shelltrace
Bivalve Growth and Trace Element Accumulation Model
v3.5.1
·
Oct 6, 2017
·
GPL-3
Description
Contains all the formulae of the growth and trace element uptake model described in the equally-named Geoscientific Model Development paper (de Winter, 2017, <doi:10.5194/gmd-2017-137>). The model takes as input a file with X- and Y-coordinates of digitized growth increments recognized on a longitudinal cross section through the bivalve shell, as well as a BMP file of an elemental map of the cross section surface with chemically distinct phases separated by phase analysis. It proceeds by a step-by-step process described in the paper, by which digitized growth increments are used to calculate changes in shell height, shell thickness, shell volume, shell mass and shell growth rate through the bivalve's life time. Then, results of this growth modelling are combined with the trace element mapping results to trace the incorporation of trace elements into the bivalve shell. Results of various modelling parameters can be exported in the form of XLSX files.
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| Flavor | Status |
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| r-devel-linux-x86_64-debian-clang | ERROR |
| r-devel-linux-x86_64-debian-gcc | NOTE |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (15 non-OK)
NOTE
r-devel-linux-x86_64-debian-clang
CRAN incoming feasibility
Maintainer: ‘Niels J. de Winter <niels.de.winter@vub.be>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = c("Niels", "J."),
family = "de Winter",
role = c("aut", "cre"),
email = "niels.de.winter@vub.be")
as necessary.
Package CITATION file contains call(s) to old-style personList() or
as.personList(). Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry(). Please
use bibentry() instead.
Found the following URLs which should use \doi (with the DOI name only):
File ‘BMP.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘IncG.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘M_el_mat.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘M_el_mat_c.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘O1_input.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘O1_phase.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_Convert_cross_section.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_Export.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_Mass_gain.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_Shell_height.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_Shell_thickness.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_Volumes.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_Z_matrices.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_accumulation.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_combined_run.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_el_time.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_ellipse_parameters.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_growth_run.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_height.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_import_BMP.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_import_TIF.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_import_phases.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_incr_area.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_incr_cross_section.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_length.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_phase_export.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_phase_matrix_BMP.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_phase_matrix_TIF.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_phase_run.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_phase_stats.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_plot_cross_section.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_plot_incr_CS.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_plot_incr_fill.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_run_sec2.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_run_sec3.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_run_sec4.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_run_sec5.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_run_sec6.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_subincr_area.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_subincr_av_thickness.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_subincr_av_thickness_X.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_subincr_phases.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_subincr_shell_height.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘ShellTrace-package.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘TIF.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Z_mat.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘cross_section.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘el_time.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘image_length.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘incr_matrix0.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘incr_matrix1.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘incr_matrix2.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘incr_matrix3.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘lengthfactor.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘phase_mat.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘phase_stat.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘phasemat.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘pixelsize.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘pma.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘subincr_matrix0.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘subincr_matrix1.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘subincr_matrix2.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘subincr_matrix3.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘subincr_matrix4.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘subincr_matrix5.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘subincr_matrix6.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
ERROR
r-devel-linux-x86_64-debian-clang
package dependencies
Package required but not available: ‘xlsx’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
NOTE
r-devel-linux-x86_64-debian-gcc
CRAN incoming feasibility
Maintainer: ‘Niels J. de Winter <niels.de.winter@vub.be>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = c("Niels", "J."),
family = "de Winter",
role = c("aut", "cre"),
email = "niels.de.winter@vub.be")
as necessary.
Package CITATION file contains call(s) to old-style personList() or
as.personList(). Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry(). Please
use bibentry() instead.
Found the following URLs which should use \doi (with the DOI name only):
File ‘BMP.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘IncG.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘M_el_mat.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘M_el_mat_c.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘O1_input.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘O1_phase.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_Convert_cross_section.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_Export.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_Mass_gain.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_Shell_height.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_Shell_thickness.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_Volumes.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_Z_matrices.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_accumulation.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_combined_run.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_el_time.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_ellipse_parameters.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_growth_run.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_height.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_import_BMP.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_import_TIF.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_import_phases.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_incr_area.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_incr_cross_section.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_length.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_phase_export.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_phase_matrix_BMP.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_phase_matrix_TIF.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_phase_run.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_phase_stats.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_plot_cross_section.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_plot_incr_CS.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_plot_incr_fill.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_run_sec2.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_run_sec3.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_run_sec4.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_run_sec5.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_run_sec6.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_subincr_area.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_subincr_av_thickness.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_subincr_av_thickness_X.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_subincr_phases.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Oyster_subincr_shell_height.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘ShellTrace-package.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘TIF.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘Z_mat.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘cross_section.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘el_time.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘image_length.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘incr_matrix0.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘incr_matrix1.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘incr_matrix2.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘incr_matrix3.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘lengthfactor.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘phase_mat.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘phase_stat.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘phasemat.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘pixelsize.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘pma.Rd’:
https://doi.org/10.5194/gmd-2017-137
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘subincr_matrix0.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘subincr_matrix1.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘subincr_matrix2.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘subincr_matrix3.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘subincr_matrix4.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘subincr_matrix5.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
File ‘subincr_matrix6.Rd’:
https://doi.org/10.5194/gmd-2017-137-supplement
OK
r-devel-linux-x86_64-fedora-clang
*
OK
r-devel-linux-x86_64-fedora-gcc
*
OK
r-devel-macos-arm64
*
OK
r-devel-windows-x86_64
*
OK
r-oldrel-macos-arm64
*
OK
r-oldrel-macos-x86_64
*
OK
r-oldrel-windows-x86_64
*
OK
r-patched-linux-x86_64
*
OK
r-release-linux-x86_64
*
OK
r-release-macos-arm64
*
OK
r-release-macos-x86_64
*
OK
r-release-windows-x86_64
*
Check History
ERROR 12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 9, 2026
ERROR
r-devel-linux-x86_64-debian-clang
CRAN incoming feasibility
Maintainer: ‘Niels J. de Winter <niels.de.winter@vub.be>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = c("Niels", "J."),
family = "de Winter",
role = c("aut", "cre"),
email = "niels.de.winter@vub.be")
as necessary.
Package CITATION file contains call(s) to old-style personList() or
as.personList(). Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style
NOTE
r-devel-linux-x86_64-debian-gcc
CRAN incoming feasibility
Maintainer: ‘Niels J. de Winter <niels.de.winter@vub.be>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = c("Niels", "J."),
family = "de Winter",
role = c("aut", "cre"),
email = "niels.de.winter@vub.be")
as necessary.
Package CITATION file contains call(s) to old-style personList() or
as.personList(). Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style
Dependency Network
Version History
new
3.5.1
Mar 9, 2026