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Replace packrat with renv

pull/95/head
JulioV 2020-05-01 19:46:04 -04:00
parent 07fe3e10af
commit f0674122ff
27 changed files with 850 additions and 933 deletions
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2
.gitignore vendored
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@ -108,3 +108,5 @@ reports/
.RData .RData
.Rhistory .Rhistory
sn_profile_*/ sn_profile_*/
renv/

10
.travis.yml
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@ -20,9 +20,11 @@ install:
- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml - conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml
- conda activate test-environment - conda activate test-environment
before_script: before_script:
- snakemake packrat_install # Install renv and library
- snakemake packrat_init - snakemake renv_install
- snakemake packrat_restore - snakemake renv_init
- snakemake renv_restore
script: script:
- cp -r tests/data/raw/* data/raw - cp -r tests/data/raw/* data/raw
- snakemake --profile tests/settings -R sms_features - snakemake --profile tests/settings -R sms_features
@ -40,4 +42,4 @@ notifications:
cache: cache:
directories: directories:
- /usr/local/lib/R - /usr/local/lib/R

2
Snakefile
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@ -1,5 +1,5 @@
configfile: "config.yaml" configfile: "config.yaml"
include: "rules/packrat.snakefile" include: "rules/renv.snakefile"
include: "rules/preprocessing.snakefile" include: "rules/preprocessing.snakefile"
include: "rules/features.snakefile" include: "rules/features.snakefile"
include: "rules/models.snakefile" include: "rules/models.snakefile"

889
packrat/packrat.lock
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@ -1,889 +0,0 @@
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19
packrat/packrat.opts
View File

@ -1,19 +0,0 @@
auto.snapshot: FALSE
use.cache: FALSE
print.banner.on.startup: auto
vcs.ignore.lib: TRUE
vcs.ignore.src: FALSE
external.packages:
local.repos:
load.external.packages.on.startup: TRUE
ignored.packages:
ignored.directories:
data
inst
quiet.package.installation: TRUE
snapshot.recommended.packages: TRUE
snapshot.fields:
Imports
Depends
LinkingTo
symlink.system.packages: TRUE

793
renv.lock 100644
View File

@ -0,0 +1,793 @@
{
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{
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}
]
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"testthat": {
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"withr": {
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}
}
}

19
rules/renv.snakefile 100644
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@ -0,0 +1,19 @@
## renv_install: installs renv onto machine
rule renv_install:
shell:
"R -e 'install.packages(\"renv\", repos=\"http://cran.us.r-project.org\")'"
## renv_install: initialize a renv environment for this project
rule renv_init:
shell:
"R -e 'renv::init()'"
## renv_snap : Look for new R packages in files & archives them
rule renv_snap:
shell:
"R -e 'renv::snapshot()'"
## renv_restore: Installs archived packages onto a new machine
rule renv_restore:
shell:
"R -e 'renv::restore()'"

2
src/data/application_genres.R
View File

@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library(tidyr) library(tidyr)
library(dplyr) library(dplyr)

2
src/data/download_dataset.R
View File

@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library(RMySQL) library(RMySQL)
library(stringr) library(stringr)

2
src/data/download_participants.R
View File

@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library(RMySQL) library(RMySQL)

2
src/data/phone_sensed_bins.R
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@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library(dplyr) library(dplyr)
library(tidyr) library(tidyr)

2
src/data/phone_valid_sensed_days.R
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@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library(dplyr) library(dplyr)

2
src/data/readable_datetime.R
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@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library("tidyverse") library("tidyverse")
library(readr) library(readr)

2
src/data/resample_fused_location.R
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@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library(dplyr) library(dplyr)
library(readr) library(readr)

2
src/data/unify_ios_android.R
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@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library(dplyr) library(dplyr)
library(stringr) library(stringr)

2
src/features/activity_recognition_deltas.R
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@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library("tidyverse") library("tidyverse")

2
src/features/battery_deltas.R
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@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library("tidyverse") library("tidyverse")

2
src/features/bluetooth_features.R
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@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library(dplyr) library(dplyr)
library(tidyr) library(tidyr)

2
src/features/call_features.R
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@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library(dplyr) library(dplyr)
library(entropy) library(entropy)

2
src/features/location_barnett_features.R
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@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library(dplyr) library(dplyr)

2
src/features/screen_deltas.R
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@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library(dplyr) library(dplyr)
library(tidyr) library(tidyr)

2
src/features/sms_features.R
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@ -1,7 +1,7 @@
# If you want to implement extra features, source(..) a new file and duplicate the line "features <- merge(...)", then # If you want to implement extra features, source(..) a new file and duplicate the line "features <- merge(...)", then
# swap base_sms_features(...) for your own function # swap base_sms_features(...) for your own function
source("packrat/init.R") source("renv/activate.R")
source("src/features/sms/sms_base.R") source("src/features/sms/sms_base.R")
library(dplyr, warn.conflicts = FALSE) library(dplyr, warn.conflicts = FALSE)

2
src/features/wifi_features.R
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@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library(dplyr) library(dplyr)

2
src/models/clean_features_for_model.R
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@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library(tidyr) library(tidyr)
library(dplyr) library(dplyr)

11
src/models/merge_features_for_individual_model.R
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@ -1,8 +1,17 @@
source("packrat/init.R") source("renv/activate.R")
library(tidyr) library(tidyr)
library(purrr) library(purrr)
library(dplyr) library(dplyr)
library("methods")
library("mgm")
library("qgraph")
library("dplyr")
library("scales")
library("ggplot2")
library("purrr")
library("tidyr")
library("reshape2")
feature_files <- snakemake@input[["feature_files"]] feature_files <- snakemake@input[["feature_files"]]
phone_valid_sensed_days <- snakemake@input[["phone_valid_sensed_days"]] phone_valid_sensed_days <- snakemake@input[["phone_valid_sensed_days"]]

2
src/models/merge_features_for_population_model.R
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@ -1,4 +1,4 @@
source("packrat/init.R") source("renv/activate.R")
library(tidyr) library(tidyr)
library(purrr) library(purrr)

2
src/visualization/compliance_report.Rmd
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@ -18,7 +18,7 @@ output:
--- ---
```{r include=FALSE} ```{r include=FALSE}
source("packrat/init.R") source("renv/activate.R")
``` ```
## Overall phone compliance ## Overall phone compliance