Bivalve Growth and Trace Element Accumulation Model

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Documentation for package ‘shelltrace’ version 3.5.1

• DESCRIPTION file.
• Package NEWS.

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