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shelltrace  

Bivalve Growth and Trace Element Accumulation Model
View on CRAN: Click here


Download and install shelltrace package within the R console
Install from CRAN:
install.packages("shelltrace")

Install from Github:
library("remotes")
install_github("cran/shelltrace")

Install by package version:
library("remotes")
install_version("shelltrace", "3.5.1")



Attach the package and use:
library("shelltrace")
Maintained by
Niels J. de Winter
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-10-06
Latest Update: 2017-10-06
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, ). 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.
How to cite:
Niels J. de Winter (2017). shelltrace: Bivalve Growth and Trace Element Accumulation Model. R package version 3.5.1, https://cran.r-project.org/web/packages/shelltrace
Previous versions and publish date:
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Functions, R codes and Examples using the shelltrace R package
Some associated functions: BMP . IncG . M_el_mat . M_el_mat_c . O1_input . O1_phase . Oyster_Convert_cross_section . Oyster_Export . Oyster_Mass_gain . Oyster_Shell_height . Oyster_Shell_thickness . Oyster_Volumes . Oyster_Z_matrices . Oyster_accumulation . Oyster_combined_run . Oyster_el_time . Oyster_ellipse_parameters . Oyster_growth_run . Oyster_height . Oyster_import_BMP . Oyster_import_TIF . Oyster_import_phases . Oyster_incr_area . Oyster_incr_cross_section . Oyster_length . Oyster_phase_export . Oyster_phase_matrix_BMP . Oyster_phase_matrix_TIF . Oyster_phase_run . Oyster_phase_stats . Oyster_plot_cross_section . Oyster_plot_incr_CS . Oyster_plot_incr_fill . Oyster_run_sec2 . Oyster_run_sec3 . Oyster_run_sec4 . Oyster_run_sec5 . Oyster_run_sec6 . Oyster_subincr_area . Oyster_subincr_av_thickness . Oyster_subincr_av_thickness_X . Oyster_subincr_phases . Oyster_subincr_shell_height . ShellTrace-package . TIF . Z_mat . cross_section . el_time . image_length . incr_matrix0 . incr_matrix1 . incr_matrix2 . incr_matrix3 . lengthfactor . phase_mat . phase_stat . phasemat . pixelsize . pma . subincr_matrix0 . subincr_matrix1 . subincr_matrix2 . subincr_matrix3 . subincr_matrix4 . subincr_matrix5 . subincr_matrix6 . 
Some associated R codes: BMP.R . IncG.R . M_el_mat.R . M_el_mat_c.R . O1_input.R . O1_phase.R . Oyster_Convert_cross_section.R . Oyster_Export.R . Oyster_Mass_gain.R . Oyster_Shell_height.R . Oyster_Shell_thickness.R . Oyster_Volumes.R . Oyster_Z_matrices.R . Oyster_accumulation.R . Oyster_combined_run.R . Oyster_el_time.R . Oyster_ellipse_parameters.R . Oyster_growth_run.R . Oyster_height.R . Oyster_import_BMP.R . Oyster_import_TIF.R . Oyster_import_phases.R . Oyster_incr_area.R . Oyster_incr_cross_section.R . Oyster_length.R . Oyster_phase_export.R . Oyster_phase_matrix_BMP.R . Oyster_phase_matrix_TIF.R . Oyster_phase_run.R . Oyster_phase_stats.R . Oyster_plot_cross_section.R . Oyster_plot_incr_CS.R . Oyster_plot_incr_fill.R . Oyster_run_sec2.R . Oyster_run_sec3.R . Oyster_run_sec4.R . Oyster_run_sec5.R . Oyster_run_sec6.R . Oyster_subincr_area.R . Oyster_subincr_av_thickness.R . Oyster_subincr_av_thickness_X.R . Oyster_subincr_phases.R . Oyster_subincr_shell_height.R . ShellTrace-internal.R . TIF.R . Z_mat.R . cross_section.R . el_time.R . image_length.R . incr_matrix0.R . incr_matrix1.R . incr_matrix2.R . incr_matrix3.R . lengthfactor.R . phase_mat.R . phase_stat.R . phasemat.R . pixelsize.R . pma.R . subincr_matrix0.R . subincr_matrix1.R . subincr_matrix2.R . subincr_matrix3.R . subincr_matrix4.R . subincr_matrix5.R . subincr_matrix6.R .  Full shelltrace package functions and examples
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