Version: | 0.1.3 |
Title: | Reproducible Research Tools |
Description: | Reproducible research tools automates the creation of an analysis directory structure and work flow. There are R markdown skeletons which encapsulate typical analytic work flow steps. Functions will create appropriate modules which may pass data from one step to another. |
Maintainer: | Brian Fannin <captain@pirategrunt.com> |
URL: | https://pirategrunt.com/represtools/ |
BugReports: | https://github.com/PirateGrunt/represtools/issues |
Depends: | R (≥ 3.2.0) |
License: | GPL (≥ 3) |
SystemRequirements: | GNU make |
LazyData: | true |
Imports: | whisker |
Suggests: | testthat, knitr, rmarkdown |
RoxygenNote: | 6.1.1 |
VignetteBuilder: | knitr |
Encoding: | UTF-8 |
NeedsCompilation: | no |
Packaged: | 2019-10-03 16:19:33 UTC; brian |
Author: | Brian Fannin [aut, cre] |
Repository: | CRAN |
Date/Publication: | 2019-10-03 17:30:03 UTC |
represtools.
Description
represtools.
Create an analysis file
Description
Create an analysis file
Usage
Analyze(fileStem, inputFiles, title)
Arguments
fileStem |
The file stem |
inputFiles |
A vector of files to load |
title |
Title of the document |
Create a cook file
Description
Create a cook file
Usage
Cook(fileStem, inputFiles, title)
Arguments
fileStem |
The file stem |
inputFiles |
A vector of files to load |
title |
Title of the Cook document |
I'm throwing in the towel on this function. I'm just not clear on the behavior that I'd like:
Description
This will apply functions to a vector of objects.
Usage
DescribeObjects(objects, FUNS, env)
Arguments
objects |
A list of objects to be described |
FUNS |
the functions which will describe the objects |
env |
An enviroment. If missing, the global environment will be used. |
Details
1. Given a vector of objects, apply a vector of functions. This is most common when I want to apply both 'str' and 'summary' to a data frame.
2. How is that implemented in practice? I either want the output printed or I want to capture the output to print later, but I'm not sure. The easiest option would be to print everything.
3. And that's what I'll do.
Describe the objects
This may be used to quickly summarize a set of objects. Note that functions are called for their side effects of printing output
x may be given as a character vector or a list.
Examples
## Not run:
myFit1 <- lm(myData, y ~ x1 + x2)
myFit2 <- lm(myData, y ~ x3)
DesribeObjects(list(myFit1, myFit2), broom::tidy)
## End(Not run)
Create a gather file
Description
Create a gather file
Usage
Gather(fileStem, title)
Arguments
fileStem |
The file stem |
title |
Title of the Gather document |
Read a SQL file
Description
Read a SQL file
Usage
GetSQL(filename, warn = FALSE)
Arguments
filename |
A character variable with a filename |
warn |
Warn if there is a missing final end of line. Default is TRUE |
Value
String
List objects
Description
Form a character vector of the names of objects, based on patterns.
Usage
ListObjects(patterns = c("^df", "^plt", "^fit"), env)
Arguments
patterns |
A vector of patterns |
env |
An enviroment. If missing, the global environment will be used. |
Details
This will collect objects based on a vector of character patterns.
Value
character vector
LoadObjects
Description
This function will load a set of objects stored in .rda files. By default, objects are loaded into the Global environment.
Usage
LoadObjects(params, env = .GlobalEnv, loadFiles)
Arguments
params |
A list of parameters. Should include the named items inputDir and inputFiles. |
env |
An environment in which to load objects. Defaults to the global environment. |
loadFiles |
A character vector of files containing saved data. |
Details
The params object is defined within an RMarkdown file and contains named items "inputDir" and "inputFiles". As an expedient, one may pass a vector of filenames. This vector will only be used if the params argument has been omitted.
Value
Character vector containing the names of loaded objects.
Examples
## Not run:
loadedObjects <- LoadObjects(params)
## End(Not run)
Run the make command
Description
This will run the make
program with whatever target the user selects. The default target is "all". The function works by calling
the system2
function. It is presumed that an appropriate make
utilty exists on the user's computer. Further
note that the default makefile for an analysis project uses GNU extensions like wildcards.
Usage
Make(target = "all", command = "", ...)
Arguments
target |
The make target to run |
command |
User-supplied location of the |
... |
Additional arguments to the |
Details
The function will to try to confirm
See Also
Examples
## Not run:
Make()
Make("clean", command = "/usr/bin/gmake")
Make("gather")
Make("MyFile.rda")
## End(Not run)
NamesToObjects
Description
Returns a list of the objects named in x
Usage
NamesToObjects(x, envir)
Arguments
x |
Vector or list of named objects |
envir |
Environment in which to search |
Details
Return a list of named objects
x is given as either a character vector containing names of objects to return, or a list. If x is a list, it will first be converted to character. If objects do not exist, no error or warning will be generated.
Value
A list of objects
Examples
## Not run:
mojo <- 4
gonzo <- "Moe"
lstObjects <- NamesToObjects(c("mojo", "gonzo"))
## End(Not run)
Create a new Research
Description
Create a new Research
Usage
NewResearch(path = ".", RStudio = TRUE, useExistingDirectory = FALSE)
Arguments
path |
A character variable indicating the name of the project to create |
RStudio |
Boolean indicating whether or not to create an RStudio project. Default is TRUE. |
useExistingDirectory |
Overwrite the directory if it already exists. Default is FALSE. |
Value
NewResearch will invisibly return the name of the project.
OutputFile
Description
Construct an output file from a params list.
Usage
OutputFile(params)
Arguments
params |
List object with output directory and file stem elements |
Create a presentation file
Description
Create a presentation file
Usage
Present(fileStem, inputFiles, title, outputFormat)
Arguments
fileStem |
The file stem |
inputFiles |
A vector of files to load |
title |
Title of the document |
outputFormat |
A string indicating the outputFormat |