7 9 Amy Santa Rosa 1989-01-01 F NA
#> 8 10 Amy96 Santa Rosa 1996-01-01 U Amy
#> 9 11 Babaganouj Santa Rosa 1992-01-01 M NA
#> 10 12 BabyFace Santa Rosa 1991-01-01 M NA
#> .. ... ... ... ... ... ...
# Get any table from PACE without warning messages
# Note that foreign key IDs aren't set!!
get_pace_tbl(pace_db, "tblIndividualDeath")
#> Source: local data frame [1,055 x 7]
#>
#> ID IndividualID DateOfDeath CauseOfDeathID SourceOfInformation
#> 1 1 1 1997-03-15 5 NA
#> 2 2 2 2004-02-13 5 NA
#> 3 3 6 1997-02-28 5 NA
#> 4 4 8 2004-02-20 5 NA
#> 5 5 9 1997-02-24 5 NA
#> 6 6 10 1997-01-28 5 NA
#> 7 7 12 1997-03-15 5 NA
#> 8 8 15 2000-05-23 5 NA
#> 9 9 16 1997-03-15 5 NA
#> 10 10 17 1989-04-18 5 NA
#> .. .. ... ... ... ...
#> Variables not shown: DateOfDeathFromCensus (chr), Comments (chr)