Results

Should be

• easy to access (for further processing)
• verifiable
• reproducible

Desired format

library(archivist.github)
archive(survplot, alink = TRUE) # results='asis'

archivist::aread('archivistR/eRum2016/817107d0e62a9500c4ddb1770bd03378')

Desired format

ahistory(BRCA.rnaseq.TP53, format = "kable", alink = TRUE )

head(getTagsRemote("63678e012c5b7f40966c32eec91f828b", tag=""))

[1] "format:rda"                  "name:BRCA.rnaseq"           
[3] "class:data.frame"            "varname:bcr_patient_barcode"
[5] "varname:?|100130426"         "varname:?|100133144"        

asession("63678e012c5b7f40966c32eec91f828b")

package          * version      date       source                          
 archivist        * 2.1          2016-07-27 CRAN (R 3.3.1)                  
 archivist.github * 0.2.2        2016-08-30 CRAN (R 3.3.1)                  
 assertthat         0.1          2013-12-06 CRAN (R 3.3.1)                  
 bitops             1.0-6        2013-08-17 CRAN (R 3.3.1)                  

Problems with reproducibility

The reproducibility is sometimes impossible due to different

improve accessibility

Provide results with unique hooks, so that one can
verify, use and modify them.

install.packages('archivist')

Store results in the repository with their metadata
- searching for objects with specific attributes is possible.

library(archivist)
prod_model <- lm(Sepal.Length ~ ., data = iris)
asave(prod_model, repoDir="eRum2016")

[1] "43c5d536cfb4d46c2862e6f4cb385c27"
attr(,"data")
[1] "f6ba0d40e585d1f9c294069d68f8e01e"

archivist worklfow

add hooks to print

library(survminer) # results='asis'
addHooksToPrint(class="ggsurvplot") 
survplot

Load: archivist::aread('archivistR/eRum2016/817107d0e62a9500c4ddb1770bd03378') Greater example by pbiecek

Objects’ Exploration

lapply(asearch("pbiecek/graphGallery",
               patterns = c("class:lm", "coefname:Sepal.Length")),
       coef)

$`18a98048f0584469483afb65294ce3ed`
 (Intercept) Sepal.Length 
   -7.101443     1.858433 

$`2a6e492cb6982f230e48cf46023e2e4f`
      (Intercept)      Sepal.Length Speciesversicolor  Speciesvirginica 
       -1.7023422         0.6321099         2.2101378         3.0900021 

archivist + shiny

Source: Shiny + archivist = reproducible interactive exploration by pbiecek

cache engine

aread("MarcinKosinski/Museum/c647") -> manyComputations
system.time(cache(FUN = manyComputations, rnorm, 1000,
                  cacheRepo = "eRum2016"))

   user  system elapsed 
  89.753   0.163   89.874 

system.time(cache(FUN = manyComputations, rnorm, 1000,
                  cacheRepo = "eRum2016"))

   user  system elapsed 
  0.019   0.000   0.018 

restoring pedigree

library(RTCGA.rnaseq); data(BRCA.rnaseq)
library(dplyr); library(archivist) #for %a%
BRCA.rnaseq %a%
    select(`TP53|7157`, 
           bcr_patient_barcode) %a%
    rename(TP53 = `TP53|7157`) %a%
    filter(substr(bcr_patient_barcode, 
                  14, 15) == "01" ) -> 
    BRCA.rnaseq.TP53

ahistory(BRCA.rnaseq.TP53)

More Usecases

archivist.github

Thanks for your attention

pbiecek.github.io/archivist/

Remark

Examples would not work without few settings

aoptions("user", "archivistR")
aoptions("repo", "eRum2016")
aoptions("repoDir", "eRum2016")

Source code of a presentation is on this repository.