Package 'qcTAF'

Title: TAF Checks
Description: Tools to check TAF analyses.
Authors: Arni Magnusson [aut, cre], Colin Millar [aut]
Maintainer: Arni Magnusson <[email protected]>
License: GPL-3
Version: 2026.05.23
Built: 2026-06-09 03:48:04 UTC
Source: https://github.com/ices-tools-prod/qcTAF

Help Index

TAF Checks

Description

Tools to check TAF analyses.

Details

Quality control:

qc run all quality checks
qc.boot.exists boot directory exists
qc.data.bib.exists ⁠DATA.bib⁠ exists
qc.data.bib.valid ⁠DATA.bib⁠ is valid
qc.data.bib.processed ⁠DATA.bib⁠ processed
qc.data.declared data files are declared
qc.software.bib.exists ⁠SOFTWARE.bib⁠ exists
qc.software.bib.valid ⁠SOFTWARE.bib⁠ is valid
qc.software.bib.processed ⁠SOFTWARE.bib⁠ processed
qc.software.declared software files are declared
qc.initial.data initial data files
qc.only.relative.paths scripts use only relative paths
qc.any.scripts.exist any scripts exist
qc.all.scripts.exist all scripts exist

Author(s)

Arni Magnusson and Colin Millar.

See Also

Useful links:

Quality Check

Description

Run all quality checks for a given analysis.

Usage

qc(analysis = ".")

Arguments

analysis

directory containing a TAF analysis.

Value

Logical vector indicating the result from each test.

See Also

The checks are run in the following order:

dir.exists checks if directory exists.

qc.boot.exists checks if boot directory exists.

qc.data.bib.exists checks if ⁠DATA.bib⁠ exists.

qc.data.bib.valid checks if ⁠DATA.bib⁠ is valid.

qc.data.bib.processed checks if ⁠DATA.bib⁠ entries have been processed.

qc.data.declared checks if data files are declared.

qc.software.bib.exists checks if ⁠SOFTWARE.bib⁠ exists.

qc.software.bib.valid checks if ⁠SOFTWARE.bib⁠ is valid.

qc.software.bib.processed checks if ⁠SOFTWARE.bib⁠ entries have been processed.

qc.data.declared checks if software files are declared.

qc.initial.data checks if initial data files have the same contents as boot data files.

qc.any.scripts.exist checks if any scripts exist.

qc.all.scripts.exist checks if all scripts exist.

qc.only.relative.paths checks if scripts use only relative paths.

qcTAF-package gives an overview of the package.

Examples

## Not run: 
qc("rjm-347d")

## End(Not run)

All Scripts Exist

Description

Check if all TAF scripts (⁠data.R⁠, ⁠model.R⁠, ⁠output.R⁠, and ⁠report.R⁠) exist.

Usage

qc.all.scripts.exist(analysis = ".")

Arguments

analysis

directory containing a TAF analysis.

Value

TRUE if test succeeds, otherwise FALSE.

See Also

qc runs all qc.* tests.

qcTAF-package gives an overview of the package.

Examples

## Not run: 
qc.all.scripts.exist("rjm-347d")

## End(Not run)

Any Scripts Exist

Description

Check if any TAF scripts (⁠data.R⁠, ⁠model.R⁠, ⁠output.R⁠, and ⁠report.R⁠) exist.

Usage

qc.any.scripts.exist(analysis = ".")

Arguments

analysis

directory containing a TAF analysis.

Value

TRUE if test succeeds, otherwise FALSE.

See Also

qc runs all qc.* tests.

qcTAF-package gives an overview of the package.

Examples

## Not run: 
qc.any.scripts.exist("rjm-347d")

## End(Not run)

Boot Directory Exists

Description

Check if a boot directory exists.

Usage

qc.boot.exists(analysis = ".")

Arguments

analysis

directory containing a TAF analysis.

Value

TRUE if test succeeds, otherwise FALSE.

See Also

qc runs all qc.* tests.

qcTAF-package gives an overview of the package.

Examples

## Not run: 
qc.boot.exists("rjm-347d")

## End(Not run)

DATA.bib Exists

Description

Check if a ⁠DATA.bib⁠ file exists.

Usage

qc.data.bib.exists(analysis = ".")

Arguments

analysis

directory containing a TAF analysis.

Value

TRUE if test succeeds, otherwise FALSE.

See Also

qc runs all qc.* tests.

qcTAF-package gives an overview of the package.

Examples

## Not run: 
qc.data.bib.exists("rjm-347d")

## End(Not run)

DATA.bib Processed

Description

Check if a ⁠DATA.bib⁠ entries appear to have been processed, i.e., found as files and directories inside the boot folder.

Usage

qc.data.bib.processed(analysis = ".")

Arguments

analysis

directory containing a TAF analysis.

Value

TRUE if test succeeds, otherwise FALSE.

Note

qc.data.bib.processed checks if all bib entries have made it into the boot data folder: 

DATA.bib | boot/data
---------+----------
    A    |
    B   ==>
    C    |

qc.data.declared checks if all boot data files were declared as bib entries: 

DATA.bib | boot/data
---------+----------
         |    A
        <==   B
         |    C

When used together, those two functions ensure that ⁠DATA.bib⁠ and ⁠boot/data⁠ contain precisely the same entries.

See Also

qc runs all qc.* tests.

qcTAF-package gives an overview of the package.

Examples

## Not run: 
qc.data.bib.processed("rjm-347d")

## End(Not run)

DATA.bib Valid

Description

Check if a ⁠DATA.bib⁠ file is valid.

Usage

qc.data.bib.valid(analysis = ".")

Arguments

analysis

directory containing a TAF analysis.

Value

TRUE if test succeeds, otherwise FALSE.

See Also

qc runs all qc.* tests.

qcTAF-package gives an overview of the package.

Examples

## Not run: 
qc.data.bib.valid("rjm-347d")

## End(Not run)

Data Declared

Description

Check if all files in the boot data folder are declared in the ⁠DATA.bib⁠ file.

Usage

qc.data.declared(analysis = ".")

Arguments

analysis

directory containing a TAF analysis.

Value

TRUE if test succeeds, otherwise FALSE.

Note

qc.data.bib.processed checks if all bib entries have made it into the boot data folder: 

DATA.bib | boot/data
---------+----------
    A    |
    B   ==>
    C    |

qc.data.declared checks if all boot data files were declared as bib entries: 

DATA.bib | boot/data
---------+----------
         |    A
        <==   B
         |    C

When used together, those two functions ensure that ⁠DATA.bib⁠ and ⁠boot/data⁠ contain precisely the same entries.

See Also

qc runs all qc.* tests.

qcTAF-package gives an overview of the package.

Examples

## Not run: 
qc.data.declared("rjm-347d")

## End(Not run)

Initial Data

Description

Check if initial data files have the same contents as boot data files.

Usage

qc.initial.data(analysis = ".")

Arguments

analysis

directory containing a TAF analysis.

Value

TRUE if test succeeds, otherwise FALSE.

See Also

qc runs all qc.* tests.

qcTAF-package gives an overview of the package.

Examples

## Not run: 
qc.initial.data("rjm-347d")

## End(Not run)

Only Relative Paths

Description

Check if scripts (⁠*.R⁠, ⁠*.Rmd⁠, ⁠Rnw⁠, ⁠*.qmd⁠) use only relative paths.

Usage

qc.only.relative.paths(analysis = ".")

Arguments

analysis

directory containing a TAF analysis.

Value

TRUE if test succeeds, otherwise FALSE.

See Also

qc runs all qc.* tests.

qcTAF-package gives an overview of the package.

Examples

## Not run: 
qc.only.relative.paths("rjm-347d")

## End(Not run)

SOFTWARE.bib Exists

Description

Check if a ⁠SOFTWARE.bib⁠ file exists.

Usage

qc.software.bib.exists(analysis = ".")

Arguments

analysis

directory containing a TAF analysis.

Value

TRUE if test succeeds, otherwise FALSE.

See Also

qc runs all qc.* tests.

qcTAF-package gives an overview of the package.

Examples

## Not run: 
qc.software.bib.exists("rjm-347d")

## End(Not run)

SOFTWARE.bib Processed

Description

Check if a ⁠SOFTWARE.bib⁠ entries appear to have been processed, i.e., found as files and directories inside the boot folder.

Usage

qc.software.bib.processed(analysis = ".")

Arguments

analysis

directory containing a TAF analysis.

Value

TRUE if test succeeds, otherwise FALSE.

Note

qc.software.bib.processed checks if all bib entries have made it into the boot software folder: 

SOFTWARE.bib | boot/software
-------------+--------------
      A      |
      B     ==>
      C      |

qc.software.declared checks if all boot software files were declared as bib entries: 

SOFTWARE.bib | boot/software
-------------+--------------
             |      A
            <==     B
             |      C

When used together, those two functions ensure that ⁠SOFTWARE.bib⁠ and ⁠boot/software⁠ contain precisely the same entries.

See Also

qc runs all qc.* tests.

qcTAF-package gives an overview of the package.

Examples

## Not run: 
qc.software.bib.processed("rjm-347d")

## End(Not run)

SOFTWARE.bib Valid

Description

Check if a ⁠SOFTWARE.bib⁠ file is valid.

Usage

qc.software.bib.valid(analysis = ".")

Arguments

analysis

directory containing a TAF analysis.

Value

TRUE if test succeeds, otherwise FALSE.

See Also

qc runs all qc.* tests.

qcTAF-package gives an overview of the package.

Examples

## Not run: 
qc.software.bib.valid("rjm-347d")

## End(Not run)

Software Declared

Description

Check if all files in the boot software folder are declared in the ⁠SOFTWARE.bib⁠ file.

Usage

qc.software.declared(analysis = ".")

Arguments

analysis

directory containing a TAF analysis.

Value

TRUE if test succeeds, otherwise FALSE.

Note

qc.software.bib.processed checks if all bib entries have made it into the boot software folder: 

SOFTWARE.bib | boot/software
-------------+--------------
      A      |
      B     ==>
      C      |

qc.software.declared checks if all boot software files were declared as bib entries: 

SOFTWARE.bib | boot/software
-------------+--------------
             |      A
            <==     B
             |      C

When used together, those two functions ensure that ⁠SOFTWARE.bib⁠ and ⁠boot/software⁠ contain precisely the same entries.

See Also

qc runs all qc.* tests.

qcTAF-package gives an overview of the package.

Examples

## Not run: 
qc.software.declared("rjm-347d")

## End(Not run)