# Bivalve Growth and Trace Element Accumulation Model

## Documentation for package ‘shelltrace’ version 3.5.1

- DESCRIPTION file.

## Help Pages

BMP | BMP image of phase map of cross section of modern oyster.
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
image_length | Length (in mm) of the digitized phase map image.
IncG | Interpolated subincrements in cross section of modern oyster rescaled to the same X-axis.
incr_matrix0 | Matrix containing data calculated for each growth band.
incr_matrix1 | Matrix containing data calculated for each growth band.
incr_matrix2 | Matrix containing data calculated for each growth band.
incr_matrix3 | Matrix containing data calculated for each growth band.
lengthfactor | Multiplier used to convert shell cross section from pixels to mm
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
O1_input | Digitized growth increments in cross section of modern oyster.
O1_phase | Characteristics of phase in XRF map of oyster
Oyster_accumulation | Calculate trace element accumulation rates
Oyster_combined_run | Runs the growth and trace element model
Oyster_Convert_cross_section | Function that converts XY-data of digitized cross section
Oyster_ellipse_parameters | Function that calculates the parameters of the base ellipse used for bivalve growth modelling
Oyster_el_time | Calculate concentrations of trace elements per sub-increment
Oyster_Export | Function that exports data of the growth model
Oyster_growth_run | Runs the entire growth model
Oyster_height | Measured height of the shell
Oyster_import_BMP | Function that imports a BMP of an XRF map
Oyster_import_phases | Function that imports phase data
Oyster_import_TIF | Function that imports a TIF file
Oyster_incr_area | Area between shell increments
Oyster_incr_cross_section | Formula that interpolates shell increments
Oyster_length | Measured length of the shell
Oyster_Mass_gain | Formula that calculates mass increase of bivalve shell with time
Oyster_phase_export | Export results of trace element model
Oyster_phase_matrix_BMP | Function that calculates phase matrix
Oyster_phase_matrix_TIF | Function that calculates phase matrix
Oyster_phase_run | Runs the entire trace element model
Oyster_phase_stats | Function that exports phase statistics
Oyster_plot_cross_section | Plot the converted shell cross section
Oyster_plot_incr_CS | Plot the result of interpolation of sub-increments
Oyster_plot_incr_fill | Plot the result of interpolation of sub-increments with a coloured area plot
Oyster_run_sec2 | Runs complete Step 2 of the growth model
Oyster_run_sec3 | Runs complete Step 3 of the growth model
Oyster_run_sec4 | Runs complete Step 4 of the growth model
Oyster_run_sec5 | Runs complete Step 5 of the trace element model
Oyster_run_sec6 | Runs complete Step 6 of the trace element model
Oyster_Shell_height | Formula that calculates shell height through time
Oyster_Shell_thickness | Formula that calculates average shell thickness through time
Oyster_subincr_area | Formula that calculates area between sub-increments
Oyster_subincr_av_thickness | Formula that calculates average shell thickness through time
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_subincr_shell_height | A fomula to calculate shell height per sub-increment
Oyster_Volumes | Formula that calculates volume of the shell through time
Oyster_Z_matrices | Function that calculates matrices of Z-values for all sub-increments and all X-values
phasemat | Matrix of phases names for each pixel in the phase map
phase_mat | Matrix listing the amount of pixels of each phase in every subincrement
phase_stat | Statistics of elemental concentrations in XRF map of oyster
pixelsize | Size of pixels in phase map in mm
pma | Function to do an n-point moving average
ShellTrace | ShellTrace: Growth and trace element uptake modelling in bivalve shells
subincr_matrix0 | 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.
subincr_matrix3 | Matrix containing data calculated for each growth band.
subincr_matrix4 | Matrix containing data calculated for each growth band.
subincr_matrix5 | Matrix containing data calculated for each growth band.
subincr_matrix6 | Matrix containing data calculated for each growth band.
TIF | TIF image of phase map of cross section of modern oyster.
Z_mat | Z-values describing the base ellipse of the oyster