Man pages for nielsjdewinter/ShellTrace
Bivalve Growth and Trace Element Accumulation Model

BMPBMP image of phase map of cross section of modern oyster.
cross_sectionDigitized growth increments in cross section of modern oyster...
el_timeMatrix listing the concentrations of elements in every...
image_lengthLength (in mm) of the digitized phase map image.
IncGInterpolated subincrements in cross section of modern oyster...
incr_matrix0Matrix containing data calculated for each growth band.
incr_matrix1Matrix containing data calculated for each growth band.
incr_matrix2Matrix containing data calculated for each growth band.
incr_matrix3Matrix containing data calculated for each growth band.
lengthfactorMultiplier used to convert shell cross section from pixels to...
M_el_matMatrix of modelled mass accumulation rates per trace element
M_el_mat_cMatrix of modelled cumulative mass accumulation rates per...
O1_inputDigitized growth increments in cross section of modern...
O1_phaseCharacteristics of phase in XRF map of oyster
Oyster_accumulationCalculate trace element accumulation rates
Oyster_combined_runRuns the growth and trace element model
Oyster_Convert_cross_sectionFunction that converts XY-data of digitized cross section
Oyster_ellipse_parametersFunction that calculates the parameters of the base ellipse...
Oyster_el_timeCalculate concentrations of trace elements per sub-increment
Oyster_ExportFunction that exports data of the growth model
Oyster_growth_runRuns the entire growth model
Oyster_heightMeasured height of the shell
Oyster_import_BMPFunction that imports a BMP of an XRF map
Oyster_import_phasesFunction that imports phase data
Oyster_import_TIFFunction that imports a TIF file
Oyster_incr_areaArea between shell increments
Oyster_incr_cross_sectionFormula that interpolates shell increments
Oyster_lengthMeasured length of the shell
Oyster_Mass_gainFormula that calculates mass increase of bivalve shell with...
Oyster_phase_exportExport results of trace element model
Oyster_phase_matrix_BMPFunction that calculates phase matrix
Oyster_phase_matrix_TIFFunction that calculates phase matrix
Oyster_phase_runRuns the entire trace element model
Oyster_phase_statsFunction that exports phase statistics
Oyster_plot_cross_sectionPlot the converted shell cross section
Oyster_plot_incr_CSPlot the result of interpolation of sub-increments
Oyster_plot_incr_fillPlot the result of interpolation of sub-increments with a...
Oyster_run_sec2Runs complete Step 2 of the growth model
Oyster_run_sec3Runs complete Step 3 of the growth model
Oyster_run_sec4Runs complete Step 4 of the growth model
Oyster_run_sec5Runs complete Step 5 of the trace element model
Oyster_run_sec6Runs complete Step 6 of the trace element model
Oyster_Shell_heightFormula that calculates shell height through time
Oyster_Shell_thicknessFormula that calculates average shell thickness through time
Oyster_subincr_areaFormula that calculates area between sub-increments
Oyster_subincr_av_thicknessFormula that calculates average shell thickness through time
Oyster_subincr_av_thickness_XFormula that calculates average shell thickness through time
Oyster_subincr_phasesCalculates proportion of phases in each sub-increment
Oyster_subincr_shell_heightA fomula to calculate shell height per sub-increment
Oyster_VolumesFormula that calculates volume of the shell through time
Oyster_Z_matricesFunction that calculates matrices of Z-values for all...
phasematMatrix of phases names for each pixel in the phase map
phase_matMatrix listing the amount of pixels of each phase in every...
phase_statStatistics of elemental concentrations in XRF map of oyster
pixelsizeSize of pixels in phase map in mm
pmaFunction to do an n-point moving average
ShellTrace-packageShellTrace: Growth and trace element uptake modelling in...
subincr_matrix0Matrix containing data calculated for each growth band.
subincr_matrix1Matrix containing data calculated for each growth band.
subincr_matrix2Matrix containing data calculated for each growth band.
subincr_matrix3Matrix containing data calculated for each growth band.
subincr_matrix4Matrix containing data calculated for each growth band.
subincr_matrix5Matrix containing data calculated for each growth band.
subincr_matrix6Matrix containing data calculated for each growth band.
TIFTIF image of phase map of cross section of modern oyster.
Z_matZ-values describing the base ellipse of the oyster
nielsjdewinter/ShellTrace documentation built on Nov. 7, 2017, 1:36 p.m.