| Type: | Package |
| Title: | Repeatable Analysis in R |
| Version: | 2.2.1 |
| URL: | https://github.com/johnaponte/repana, https://johnaponte.github.io/repana/ |
| Description: | Set of utilities to facilitate the reproduction of analysis in R. It allow to make_structure(), clean_structure(), and run and log programs in a predefined order to allow secondary files, analysis and reports be constructed in an ordered and reproducible form. |
| License: | GPL (≥ 3) |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.1 |
| Depends: | DBI (≥ 1.0) |
| Suggests: | spelling, testthat, knitr, RSQLite, RPostgres, duckdb, pacman, targets |
| Imports: | config, dplyr, magrittr, lubridate, rmarkdown, processx, readr, rstudioapi, pool, openxlsx, tools, yaml, digest |
| Language: | en-US |
| VignetteBuilder: | knitr |
| BugReports: | https://github.com/johnaponte/repana/issues |
| NeedsCompilation: | no |
| Packaged: | 2025-02-21 20:14:26 UTC; master |
| Author: | John J. Aponte 
[aut, cre] |
| Maintainer: | John J. Aponte <john.j.aponte@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2025-02-21 20:30:05 UTC |
repana: Repeatable Analysis in R
Description
Set of utilities to facilitate the reproduction of analysis in R. It allow to make_structure(), clean_structure(), and run and log programs in a predefined order to allow secondary files, analysis and reports be constructed in an ordered and reproducible form.
Author(s)
Maintainer: John J. Aponte john.j.aponte@gmail.com (ORCID)
See Also
Useful links:
Report bugs at https://github.com/johnaponte/repana/issues
A wrap to writeDataTable
Description
Include a data.frame into a workbook applying a tableStyle and
an auto width to the column. For better results you could setup
options("openxlsx.minWidth" = 6)
Usage
addDataTable(
wb,
df,
sheet,
tableName,
tableStyle = "TableStyleMedium1",
withFilter = TRUE,
firstActiveCol = NULL,
...
)
Arguments
wb |
a workbook object |
df |
a data.frame |
sheet |
the sheet name. If missing the name of the data.frame |
tableName |
a name for the table in the excel document. If missing the name of the data.frame |
tableStyle |
a tableStyle name |
withFilter |
if TRUE the filter is included |
firstActiveCol |
First column active on the the freeze panel |
... |
other parameters for the |
Value
silently the wb
Examples
## Not run:
library(openxlxs)
options("openxlsx.minWidth" = 6)
wb <- createWorkbook(title = "Test addDataTable")
addDataTable(wb,iris)
saveWorkbook(wb, "test_addDataTable.xlsx")
## End(Not run)
Helper function to drop all tables from a database
Description
Helper function to drop all tables from a database
Usage
clean_database(con)
Arguments
con |
DBI connection |
Value
invisible, a lit with result from DBI
Clean the secondary files of the project
Description
Delete and make new database, logs and reports directory
Usage
clean_structure()
Value
Invisible, the directories defined by the clean_before_new_analysis entry in the config.yml file.
Author(s)
John J. Aponte
Get a DBI connection reading a configuration file
Description
This function get a DBI connection to a database reading the parameters from a
config.yml file using the get function.
See the vignette for details.
Usage
get_con(configname = "defaultdb", file = "config.yml")
Arguments
configname |
a string with the name of the configuration |
file |
name of the configuration to read from. |
Value
a DBI connection
Author(s)
John J. Aponte
Get the dirs section of the config.yml file
Description
It is a wrap of config::get("dirs").
Usage
get_dirs(file = "config.yml")
Arguments
file |
by default the |
Value
a list with the directory entries
Get a pool connection reading a configuration file
Description
This function get a pool connection to a database reading the parameters from a
config.yml file using the get function.
See the vignette for details.
Usage
get_pool(configname = "defaultdb", file = "config.yml")
Arguments
configname |
a string with the name of the value |
file |
name of the configuration to read from. |
Value
a dbPool connection object
Author(s)
John J. Aponte
RStudio addin app to insert a template to the heading part of a snip code
Description
RStudio addin app to insert a template to the heading part of a snip code
Usage
insert_template()
Value
The template to insert
Make the structure for a new project
Description
Make the following directories
data to keep the data necessary for the project
database to keep the secondary, modified dataset and objects
handmade to keep reports and dataset modified by hand or not make by the automatic stream
logs to keep logs of the automatic stream
reports to keep the automatic reports
The data, handmade are not clean. The rest are clean as they
should be reproduced by the automatic stream. Do not forget to include them
in .gitignore if you use git
Usage
make_structure()
Value
the dir structure
Author(s)
John J. Aponte
Render programs
Description
By default, all programs with the pattern "nn_" will be executed in order. The 'Start' and 'Stop' parameters can be used to modify the files to start or stop at a different number.
Usage
master(
start = 0,
stop = Inf,
format = "html",
logdir = config::get("dirs")$logs
)
Arguments
start |
program to start |
stop |
program to stop |
format |
Format to render the programs values accepted are "pdf", "html" and "word" |
logdir |
directory to keep the logs of the files. By default
the entry on the |
Details
The files are treated as snip files for rmarkdown and render in the log directory, with the format specified in the format parameter.
The default the log directory is configured in the config.yml file.
Value
a data.frame with the files run, running time and exit status
Runs the programs
Description
Run the programs specified by the pattern, in the order as the pattern select the files. Keep a log of the results. By default the pattern starting with two numbers and ending with .R is selected. They are run in order
Usage
master_txt(
pattern = "^[0-9][0-9].*\\.R$",
start = 1,
stop = Inf,
logdir = config::get("dirs")$logs,
rscript_path
)
Arguments
pattern |
Regular expression to select the files to run |
start |
index of the program to start |
stop |
index of the program to stop |
logdir |
directory to keep the logs of the files. By default |
rscript_path |
path to the |
Details
The program add (or create if not exists) the files run, time of execution and exit status in the file master.log of the directory logs.
WARNING: This is a legacy program. Use master instead.
Value
a data.frame with the files run, running time and exit status
A wrap to render a markdown report
Description
Render the report and copy it to the outputdir directory.
More formats are available but only three are included here
'
Usage
render_report(report, format = "pdf", outputdir = get_dirs()$reports, ...)
Arguments
report |
filename of the report |
format |
output format. "pdf","html","word" are valid entries |
outputdir |
directory to save the report |
... |
other parameters for |
Value
No return value, called for side effects to render the reports
See Also
Examples
## Not run:
render_report(myreport.rmd,"pdf")
## End(Not run)
Create configuration to use targets
Description
Create of they do not exist the following directories
R
dat
out
Usage
targets_structure()
Details
If does not exists, create a simplify version of the _targets.R script,
modify the .gitignore. Also add a config.yml and a _template.txt
files.
Examples
## Not run:
targets_structure()
## End(Not run)
Helper function to include a data.frame in the database and update the log
Description
Helper function to include a data.frame in the database and update the log
Usage
update_table(con, table, source, tablename)
Arguments
con |
DBI connection |
table |
the data.frame to be included in the database |
source |
a manual comment to identify the source of the table |
tablename |
if present, the data frame will be saved with this name. |
Value
the result from DBI
otherwise the name of the data.frame
Make a log of the updates on the database
Description
Make a log of the database updates. If the log table does not exists it creates it Make a new entry with the timestamp of the update
Usage
write_log(con, tablename, source)
Arguments
con |
DBI connection |
tablename |
the name of the table |
source |
a manual comment to identify the source of the table |
Value
the result from DBI