# shelltrace v3.5.1

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## Bivalve Growth and Trace Element Accumulation Model

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.

## Functions in shelltrace

 Name Description M_el_mat Matrix of modelled mass accumulation rates per trace element M_el_mat_c Matrix of modelled cumulative mass accumulation rates per trace element Oyster_Mass_gain Formula that calculates mass increase of bivalve shell with time Oyster_Shell_height Formula that calculates shell height through time Oyster_Convert_cross_section Function that converts XY-data of digitized cross section Oyster_Export Function that exports data of the growth model BMP BMP image of phase map of cross section of modern oyster. IncG Interpolated subincrements in cross section of modern oyster rescaled to the same X-axis. O1_input Digitized growth increments in cross section of modern oyster. O1_phase Characteristics of phase in XRF map of oyster Oyster_Shell_thickness Formula that calculates average shell thickness through time Oyster_Volumes Formula that calculates volume of the shell through time Oyster_combined_run Runs the growth and trace element model Oyster_el_time Calculate concentrations of trace elements per sub-increment Oyster_phase_matrix_BMP Function that calculates phase matrix Oyster_Z_matrices Function that calculates matrices of Z-values for all sub-increments and all X-values Oyster_accumulation Calculate trace element accumulation rates Oyster_length Measured length of the shell Oyster_phase_export Export results of trace element model Oyster_run_sec5 Runs complete Step 5 of the trace element model Oyster_ellipse_parameters Function that calculates the parameters of the base ellipse used for bivalve growth modelling Oyster_growth_run Runs the entire growth model Oyster_incr_area Area between shell increments Oyster_incr_cross_section Formula that interpolates shell increments Oyster_plot_incr_fill Plot the result of interpolation of sub-increments with a coloured area plot Oyster_run_sec6 Runs complete Step 6 of the trace element model image_length Length (in mm) of the digitized phase map image. incr_matrix0 Matrix containing data calculated for each growth band. phase_mat Matrix listing the amount of pixels of each phase in every subincrement Oyster_height Measured height of the shell Oyster_import_BMP Function that imports a BMP of an XRF map Oyster_phase_run Runs the entire trace element model Oyster_phase_stats Function that exports phase statistics Oyster_subincr_area Formula that calculates area between sub-increments Oyster_subincr_av_thickness Formula that calculates average shell thickness through time TIF TIF image of phase map of cross section of modern oyster. Z_mat Z-values describing the base ellipse of the oyster Oyster_run_sec2 Runs complete Step 2 of the growth model cross_section Digitized growth increments in cross section of modern oyster rescaled to the same X-axis. el_time Matrix listing the concentrations of elements in every subincrement incr_matrix1 Matrix containing data calculated for each growth band. incr_matrix2 Matrix containing data calculated for each growth band. subincr_matrix1 Matrix containing data calculated for each growth band. subincr_matrix2 Matrix containing data calculated for each growth band. pma Function to do an n-point moving average subincr_matrix0 Matrix containing data calculated for each growth band. subincr_matrix3 Matrix containing data calculated for each growth band. subincr_matrix4 Matrix containing data calculated for each growth band. phase_stat Statistics of elemental concentrations in XRF map of oyster Oyster_import_TIF Function that imports a TIF file Oyster_import_phases Function that imports phase data Oyster_plot_cross_section Plot the converted shell cross section Oyster_subincr_shell_height A fomula to calculate shell height per sub-increment Oyster_phase_matrix_TIF Function that calculates phase matrix Oyster_run_sec3 Runs complete Step 3 of the growth model Oyster_run_sec4 Runs complete Step 4 of the growth model Oyster_subincr_av_thickness_X Formula that calculates average shell thickness through time Oyster_subincr_phases Calculates proportion of phases in each sub-increment Oyster_plot_incr_CS Plot the result of interpolation of sub-increments phasemat Matrix of phases names for each pixel in the phase map pixelsize Size of pixels in phase map in mm ShellTrace ShellTrace: Growth and trace element uptake modelling in bivalve shells incr_matrix3 Matrix containing data calculated for each growth band. lengthfactor Multiplier used to convert shell cross section from pixels to mm subincr_matrix5 Matrix containing data calculated for each growth band. subincr_matrix6 Matrix containing data calculated for each growth band. No Results!

## Details

 Type Package Date 2017-09-27 License GPL-3 LazyData true URL https://github.com/nielsjdewinter/ShellTrace, https://doi.org/10.5194/gmd-2017-137-supplement, http://nidewint.wixsite.com/nielsdewinter BugReports https://github.com/nielsjdewinter/ShellTrace/issues RoxygenNote 6.0.1 NeedsCompilation no Packaged 2017-10-06 11:17:04 UTC; Niels Repository CRAN Date/Publication 2017-10-06 11:35:20 UTC
 imports bmp , grDevices , stats , tiff , xlsx depends R (>= 3.1.0) Contributors Niels de Winter