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 |