Should be
library(archivist.github)
archive(survplot, alink = TRUE) # results='asis'
archivist::aread('archivistR/eRum2016/817107d0e62a9500c4ddb1770bd03378')
ahistory(BRCA.rnaseq.TP53, format = "kable", alink = TRUE )
call | md5hash | |
---|---|---|
4 | BRCA.rnaseq | 63678e012c5b7f40966c32eec91f828b |
3 | select(TP53|7157 , bcr_patient_barcode) |
4a85ce61229dd743b911d7edab0310b3 |
2 | rename(TP53 = TP53|7157 ) |
103f2b82c41956e9f6437b3a0cd68679 |
1 | filter(substr(bcr_patient_barcode, 14, 15) == “01”) | 1da5a026aae19e0d0467ba3773679e28 |
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)
The reproducibility is sometimes impossible due to different
or due to the
Can’t install git2r nor devtools R packages on centOS 7.0 64 bit
pandoc version 1.12.3 or higher is required and was not found (R shiny)
rmarkdown::render freezes because pandoc freezes when LC_ALL and LANG are unset
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"
library(survminer) # results='asis'
addHooksToPrint(class="ggsurvplot")
survplot
Load: archivist::aread('archivistR/eRum2016/817107d0e62a9500c4ddb1770bd03378')
Greater example by pbiecek
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
Source: Shiny + archivist = reproducible interactive exploration by pbiecek
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
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)
call | md5hash | |
---|---|---|
4 | BRCA.rnaseq | 63678e012c5b7f40966c32eec91f828b |
3 | select(TP53|7157 , bcr_patient_barcode) |
4a85ce61229dd743b911d7edab0310b3 |
2 | rename(TP53 = TP53|7157 ) |
103f2b82c41956e9f6437b3a0cd68679 |
1 | filter(substr(bcr_patient_barcode, 14, 15) == “01”) | 1da5a026aae19e0d0467ba3773679e28 |
The list of blog-posts and conference talks about archivist
archivist.github
: R Hero saves Backup City with archivist and GitHub (Marcin Kosiński)archivist.github
CRAN Publication, Tools for Archiving, Managing and Sharing R Objects via GitHubExamples would not work without few settings
aoptions("user", "archivistR")
aoptions("repo", "eRum2016")
aoptions("repoDir", "eRum2016")
Source code of a presentation is on this repository.