Man pages for nielsjdewinter/ShellTrace
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 |
