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Bivalve Growth and Trace Element Accumulation Model

v3.5.1 · Oct 6, 2017 · GPL-3
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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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2 NOTE
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r-devel-linux-x86_64-debian-clang NOTE
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 (2 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.R
...[truncated]...
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
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.R
...[truncated]...
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

Check History

NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 6, 2026
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")
...[truncated]...
plement
  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
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")
...[truncated]...
plement
  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 12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 3, 2026
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")
...[truncated]...
plement
  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-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")
...[truncated]...
plement
  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
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
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")
...[truncated]...
plement
  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
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")
...[truncated]...
plement
  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

Dependency Network

Dependencies Reverse dependencies xlsx bmp tiff shelltrace

Version History

new 3.5.1 Mar 10, 2026