Bivalve Growth and Trace Element Accumulation Model

BMP | BMP image of phase map of cross section of modern oyster. |

cross_section | Digitized growth increments in cross section of modern oyster... |

el_time | Matrix listing the concentrations of elements in every... |

image_length | Length (in mm) of the digitized phase map image. |

IncG | Interpolated subincrements in cross section of modern oyster... |

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... |

M_el_mat | Matrix of modelled mass accumulation rates per trace element |

M_el_mat_c | Matrix of modelled cumulative mass accumulation rates per... |

O1_input | Digitized growth increments in cross section of modern... |

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... |

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... |

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... |

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... |

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... |

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-package | ShellTrace: Growth and trace element uptake modelling in... |

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 |

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