Chaining

The archivist package is very efficient and advantageous when archived artifacts were created with a chaining code offered by the magrittr package. It is higly useful because the origin of the artifact is archived, which means that the artifact can be easly reproduced and it’s origin code is stored for future use.

Below are examples of creating artifacts with a chaining code, that requires using a %>% and a %.% operators, offered by the magrittr and the dplyr package.

Since the version 1.5 of the magrittr package has changed functionality of a mentioned pipe operator %>%, we copied (in version 1.3 of the archivist) functionality from version 1.0.1 and added old operator to the archivist package as %a% operator.

Let us prepare a Repository where archived artifacts will be stored.

library(archivist)
exampleRepoDir <- getwd()
createLocalRepo(exampleRepoDir, default = TRUE)

Chaining code

Then one might create artifacts like those below. The code lines are ordered in chaining code, which will be used by the asave function to store an artifact and archive it’s origin code as a name of this artifact.

# example 1
library(dplyr)

data("hflights", package = "hflights")
hflights %a%
   group_by(Year, Month, DayofMonth) %a%
   select(Year:DayofMonth, ArrDelay, DepDelay) %a%
   summarise(
      arr = mean(ArrDelay, na.rm = TRUE),
      dep = mean(DepDelay, na.rm = TRUE)
   ) %a%
   filter(arr > 30 | dep > 30) -> example1

One may see a vast difference in code evalution when using chaining code. Here is an example of a traditional R call and one that uses the chaining code philosophy.

# example 2
library(Lahman)

# Traditional R code
players <- group_by(Batting, playerID)
games <- summarise(players, total = sum(G))
head(arrange(games, desc(total)), 5)

Source: local data frame [5 x 2]

   playerID total
      (chr) (int)
1  rosepe01  3562
2 yastrca01  3308
3 aaronha01  3298
4 henderi01  3081
5  cobbty01  3035

# Corresponding chaining code
Batting %a%
   group_by(playerID) %a%
   summarise(total = sum(G)) %a%
   arrange(desc(total)) %a%
   head(5) %a%
   asave( repoDir = exampleRepoDir )

[1] "b5ba48251904ce231c382594cdc75bb2"

setLocalRepo

To simplify the code one can set globally the path to Repository using code as below. Now one no longer need to specify the repoDir parameter with every call.

setLocalRepo( exampleRepoDir )

Archiving artifacts

Many of various operations can be performed on a single data.frame before one consideres to archive these artifacts. Archivist guarantees that all of them will be archived, which means a code alone will no longer be needed to be stored in a separate file. Also an artifact may be saved during operations are performed and used in further code evaluations. This can be done when argument in asave is specified.

# example 3
aread('MarcinKosinski/Museum/3374db20ecaf2fa0d070d') -> crime.by.state
crime.by.state %a%
   filter(State=="New York", Year==2005) %a%
   arrange(desc(Count)) %a%
   select(Type.of.Crime, Count) %a%
   mutate(Proportion=Count/sum(Count)) %a%
   asave( exampleRepoDir, value = TRUE) %a%
   group_by(Type.of.Crime) %a%
   summarise(num.types = n(), counts = sum(Count)) %a%
   asave( )

[1] "9a3dd58b75558273c53a441ec823b219"

Dozens of artifacts may now be stored in one Repository. Every artifact may have an additional Tag specified by an user. This will simplify searching for this artifact in the future.

# example 4
library(ggplot2)

diamonds %a% 
   group_by(cut, clarity, color) %a%  
   summarize(
      meancarat = mean(carat, na.rm = TRUE), 
      ndiamonds = length(carat)
   ) %a% 
   head( 10) %a%
   asave(userTags = c("tags", "operations on diamonds"))

[1] "33576ab6aa88e5aedb4887aeffd84fa9"

Restoring origin code - Artifact’s Pedigree

# results = 'asis'
hash2 <- searchInLocalRepo( pattern = "operations on diamonds" )
ahistory(hash2, format = "kable")

	call	md5hash
5	env[[nm]]	926dab1fe6e71b197a17909fcd0e5995
4	group_by(cut, clarity, color)	860466a792815080957a34021d04c5c6
3	summarize(meancarat = mean(carat, na.rm = TRUE), ndiamonds = length(carat))	820c5bf2ce98bbb4b787830fe52d98f3
2	head(10)	33576ab6aa88e5aedb4887aeffd84fa9
1	asave(userTags = c(“tags”, “operations on diamonds”))	434d4891ac1569883f80b2ec9fef0b95