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.
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_Convert_cross_section
                        Function that converts XY-data of digitized
                        cross section
Oyster_Export           Function that exports data of the growth model
Oyster_Mass_gain        Formula that calculates mass increase of
                        bivalve shell with time
Oyster_Shell_height     Formula that calculates shell height through
                        time
Oyster_Shell_thickness
                        Formula that calculates average shell thickness
                        through time
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
Oyster_accumulation     Calculate trace element accumulation rates
Oyster_combined_run     Runs the growth and trace element model
Oyster_el_time          Calculate concentrations of trace elements per
                        sub-increment
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_height           Measured height of the shell
Oyster_import_BMP       Function that imports a BMP of an XRF map
Oyster_import_TIF       Function that imports a TIF file
Oyster_import_phases    Function that imports phase data
Oyster_incr_area        Area between shell increments
Oyster_incr_cross_section
                        Formula that interpolates shell increments
Oyster_length           Measured length of the shell
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_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
ShellTrace              ShellTrace: Growth and trace element uptake
                        modelling in bivalve shells
TIF                     TIF image of phase map of cross section of
                        modern oyster.
Z_mat                   Z-values describing the base ellipse of the
                        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.
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
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
phasemat                Matrix of phases names for each pixel in the
                        phase map
pixelsize               Size of pixels in phase map in mm
pma                     Function to do an n-point moving average
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.
