| Type: | Package |
| Title: | Bivalve Growth and Trace Element Accumulation Model |
| Version: | 3.5.1 |
| Date: | 2017-09-27 |
| Author: | Niels J. de Winter |
| Maintainer: | Niels J. de Winter <niels.de.winter@vub.be> |
| Depends: | R (≥ 3.1.0) |
| Imports: | xlsx, bmp, tiff, grDevices, stats |
| Description: | Contains all the formulae of the growth and trace element uptake model described in the equally-named Geoscientific Model Development paper (de Winter, 2017, <doi:10.5194/gmd-2017-137>). The model takes as input a file with X- and Y-coordinates of digitized growth increments recognized on a longitudinal cross section through the bivalve shell, as well as a BMP file of an elemental map of the cross section surface with chemically distinct phases separated by phase analysis. It proceeds by a step-by-step process described in the paper, by which digitized growth increments are used to calculate changes in shell height, shell thickness, shell volume, shell mass and shell growth rate through the bivalve's life time. Then, results of this growth modelling are combined with the trace element mapping results to trace the incorporation of trace elements into the bivalve shell. Results of various modelling parameters can be exported in the form of XLSX files. |
| License: | GPL-3 |
| LazyData: | true |
| URL: | https://github.com/nielsjdewinter/ShellTrace, https://doi.org/10.5194/gmd-2017-137-supplement, http://nidewint.wixsite.com/nielsdewinter |
| BugReports: | https://github.com/nielsjdewinter/ShellTrace/issues |
| RoxygenNote: | 6.0.1 |
| NeedsCompilation: | no |
| Packaged: | 2017-10-06 11:17:04 UTC; Niels |
| Repository: | CRAN |
| Date/Publication: | 2017-10-06 11:35:20 UTC |
BMP image of phase map of cross section of modern oyster.
Description
An image of the microXRF phase map of the cross section used for this model from the Crassostre gigas #1 oyster used as an example in de Winter (2017)
Usage
data(BMP)
Format
A BMP image imported into R as a large data array
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Interpolated subincrements in cross section of modern oyster rescaled to the same X-axis.
Description
A dataset containing X- and Y-coordinates of subincrements interpolated between digitized growth increments from the Crassostrea gigas #1 oyster used as an example in de Winter (2017) sampled to fit a common X-axis. A Xstep of 0.1, a Tstep of 1 and a growth season of 250 days are used.
Usage
data(IncG)
Format
A large data frame with 101 rows and 1291 variables:
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Matrix of modelled mass accumulation rates per trace element
Description
A dataset containing trace element accumulation modelled for every based on the a phase map of the XRF mapped surface of the Crassostrea gigas #1 oyster used as an example in de Winter (2017)
Usage
data(M_el_mat)
Format
A data frame with 5 rows and 24 variables:
- C
Mass accumulation of C in subincrement
- O
Mass accumulation of O in subincrement
- Na
Mass accumulation of Na in subincrement
- Mg
Mass accumulation of Mg in subincrement
- Al
Mass accumulation of Al in subincrement
- Si
Mass accumulation of Si in subincrement
- P
Mass accumulation of P in subincrement
- S
Mass accumulation of S in subincrement
- Cl
Mass accumulation of Cl in subincrement
- K
Mass accumulation of K in subincrement
- Ca
Mass accumulation of Ca in subincrement
- Ti
Mass accumulation of Ti in subincrement
- Cr
Mass accumulation of Cr in subincrement
- Mn
Mass accumulation of Mn in subincrement
- Fe
Mass accumulation of Fe in subincrement
- Ni
Mass accumulation of Ni in subincrement
- Cu
Mass accumulation of Cu in subincrement
- Zn
Mass accumulation of Zn in subincrement
- Br
Mass accumulation of Br in subincrement
- Rb
Mass accumulation of Rb in subincrement
- Sr
Mass accumulation of Sr in subincrement
- Rh
Mass accumulation of Rh in subincrement
- Ba
Mass accumulation of Ba in subincrement
- Pb
Mass accumulation of Pb in subincrement
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Matrix of modelled cumulative mass accumulation rates per trace element
Description
A dataset containing mass accumulation of trace elements modelled for every based on the a phase map of the XRF mapped surface of the Crassostrea gigas #1 oyster used as an example in de Winter (2017)
Usage
data(M_el_mat_c)
Format
A data frame with 5 rows and 24 variables:
- C
Cumulative mass accumulation of C in subincrement
- O
Cumulative mass accumulation of O in subincrement
- Na
Cumulative mass accumulation of Na in subincrement
- Mg
Cumulative mass accumulation of Mg in subincrement
- Al
Cumulative mass accumulation of Al in subincrement
- Si
Cumulative mass accumulation of Si in subincrement
- P
Cumulative mass accumulation of P in subincrement
- S
Cumulative mass accumulation of S in subincrement
- Cl
Cumulative mass accumulation of Cl in subincrement
- K
Cumulative mass accumulation of K in subincrement
- Ca
Cumulative mass accumulation of Ca in subincrement
- Ti
Cumulative mass accumulation of Ti in subincrement
- Cr
Cumulative mass accumulation of Cr in subincrement
- Mn
Cumulative mass accumulation of Mn in subincrement
- Fe
Cumulative mass accumulation of Fe in subincrement
- Ni
Cumulative mass accumulation of Ni in subincrement
- Cu
Cumulative mass accumulation of Cu in subincrement
- Zn
Cumulative mass accumulation of Zn in subincrement
- Br
Cumulative mass accumulation of Br in subincrement
- Rb
Cumulative mass accumulation of Rb in subincrement
- Sr
Cumulative mass accumulation of Sr in subincrement
- Rh
Cumulative mass accumulation of Rh in subincrement
- Ba
Cumulative mass accumulation of Ba in subincrement
- Pb
Cumulative mass accumulation of Pb in subincrement
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Digitized growth increments in cross section of modern oyster.
Description
A dataset containing X- and Y-coordinates of digitized growth increments from the Crassostrea gigas #1 oyster used as an example in de Winter (2017)
Usage
data(O1_input)
Format
A data frame with 181 rows and 26 variables:
- x_base
X-coordinate in pixels of bottom line on image
- y_base
Y-coordinate in pixels of bottom line on image, second row value represents the day of the year
- EMPTY1
Empty column
- x_top
X-coordinate in pixels of top of Crassostrea gigas shell #1 (increment 0)
- y_top
Y-coordinate in pixels of top of Crassostrea gigas shell #1 (increment 0), second row value represents the age in days (=0)
- EMPTY2
Empty column
- x_1
X-coordinate in pixels of increment 1
- y_1
Y-coordinate in pixels of increment 1, second row value represents the age in days
- EMPTY3
Empty column
- x_2
X-coordinate in pixels of increment 2
- y_2
Y-coordinate in pixels of increment 2, second row value represents the age in days
- EMPTY4
Empty column
- x_3
X-coordinate in pixels of increment 3
- y_3
Y-coordinate in pixels of increment 3, second row value represents the age in days
- EMPTY5
Empty column
- x_4
X-coordinate in pixels of increment 4
- y_4
Y-coordinate in pixels of increment 4, second row value represents the age in days
- EMPTY6
Empty column
- x_5
X-coordinate in pixels of increment 5
- y_5
Y-coordinate in pixels of increment 5, second row value represents the age in days
- EMPTY7
Empty column
- x_6
X-coordinate in pixels of increment 6
- y_6
Y-coordinate in pixels of increment 6, second row value represents the age in days
- EMPTY8
Empty column
- x_bottom
X-coordinate in pixels of bottom of Crassostrea gigas shell #1
- y_bottom
Y-coordinate in pixels of bottom of Crassostrea gigas shell #1, second row value represents the age in days (= age of death)
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Characteristics of phase in XRF map of oyster
Description
A dataset containing trace element concentrations and RGB colour values of a phase map of the XRF mapped surface of the Crassostrea gigas #1 oyster used as an example in de Winter (2017)
Usage
data(O1_phase)
Format
A data frame with 5 rows and 30 variables:
- Description
Desription of phase
- Name
Name of phase
- R
R-value of phase colour
- G
G-value of phase colour
- B
B-value of phase colour
- density
specific density of different phases
- C
Concentration of C in phase
- O
Concentration of O in phase
- Na
Concentration of Na in phase
- Mg
Concentration of Mg in phase
- Al
Concentration of Al in phase
- Si
Concentration of Si in phase
- P
Concentration of P in phase
- S
Concentration of S in phase
- Cl
Concentration of Cl in phase
- K
Concentration of K in phase
- Ca
Concentration of Ca in phase
- Ti
Concentration of Ti in phase
- Cr
Concentration of Cr in phase
- Mn
Concentration of Mn in phase
- Fe
Concentration of Fe in phase
- Ni
Concentration of Ni in phase
- Cu
Concentration of Cu in phase
- Zn
Concentration of Zn in phase
- Br
Concentration of Br in phase
- Rb
Concentration of Rb in phase
- Sr
Concentration of Sr in phase
- Rh
Concentration of Rh in phase
- Ba
Concentration of Ba in phase
- Pb
Concentration of Pb in phase
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Function that converts XY-data of digitized cross section
Description
Takes XY data of digitized growth increments in a shell cross section and converts them to a common X-axis with the correct lengths in millimeters. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_Convert_cross_section(raw_data, image_length, Xstep = 0.1)
Arguments
raw_data |
Numeric data frame containing the X- and Y-coordinates digitized in Adobe Illustrator or another image processing software |
image_length |
Measured maximum length of the area of the cross section that is represented in "raw_data" |
Xstep |
The step size (dx) in X-direction used to interpolate coordinates of shell increments |
Details
First step in growth modelling: Converting XY data of increments to a common X-axis
Value
List of two data sets and one value:
cross_section |
Digitized cross section of the shell with shell top, bottom and growth increments relative to a common X-axis |
year_trace |
Digitized cross section of shell increments without addition of top and bottom of the shell to the increment Y-values |
lengthfactor |
Factor of actual shell length relative to shell length in cross section |
incr_matrix |
Matrix containing ages and calibrated ages for each shell increment |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 - A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https:\doi.org\10.5194\gmd-2017-137, in review, 2017.
Examples
Llist<-Oyster_Convert_cross_section(O1_input, image_length, Xstep=1)
Function that exports data of the growth model
Description
Function that exports the results of the bivalve growth model as tables in the form of XLSX files. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_Export(subincr_matrix, name_file)
Arguments
subincr_matrix |
Data frame that contains characteristics of every sub-increment |
name_file |
String containing the name of the file to be exported |
Details
Results are exported as "<name file>.xlsx?" in the working directory
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_av_thickness"
Examples
## Not run:
Oyster_Export(subincr_matrix6, "test_export")
## End(Not run)
Formula that calculates mass increase of bivalve shell with time
Description
Formula that takes the modelled volume of a bivalve shell by sub-increment and calculates mass increase using variable shell density. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_Mass_gain(subincr_matrix, phase_mat, phases)
Arguments
subincr_matrix |
Data frame that contains characteristics of every sub-increment |
phase_mat |
Matrix of amounts of pixels of each phase per sub-increment |
phases |
Matrix containing colour, density and trace element data of the phases in the XRF phase map |
Details
Calculates mass gain from modelled changes in volume based on the shell density
Value
subincr_matrix |
Updated data frame that contains characteristics of every sub-increment with modelled shell mass calculations added to the matrix |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_av_thickness"
Examples
subincr_matrix6<-Oyster_Mass_gain(subincr_matrix5, phase_mat, O1_phase)
Formula that calculates shell height through time
Description
Formula that calculates shell height at the moment of deposition of each shell increment from X- and Y-coordinates of the shell increments and adds the result to the matrix of increment characteristics. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_Shell_height(cross_section, incr_matrix)
Arguments
incr_matrix |
Matrix listing characteristics of each digitized increment |
cross_section |
Digitized cross section of the shell with shell top, bottom and growth increments relative to a common X-axis |
Details
Shell height is calculated via the Pythagorean Theorem using the X- and Y-coordinates of both ends of the shell increment with extreme X-values
Value
incr_matrix |
Updated matrix listing characteristics of each digitized increment, shell height values as well as the coordinates of both ends of the shell increments are added |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
Examples
incr_matrix3<-Oyster_Shell_height(cross_section, incr_matrix2)
Formula that calculates average shell thickness through time
Description
Formula that calculates average shell thickness at the moment of deposition of each shell increment from X- and Y-coordinates of the shell increments and adds the result to the matrix of increment characteristics. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_Shell_thickness(cross_section, incr_matrix)
Arguments
incr_matrix |
Matrix listing characteristics of each digitized increment |
cross_section |
Digitized cross section of the shell with shell top, bottom and growth increments relative to a common X-axis |
Details
Shell thickness is calculated as the average difference in Y-values between the shell increment and the top of the shell (Increment 0)
Value
incr_matrix |
Updated matrix listing characteristics of each digitized increment, shell thickness values are added |
A plot of the change in shell thickness with shell age based on the digitized growth increments is produced in a new window
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
Examples
incr_matrix2<-Oyster_Shell_thickness(cross_section, incr_matrix1)
Formula that calculates volume of the shell through time
Description
Formula that calculates the volume of the bivalve shell during the time of deposition of each sub-increment. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_Volumes(subincr_matrix, Z_mat, IncG, Xstep = 0.1)
Arguments
subincr_matrix |
Data frame that contains characteristics of every sub-increment |
Z_mat |
Matrix of Z-values for each X-value and each sub-increment |
IncG |
Matrix of X- and Y-coordinates of all interpolated sub-increments |
Xstep |
Step value in X-direction for the interpolation of sub-increments |
Details
Volume is calculated for each sub-increment and each X-value based on cross sections perpendicular to the XY-plane. Area of the shell in this cross section is calculated by constructing a circle section through the intercept with the base ellipse and the top of the shell sub-increment. See paper de Winter, GMD (in review) for details and illustrations
Value
A list of two data frames:
subincr_matrix |
Updated data frame that contains characteristics of every sub-increment with modelled shell volumes added to the matrix |
IncGAnet |
Matrix of areas of cross sections in YZ-directions sorted by X-values and by sub-increment |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_av_thickness"
Examples
## Not run:
diagL<-Oyster_Volumes(subincr_matrix4, Z_mat, IncG, Xstep = 1)
## End(Not run)
Function that calculates matrices of Z-values for all sub-increments and all X-values
Description
Function that calculates Z-values that form the edge of the shell in terms of distance from the X-axis in direction of the width of the shell. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_Z_matrices(IncG, subincr_matrix)
Arguments
IncG |
Matrix of X- and Y-coordinates of all interpolated sub-increments |
subincr_matrix |
Data frame that contains characteristics of every sub-increment |
Details
Z-values are calculated using the standard formulae of an ellipse, the parameters calculated in "Oyster_Oval_parameters" and the X-coordinates of each sub-increment
Value
Z-mat |
Matrix of Z-values for each X-value and each sub-increment |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_av_thickness"
Examples
Z_mat<-Oyster_Z_matrices(IncG, subincr_matrix4)
Calculate trace element accumulation rates
Description
Function that combines the concentrations of trace elements per sub-increment with a smoothed record of mass accumulation with time to calculate the rate of accumulation of each element through the lifetime of the bivalve. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_accumulation(el_time, subincr_matrix, npma = 10)
Arguments
el_time |
Matrix of trace element concentrations through time |
subincr_matrix |
Data frame that contains characteristics of every sub-increment |
npma |
Integer n-value determining the window size of the moving average smoothing of the mass accumulation record |
Details
A record of mass accumulation of the shell is smoothed using a moving average. This mass accumulation record is multiplied with the records of trace element concentrations per sub-increment to obtain a record of mass accumulation of each trace element through time and a record of cumulative trace element accumulation through time
Value
Matrices of trace element accumulation per sub-increment and cumulative trace element accumulation
M_el_mat |
Matrix of mass accumulation per trace element |
M_el_mat_c |
Matrix of cumulative mass accumulation per trace element |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_el_time"
Examples
AccL<-Oyster_accumulation(el_time, subincr_matrix6, npma = 10)
Runs the growth and trace element model
Description
Function that runs the bivalve growth and trace element model from start to finish, combining Step 2-6. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_combined_run(raw_data, image_length, season_length=250, Xstep=0.1, Tstep=1,
Oyster_height, Oyster_length, name_file="Oyster_growth_model", phases_name,
image_name, image_ext, npma=10, name_shell)
Arguments
raw_data |
Numeric data frame containing the X- and Y-coordinates digitized in Adobe Illustrator or another image processing software |
image_length |
Measured maximum length of the area of the cross section that is represented in "raw_data" |
season_length |
Length (in days) of the growth season of the studied bivalve |
Xstep |
The step size (dx) in X-direction used to interpolate coordinates of shell increments |
Tstep |
The step size (dt) in time (days) used to interpolate the existing shell increments |
Oyster_height |
Measured maximum height of the shell |
Oyster_length |
Measured maximum length of the shell in anterio-posterior direction |
name_file |
string indicating the name that should be added to all exported model results |
phases_name |
String of full name (including extension!) of the CSV file that contains information about the phases in the map |
image_name |
String of full name of the BMP that needs to be imported, excluding extension |
image_ext |
Extention of phase map file ("BMP" or "TIF") |
npma |
Window size of the moving average used to smooth mass gain record from the bivalve growth model |
name_shell |
string indicating the name that should be added to all exported model results |
Details
Oyster_growth_run and Oyster_phase_run, bundling and exporting the model results
Value
Exports matrices containing oyster growth parameters for each sub-increment as well as matrices containing trace element accumulation rates and concentration changes through the shells life time resulting from the trace element model. All these matrices are also exported as a list containing:
subincr_matrix |
Revised version of the "incr_matrix" data frame that contains characteristics calculated for every sub-increment |
phase_stat |
matrix of statistics of trace elements and phases in the total map |
el_time |
Matrix of trace element concentrations through time |
M_el_mat |
Matrix of mass accumulation per trace element |
M_el_mat_c |
Matrix of cumulative mass accumulation per trace element |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_growth_run" and "Oyster_phase_run"
Calculate concentrations of trace elements per sub-increment
Description
Function that takes the matrix of phase pixels per sub-increment together with the matrix of concentrations per phase to calculate the concentration of each trace element in every sub-increment. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_el_time(phase_mat, phases)
Arguments
phase_mat |
Matrix of amounts of pixels of each phase per sub-increment |
phases |
Matrix containing colour and trace element data of the phases in the XRF phase map |
Details
For every sub-increment, the relative contribution of phases is multiplied with the trace element concentrations of the phases to calculate the average concentration of trace elements in each sub-increment
Value
Matrix of trace element concentrations per sub-increment
el_time |
Matrix of trace element concentrations through time |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_Volumes"
Examples
el_time<-Oyster_el_time(phase_mat, O1_phase)
Function that calculates the parameters of the base ellipse used for bivalve growth modelling
Description
Calculates the parameters a and b of the ellipse that forms the base of the shell in growth modelling. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_ellipse_parameters(subincr_matrix, IncG, Oyster_height, Oyster_length)
Arguments
subincr_matrix |
Data frame that contains characteristics of every sub-increment |
IncG |
Matrix of X- and Y-coordinates of all interpolated sub-increments |
Oyster_height |
Measured maximum height of the shell |
Oyster_length |
Measured maximum length of the shell in anterio-posterior direction |
Details
Parameters of the base ellipse of the shell are calculated by calculating the ratio between measured shell height and length and the endpoints of all sub-increments
Value
subincr_matrix |
Updated data frame that contains characteristics of every sub-increment, with ellipse parameters added |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_av_thickness"
Examples
subincr_matrix4<-Oyster_ellipse_parameters(subincr_matrix3,IncG,Oyster_height,Oyster_height)
Runs the entire growth model
Description
Function that runs all functions contained in Step 2-4 of the growth model. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_growth_run(LOG=T, raw_data, image_length, season_length=250,
Xstep=0.1, Tstep=1, Oyster_height, Oyster_length,
name_file="Oyster_growth_model")
Arguments
LOG |
Boolean parameter specifying if a LOG should be printed detailing the parameters entered into this function |
raw_data |
Numeric data frame containing the X- and Y-coordinates digitized in Adobe Illustrator or another image processing software |
image_length |
Measured maximum length of the area of the cross section that is represented in "raw_data" |
season_length |
Length (in days) of the growth season of the studied bivalve |
Xstep |
The step size (dx) in X-direction used to interpolate coordinates of shell increments |
Tstep |
The step size (dt) in time (days) used to interpolate the existing shell increments |
Oyster_height |
Measured maximum height of the shell |
Oyster_length |
Measured maximum length of the shell in anterio-posterior direction |
name_file |
string indicating the name that should be added to all exported model results |
Details
Runs Oyser_run_sec2, Oyser_run_sec3, Oyser_run_sec4 and Oyster_Export
Value
Matrix containing all parameters of the shell calculated per sub-increment and CSV file containing this matrix
subincr_matrix |
Revised version of the "incr_matrix" data frame that contains characteristics calculated for every sub-increment |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
Examples
## Not run:
GList<-Oyster_growth_run(TRUE, O1_input, image_length, season_length=250,
Xstep=1, Tstep=1, Oyster_height, Oyster_length,name_file="test_export")
## End(Not run)
Measured height of the shell
Description
A single value containing the measured height in mm of the Crassostrea gigas #1 oyster used as an example in de Winter (2017) GMD.
Usage
data(Oyster_height)
Format
A single value:
Height in mm of the Crassostrea gigas #1 shell
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Function that imports a BMP of an XRF map
Description
Function that imports a BMP file into R. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_import_BMP(file_name)
Arguments
file_name |
String of full name of the BMP that needs to be imported, excluding the extension |
Details
Requires "bmp" package to work
Value
BMP |
"BMP" file representing the BMP image in R session |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_av_thickness"
Function that imports a TIF file
Description
Function that imports an image in TIF or TIFF format of an XRF map. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_import_TIF(file_name)
Arguments
file_name |
String of full name of the TIF(F) that needs to be imported, including extension |
Details
Requires "tiff" package to work
Value
TIF |
"TIF" file representing the TIF(F) image in R session |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_av_thickness"
Function that imports phase data
Description
Function that imports a table (in CSV format) containing the specifics of phases that make up the phase XRF map used in the trace element model. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_import_phases(file_name)
Arguments
file_name |
String containing the name of the CSV file to be imported, including its extension |
Details
This funcion imports a table containing trace element concentration and RGB colour data. Table needs to be of the same format as the example shown in de Winter, N.J., GMD, in review. The amount of phases represented in the table byrows is unlimited)
Value
phases |
Matrix containing colour, density and trace element data of the phases in the XRF phase map |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_av_thickness"
Area between shell increments
Description
Calculates the area between this shell increment and the previous increment and the cumulative shell cross section area at the moment of deposition of the current increment and adds these to the previously created increment matrix. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_incr_area(cross_section, incr_matrix)
Arguments
cross_section |
Digitized cross section of the shell with shell top, bottom and growth increments relative to a common X-axis |
incr_matrix |
Matrix containing ages and calibrated ages for each shell increment |
Details
Areas between shell increments are calculated by iterating through increments in X-direction (dx) and adding differences in Y-values between increments
Value
incr_matrix |
Matrix containing ages and calibrated ages for each shell increment |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
Examples
incr_matrix1<-Oyster_incr_area(cross_section, incr_matrix0)
Formula that interpolates shell increments
Description
Formula that takes the coordinates of digitized shell increments and interpolates a number of sub-increments between them to increase the time resolution of the growth model. The number of interpolated shell increments as well as the relative thickness of these increments is determined by a sinusoidal seasonal model that simulates seasonal variations in shell growth rate. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_incr_cross_section(incr_matrix, cross_section, season_length,
Tstep=1, Xstep=0.1)
Arguments
incr_matrix |
Matrix listing characteristics of each digitized increment |
cross_section |
Digitized cross section of the shell with shell top, bottom and growth increments relative to a common X-axis |
season_length |
Length (in days) of the growth season of the studied bivalve |
Tstep |
The step size (dt) in time (days) used to interpolate the existing shell increments |
Xstep |
The step size (dx) in X-direction used to interpolate coordinates of shell increments |
Details
Sub-increments are reconstructed by interpolating Y-values between the digitized shell increments
Value
List of two data frames:
IncG |
Matrix of X- and Y-coordinates of all interpolated sub-increments |
subincr_matrix |
Revised version of the "incr_matrix" data frame that contains characteristics (sub-increment number, X-value of start of increment) recalculated for every sub-increment |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
Examples
Lsub<-Oyster_incr_cross_section(incr_matrix3, cross_section, season_length=250,
Tstep=1, Xstep=1)
Measured length of the shell
Description
A single value containing the measured length (in anterio-posterior direction) in mm of the Crassostrea gigas #1 oyster used as an example in de Winter (2017) GMD.
Usage
data(Oyster_length)
Format
A single value:
Lenght in mm of the Crassostrea gigas #1 shell
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Export results of trace element model
Description
A function that takes all the matrices with results of the trace element model and exports them as XLSX files. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_phase_export(phase_stat, el_time, M_el_mat, M_el_mat_c, name_shell)
Arguments
phase_stat |
matrix of statistics of trace elements and phases in the total map |
el_time |
Matrix of trace element concentrations through time |
M_el_mat |
Matrix of mass accumulation per trace element |
M_el_mat_c |
Matrix of cumulative mass accumulation per trace element |
name_shell |
Name of the shell used in the model to be incorporated into the file names |
Details
All matrices fed to the function are exported as XLSX files in the working directory using the " write.xlsx" function of the "xlsx" package
Value
XLSX files of all result matrices of the trace element model
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_Export"
Examples
## Not run:
Oyster_phase_export(phase_stat, el_time, M_el_mat, M_el_mat_c, "test")
## End(Not run)
Function that calculates phase matrix
Description
Function that calculates a matrix of phase numbers for every pixel in the imported BMP file. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_phase_matrix_BMP(BMP, phases)
Arguments
BMP |
"BMP" file representing the BMP image in R session |
phases |
Matrix containing colour, density and trace element data of the phases in the XRF phase map |
Details
This function compares the colour data from the "BMP" object with colour codes of phases in "phases" table to assign a phase to every pixel in the BMP
Value
phasemat |
matrix of phases of each pixel sorted by X- and Y-coordinate of the pixel |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_av_thickness"
Examples
## Not run:
phasemat<-Oyster_phase_matrix_BMP(BMP, O1_phase)
## End(Not run)
Function that calculates phase matrix
Description
Function that calculates a matrix of phase numbers for every pixel in the imported TIF file. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_phase_matrix_TIF(TIF, phases)
Arguments
TIF |
"TIF" file representing the TIF(F) image in R session |
phases |
Matrix containing colour and trace element data of the phases in the XRF phase map |
Details
This function compares the colour data from the "TIF" object with colour codes of phases in "phases" table to assign a phase to every pixel in the TIF(F)
Value
phasemat |
matrix of phases of each pixel sorted by X- and Y-coordinate of the pixel |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_av_thickness"
Examples
## Not run:
phasemat<-Oyster_phase_matrix_TIF(TIF, O1_phase)
## End(Not run)
Runs the entire trace element model
Description
Function that runs all functions contained in Step 5 and 6 of the trace element model. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_phase_run(LOG=T, phases_name, image_name, image_ext, IncG,
pixelsize, subincr_matrix, npma=10, name_shell, name_file)
Arguments
LOG |
Boolean parameter specifying if a LOG should be printed detailing the parameters entered into this function |
phases_name |
String of full name (including extension!) of the CSV file that contains information about the phases in the map |
image_name |
String of full name of the BMP that needs to be imported, excluding extension |
image_ext |
Extention of phase map file ("BMP" or "TIF") |
IncG |
Matrix of X- and Y-coordinates of all interpolated sub-increments |
pixelsize |
Size of pixels in phase map in micrometeres |
subincr_matrix |
Revised version of the "yearly_matrix" data frame that contains characteristics calculated for every sub-increment |
npma |
Window size of the moving average used to smooth mass gain record from the bivalve growth model |
name_shell |
string indicating the name that should be added to all exported model results |
name_file |
string indicating the name of the exported results file |
Details
Runs Oyser_run_sec5, Oyser_run_sec6 and Oyster_phase_export
Value
XLSX files of all result matrices of the trace element model as well as a list containing these matrices:
phase_stat |
matrix of statistics of trace elements and phases in the total map |
el_time |
Matrix of trace element concentrations through time |
M_el_mat |
Matrix of mass accumulation per trace element |
M_el_mat_c |
Matrix of cumulative mass accumulation per trace element |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
Function that exports phase statistics
Description
Function that searches through the matrix of phases per pixel and exports the statistics of representation of different phases in the map as well as the bulk composition of pixels in the map. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_phase_stats(phasemat, phases)
Arguments
phasemat |
matrix of phases of each pixel sorted by X- and Y-coordinate of the pixel |
phases |
Matrix containing colour and trace element data of the phases in the XRF phase map |
Details
Phase statistics are calculated by looping through the matrix of phases created from the XRF phase map and comparing with the "phases" statistics table
Value
phase_stat |
matrix of statistics of trace elements and phases in the total map |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_phase_matrix_BMP"
Examples
phase_stat<-Oyster_phase_stats(phasemat, O1_phase)
Plot the converted shell cross section
Description
Simple function that returns a plot of the shell cross section after it has been converted to a common X-axis. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_plot_cross_section(cross_section)
Arguments
cross_section |
Digitized cross section of the shell with shell top, bottom and growth increments relative to a common X-axis |
Details
Plotting of digitized cross section after first modelling step to verify the correct digitization of the shell increments
Value
Opens a new plotting window to plot the shell cross section based on its X- and Y-coordinates
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
Examples
Oyster_plot_cross_section(cross_section)
Plot the result of interpolation of sub-increments
Description
Formula that plots the result of the interpolation of digitized shell growth increments to reconstruct sub-increments to provide a check on the progress of the model. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_plot_incr_CS(IncG, incr_matrix, Tstep)
Arguments
IncG |
Matrix of X- and Y-coordinates of all interpolated sub-increments |
incr_matrix |
Matrix listing characteristics of each digitized increment |
Tstep |
The step size (dt) in time (days) used to interpolate the existing shell increments |
Details
In order to prevent overcrowding the plot area and slowing the plotting process, only original shell increments and sub-increments halfway between original increments are plotted. Sub-increments are colored blue
Value
No data is exported, but a plot showing interpolated sub-increments is given in a separate window.
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 - A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
Examples
Oyster_plot_incr_CS(IncG,incr_matrix3,Tstep=1)
Plot the result of interpolation of sub-increments with a coloured area plot
Description
Formula that plots the result of the interpolation of digitized shell growth increments to reconstruct sub-increments to provide a check on the progress of the model. Areas between sub-increments are coloured in direction of growth using the heat colour palette. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_plot_incr_fill(IncG)
Arguments
IncG |
Matrix of X- and Y-coordinates of all interpolated sub-increments |
Details
Areas between sub-increments are represented by coloured polygons, while digitized increments are plotted using black lines. High numbers of interpolated sub-increments can cause plotting to become slow
Value
No data is exported, but a coloured plot showing interpolated sub-increments is given in a separate window.
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 - A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
Examples
Oyster_plot_incr_fill(IncG)
Runs complete Step 2 of the growth model
Description
Function that combines all functions in Step 2 of the bivalve growth model and runs them consecutively given the right input. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_run_sec2(raw_data, image_length, Xstep)
Arguments
raw_data |
Numeric data frame containing the X- and Y-coordinates digitized in Adobe Illustrator or another image processing software |
image_length |
Measured maximum length of the area of the cross section that is represented in raw_data |
Xstep |
The step size (dx) in X-direction used to interpolate coordinates of shell increments |
Details
This function runs the functions Oyster_Convert_cross_section, Oyster_plot_cross_section, Oyster_incr_area, Oyster_Shell_thickness and Oyster_Shell_height consecutively
Value
List of three items:
cross_section |
Digitized cross section of the shell with shell top, bottom and growth increments relative to a common X-axis |
incr_matrix |
Matrix listing characteristics of each digitized increment |
lengthfactor |
Factor of actual shell length relative to shell length in cross section, used to constrain pixelsize in phase map |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
Examples
List2<-Oyster_run_sec2(O1_input, image_length, Xstep=1)
Runs complete Step 3 of the growth model
Description
Function that combines all functions in Step 3 of the bivalve growth model and runs them consecutively given the right input. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_run_sec3(cross_section, incr_matrix, season_length=250, Xstep=0.1,
Tstep=1, Oyster_height, Oyster_length)
Arguments
cross_section |
Digitized cross section of the shell with shell top, bottom and growth increments relative to a common X-axis |
incr_matrix |
Matrix listing characteristics of each digitized increment |
season_length |
Length (in days) of the growth season of the studied bivalve |
Xstep |
The step size (dx) in X-direction used to interpolate coordinates of shell increments |
Tstep |
The step size (dt) in time (days) used to interpolate the existing shell increments |
Oyster_height |
Measured maximum height of the shell |
Oyster_length |
Measured maximum length of the shell in anterio-posterior direction |
Details
This function runs the functions Oyster_Increment_cross_section, Oyster_plot_Inc_CS, Oyster_Inc_fill, Oyster_subincr_area, Oyster_subincr_shell_height, Oyster_subincr_av_thickness and Oyster_ellipse_parameters consecutively
Value
List of two items:
IncG |
Matrix of X- and Y-coordinates of all interpolated sub-increments |
subincr_matrix |
Revised version of the "yearly_matrix" data frame that contains characteristics (sub-increment number, X-value of start of increment) recalculated for every sub-increment |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
Examples
List3<-Oyster_run_sec3(cross_section, incr_matrix3, season_length=250, Xstep=1,
Tstep=1, Oyster_height, Oyster_length)
Runs complete Step 4 of the growth model
Description
Function that combines all functions in Step 4 of the bivalve growth model and runs them consecutively given the right input. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_run_sec4(IncG, subincr_matrix, Xstep = 0.1)
Arguments
IncG |
Matrix of X- and Y-coordinates of all interpolated sub-increments |
subincr_matrix |
Revised version of the "yearly_matrix" data frame that contains characteristics calculated for every sub-increment |
Xstep |
The step size (dx) in X-direction used to interpolate coordinates of shell increments |
Details
This function runs the functions Oyster_Z_matrices and Oyster_Volumes consecutively
Value
A list of two items:
subincr_matrix |
Revised version of the "incr_matrix" data frame that contains characteristics calculated for every sub-increment |
IncGAnet |
Matrix of areas of cross sections in YZ-directions sorted by X-values and by sub-increment |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
Examples
## Not run:
List4<-Oyster_run_sec4(IncG, subincr_matrix4, Xstep = 1)
## End(Not run)
Runs complete Step 5 of the trace element model
Description
Function that combines all functions in Step 5 of the bivalve trace element model and runs them consecutively given the right input. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_run_sec5(phases_name, image_name, image_ext)
Arguments
phases_name |
String of full name (including extension!) of the CSV file that contains information about the phases in the map |
image_name |
String of full name of the BMP that needs to be imported, excluding extension |
image_ext |
Extention of phase map file ("BMP" or "TIF") |
Details
This function runs the functions Oyster_import_phases, Oyster_phase_matrix_BMP, Oyster_phase_matrix_TIF and Oyster_phase_stat consecutively
Value
List of two items:
phasemat |
matrix of phases of each pixel sorted by X- and Y-coordinate of the pixel |
phase_stat |
matrix of statistics of trace elements and phases in the total map |
phases |
Matrix containing colour, density and trace element data of the phases in the XRF phase map |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
Runs complete Step 6 of the trace element model
Description
Function that combines all functions in Step 6 of the bivalve trace element model and runs them consecutively given the right input. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_run_sec6(phasemat, IncG, pixelsize, phases, subincr_matrix, npma,
name_file)
Arguments
phasemat |
matrix of phases of each pixel sorted by X- and Y-coordinate of the pixel |
IncG |
Matrix of X- and Y-coordinates of all interpolated sub-increments |
pixelsize |
size of pixels in the phase map in micrometer |
phases |
Matrix containing colour and trace element data of the phases in the XRF phase map |
subincr_matrix |
Data frame that contains characteristics of every sub-increment |
npma |
Integer n-value determining the window size of the moving average smoothing of the mass accumulation record |
name_file |
string indicating the name of the exported results file |
Details
This function runs the functions Oyster_subincr_phases, Oyster_Mass_gain Oyster_el_time and Oyster_accumulation consecutively
Value
List of three items:
el_time |
Matrix of trace element concentrations through time |
M_el_mat |
Matrix of mass accumulation per trace element |
M_el_mat_c |
Matrix of cumulative mass accumulation per trace element |
subincr_matrix |
Data frame that contains characteristics of every sub-increment |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
Examples
## Not run:
List6<-Oyster_run_sec6(phasemat, IncG, pixelsize, O1_phase, subincr_matrix5, npma=10,
"test_export")
## End(Not run)
Formula that calculates area between sub-increments
Description
Formula that calculates cross section area between each sub-increment and the previous sub-increment. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_subincr_area(IncG, subincr_matrix, Xstep)
Arguments
IncG |
Matrix of X- and Y-coordinates of all interpolated sub-increments |
subincr_matrix |
Data frame that contains characteristics of every sub-increment |
Xstep |
Step value in X-direction for the interpolation of sub-increments |
Details
Areas between sub-increments are calculated by averaging the difference in Y-values between sub-increments and multiplying them with the step in X-values (dx)
Value
subincr_matrix |
Revised version of the "incr_matrix" data frame that contains cross section area recalculated for every sub-increment |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_Shell_length"
Examples
subincr_matrix1<-Oyster_subincr_area(IncG, subincr_matrix0, Xstep=1)
Formula that calculates average shell thickness through time
Description
Formula that calculates average shell thickness at the moment of deposition of each shell sub-increment from cross section area and shell length and adds the result to the matrix of increment characteristics. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_subincr_av_thickness(subincr_matrix)
Arguments
subincr_matrix |
Data frame that contains characteristics of every sub-increment |
Details
Shell thickness is calculated as the ratio between cross section area and shell length (Increment 0)
Value
subincr_matrix |
Revised version of the "incr_matrix" data frame that contains average shell thickness recalculated for every sub-increment |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_av_thickness"
Examples
subincr_matrix3<-Oyster_subincr_av_thickness(subincr_matrix2)
Formula that calculates average shell thickness through time
Description
Formula that calculates average shell thickness at the moment of deposition of each shell sub-increment from X- and Y-coordinates of the shell increments and adds the result to the matrix of increment characteristics. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_subincr_av_thickness_X(IncG, subincr_matrix)
Arguments
IncG |
Matrix of X- and Y-coordinates of all interpolated sub-increments |
subincr_matrix |
Data frame that contains characteristics of every sub-increment |
Details
Shell thickness is calculated as the average difference in Y-values between the shell sub-increment and the top of the shell (Increment 0)
Value
subincr_matrix |
Revised version of the "incr_matrix" data frame that contains average shell thickness recalculated for every sub-increment |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_av_thickness"
Examples
subincr_matrix3<-Oyster_subincr_av_thickness_X(IncG, subincr_matrix2)
Calculates proportion of phases in each sub-increment
Description
Function that takes the matrix of sub-increment positions and the matrix of phases and calculates the amount of pixels of each phase that is contained in each sub-increment based on pixelsize and phase characteristics. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_subincr_phases(IncG, phasemat, pixelsize, phases)
Arguments
IncG |
Matrix of X- and Y-coordinates of all interpolated sub-increments |
phasemat |
matrix of phases of each pixel sorted by X- and Y-coordinate of the pixel |
pixelsize |
size of pixels in the phase map in millimeter |
phases |
Matrix containing colour and trace element data of the phases in the XRF phase map |
Details
For every sub-increment, all pixels that cover area in the sub-increment are identified based on the pixel size of the phase map and the X- and Y-positions of the sub-increments. The amount of pixels of each phase in the sub-increment is saved in a new matrix of phases per sub-increment
Value
A matrix of the amount of pixels for each phase found in every sub-increment
phase_mat |
Matrix of amounts of pixels of each phase per sub-increment |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_Suby_av_thickness"
Examples
## Not run:
phase_mat<-Oyster_subincr_phases(IncG, phasemat, pixelsize, O1_phase)
## End(Not run)
A fomula to calculate shell height per sub-increment
Description
Formula that calculates shell height at the time of deposition of each sub-increment. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
Oyster_subincr_shell_height(subincr_matrix, IncG, Xstep)
Arguments
subincr_matrix |
Data frame that contains characteristics of every sub-increment |
IncG |
Matrix of X- and Y-coordinates of all interpolated sub-increments |
Xstep |
Step value in X-direction for the interpolation of sub-increments |
Details
Shell height is calculated via the Pythagorean Theorem using the X- and Y-coordinates of both ends of the shell sub-increment with extreme X-values
Value
subincr_matrix |
Revised version of the "incr_matrix" data frame that contains shell height recalculated for every sub-increment |
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
"Oyster_Shell_height"
Examples
subincr_matrix2<-Oyster_subincr_shell_height(subincr_matrix1,IncG,Xstep=1)
ShellTrace: Growth and trace element uptake modelling in bivalve shells
Description
This package contains formulae used to model the growth and development of bivalve shells based on digitized coordinated of shell increments in a longitudinal cross section thorugh the shell. The growth model is combined with XRF mapping results of the same cross section and a seasonal growth rate model to model trace element concentrations and uptake rates into the bivalve shell. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Details
Formulae in this package form the several steps of the model, and are not meant to be used individually. The order and application of these functions is outlined in the publication in Geoscientific Model Development that bears the name of the model (de Winter, in review)
Author(s)
Niels J. de Winter
Maintainer: Niels J. de Winter
References
de Winter, N. J.: ShellTrace v1.0 - A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
See Also
GitHub
Manuscript
Supplementary data
Author website
Examples
print("de Winter, N. J.: ShellTrace v1.0 - A new approach for
modelling growth and trace element uptake in marine bivalve shells:
Model verification on pacific oyster shells (Crassostrea gigas),
Geosci. Model Dev. Discuss., in review, 2017.")
TIF image of phase map of cross section of modern oyster.
Description
An image of the microXRF phase map of the cross section used for this model from the Crassostre gigas #1 oyster used as an example in de Winter (2017)
Usage
data(TIF)
Format
A TIF image imported into R as a large data array
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Z-values describing the base ellipse of the oyster
Description
A dataset containing Z-coordinates of the base ellipse calculated for all subincrements in the Crassostrea gigas #1 oyster used as an example in de Winter (2017). A Xstep of 0.1, a Tstep of 1 and a growth season of 250 days are used.
Usage
data(Z_mat)
Format
A large data frame with 101 rows and 1291 variables:
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Digitized growth increments in cross section of modern oyster rescaled to the same X-axis.
Description
A dataset containing X- and Y-coordinates of digitized growth increments from the Crassostrea gigas #1 oyster used as an example in de Winter (2017) resampled to fit the same X-axis.
Usage
data(cross_section)
Format
A data frame with 101 rows and 10 variables:
- 0
X-coordinates in mm
- 44
Empty column, title contains day of the year the shell started growing (estimated)
- 0
Y-coordinates of digitized increment 0 (top of shell), title contains age in days
- 30
Y-coordinates of digitized increment 1, title contains age in days
- 90
Y-coordinates of digitized increment 2, title contains age in days
- 270
Y-coordinates of digitized increment 3, title contains age in days
- 420
Y-coordinates of digitized increment 4, title contains age in days
- 780
Y-coordinates of digitized increment 5, title contains age in days
- 1050
Y-coordinates of digitized increment 6, title contains age in days
- 1290
Y-coordinates of digitized increment 7 (bottom of shell), title contains age in days
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Matrix listing the concentrations of elements in every subincrement
Description
A dataset containing the concentrations of every element measured in the phase map of the XRF mapped surface of the Crassostrea gigas #1 oyster used as an example in de Winter (2017) reconstructed in every subincrement.
Usage
data(el_time)
Format
A data frame with 24 rows and 1291 variables:
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Length (in mm) of the digitized phase map image.
Description
A single value of the image length in mm
Usage
data(image_length)
Format
A single value:
Length in mm of digitized shell cross section
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Matrix containing data calculated for each growth band.
Description
A dataset containing specific parameters calculated for all digitized growth increments from the Crassostre gigas #1 oyster used as an example in de Winter (2017) sorted per increment.
Usage
data(incr_matrix0)
Format
A data frame with 8 rows and 3 variables:
- growth band
name of the growth increment
- age (days)
Age associated with the deposition of the growth increment
- age_cal (days)
Age associated with the deposition of the growth increment, calibrated to the seasonal cycle
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Matrix containing data calculated for each growth band.
Description
A dataset containing specific parameters calculated for all digitized growth increments from the Crassostre gigas #1 oyster used as an example in de Winter (2017) sorted per increment.
Usage
data(incr_matrix1)
Format
A data frame with 8 rows and 5 variables:
- growth band
name of the growth increment
- age (days)
Age associated with the deposition of the growth increment
- age_cal (days)
Age associated with the deposition of the growth increment, calibrated to the seasonal cycle
- incr_area
area between subsequent increments
- incr_cumarea
area between increment and the top of the shell
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Matrix containing data calculated for each growth band.
Description
A dataset containing specific parameters calculated for all digitized growth increments from the Crassostre gigas #1 oyster used as an example in de Winter (2017) sorted per increment.
Usage
data(incr_matrix2)
Format
A data frame with 8 rows and 6 variables:
- growth band
name of the growth increment
- age (days)
Age associated with the deposition of the growth increment
- age_cal (days)
Age associated with the deposition of the growth increment, calibrated to the seasonal cycle
- incr_area
area between subsequent increments
- incr_cumarea
area between increment and the top of the shell
- av_thickness
average thickness of area between increment and the top of the shell
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Matrix containing data calculated for each growth band.
Description
A dataset containing specific parameters calculated for all digitized growth increments from the Crassostre gigas #1 oyster used as an example in de Winter (2017) sorted per increment.
Usage
data(incr_matrix3)
Format
A data frame with 8 rows and 11 variables:
- growth band
name of the growth increment
- age (days)
Age associated with the deposition of the growth increment
- age_cal (days)
Age associated with the deposition of the growth increment, calibrated to the seasonal cycle
- incr_area
area between subsequent increments
- incr_cumarea
area between increment and the top of the shell
- av_thickness
average thickness of area between increment and the top of the shell
- p1x
X-value of first (leftmost) point in growth increment
- p1y
Y-value of first (leftmost) point in growth increment
- p2x
X-value of last (rightmost) point in growth increment
- p2y
Y-value of last (rightmost) point in growth increment
- shell_height
Height of shell during deposition of shell increment
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Multiplier used to convert shell cross section from pixels to mm
Description
A single value of the amount of mm contained in one pixel
Usage
data(lengthfactor)
Format
A single value:
Length in mm of one pixel in the digitized shell cross section
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Matrix listing the amount of pixels of each phase in every subincrement
Description
A dataset containing the amounts of pixels of each phase in the phase map of the XRF mapped surface of the Crassostrea gigas #1 oyster used as an example in de Winter (2017) represented in every subincrement.
Usage
data(phase_mat)
Format
A data frame with 4 rows and 1291 variables:
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Statistics of elemental concentrations in XRF map of oyster
Description
A dataset containing trace element concentrations and fractions of a phase map of the XRF mapped surface of the Crassostrea gigas #1 oyster used as an example in de Winter (2017)
Usage
data(phase_stat)
Format
A data frame with 5 rows and 27 variables:
- Names
Names of phases
- pixels
Amount of pixels representing the phase
- fraction
Fraction of map surface represented by phase
- C
Concentration of C in phase
- O
Concentration of O in phase
- Na
Concentration of Na in phase
- Mg
Concentration of Mg in phase
- Al
Concentration of Al in phase
- Si
Concentration of Si in phase
- P
Concentration of P in phase
- S
Concentration of S in phase
- Cl
Concentration of Cl in phase
- K
Concentration of K in phase
- Ca
Concentration of Ca in phase
- Ti
Concentration of Ti in phase
- Cr
Concentration of Cr in phase
- Mn
Concentration of Mn in phase
- Fe
Concentration of Fe in phase
- Ni
Concentration of Ni in phase
- Cu
Concentration of Cu in phase
- Zn
Concentration of Zn in phase
- Br
Concentration of Br in phase
- Rb
Concentration of Rb in phase
- Sr
Concentration of Sr in phase
- Rh
Concentration of Rh in phase
- Ba
Concentration of Ba in phase
- Pb
Concentration of Pb in phase
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Matrix of phases names for each pixel in the phase map
Description
A dataset containing names of phases for every pixel in the phase map measured on a cross section through the Crassostrea gigas #1 oyster used as an example in de Winter (2017)
Usage
data(phasemat)
Format
A large data frame with 2258 rows and 2383 variables:
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Size of pixels in phase map in mm
Description
A single value of the amount of mm contained in one pixel rounded up to the nearest micrometer.
Usage
data(pixelsize)
Format
A single value:
Length in mm of one pixel in the digitized shell cross section rounded up to the nearest micrometer
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Function to do an n-point moving average
Description
Performs a moving average smoothing on a data series. de Winter, N. J. (2017) <doi:10.5194/gmd-2017-137>
Usage
pma(x, i, n)
Arguments
x |
A numeric data frame containing the data set to be smoothed, X-values should be in the first column |
i |
The index of the column that contains the Y-values |
n |
Integer N-value determining the window size of the moving average smoothing |
Value
A numeric data frame containing three columns: One with X-values, one with Y-values and one with smoothed Y-values
Note
Please cite Geoscientific Model Development paper dealing with the ShellTrace model
Author(s)
Niels J. de Winter
Source
GitHub
Manuscript
Supplementary data
Author website
References
de Winter, N. J.: ShellTrace v1.0 ? A new approach for modelling growth and trace element uptake in marine bivalve shells: Model verification on pacific oyster shells (Crassostrea gigas), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2017-137, in review, 2017.
Examples
Nile<-as.data.frame(Nile)
Nile<-cbind(rownames(Nile),Nile)
Nile_5pma<-pma(Nile,2,5)
Matrix containing data calculated for each growth band.
Description
A dataset containing specific parameters calculated for all interpolated subincrements from the Crassostrea gigas #1 oyster used as an example in de Winter (2017) sorted per increment.
Usage
data(subincr_matrix0)
Format
A data frame with 1291 rows and 3 variables:
- Age
age (in days) of the subincrement
- p1xs
X-value of the first (leftmost) point in the subincrement
- p2xs
X-value of the last (rightmost) point in the subincrement
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Matrix containing data calculated for each growth band.
Description
A dataset containing specific parameters calculated for all interpolated subincrements from the Crassostrea gigas #1 oyster used as an example in de Winter (2017) sorted per increment.
Usage
data(subincr_matrix1)
Format
A data frame with 1291 rows and 5 variables:
- Age
age (in days) of the subincrement
- p1xs
X-value of the first (leftmost) point in the subincrement
- p2xs
X-value of the last (rightmost) point in the subincrement
- areaY
Area between subsequent subincrements
- areaC
Area between subincrement and top of shell
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Matrix containing data calculated for each growth band.
Description
A dataset containing specific parameters calculated for all interpolated subincrements from the Crassostrea gigas #1 oyster used as an example in de Winter (2017) sorted per increment.
Usage
data(subincr_matrix2)
Format
A data frame with 1291 rows and 10 variables:
- Age
age (in days) of the subincrement
- p1xs
X-value of the first (leftmost) point in the subincrement
- p2xs
X-value of the last (rightmost) point in the subincrement
- areaY
Area between subsequent subincrements
- areaC
Area between subincrement and top of shell
- p1y
Y-value of the first (leftmost) point in the subincrement
- p2y
Y-value of the last (rightmost) point in the subincrement
- shell_height
Height of shell during deposition of the subincrement
- firstl
Row number in IncG of first (leftmost) data point belonging to the subincrement
- lastl
Row number in IncG of last (rightmost) data point belonging to the subincrement
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Matrix containing data calculated for each growth band.
Description
A dataset containing specific parameters calculated for all interpolated subincrements from the Crassostrea gigas #1 oyster used as an example in de Winter (2017) sorted per increment.
Usage
data(subincr_matrix3)
Format
A data frame with 1291 rows and 11 variables:
- Age
age (in days) of the subincrement
- p1xs
X-value of the first (leftmost) point in the subincrement
- p2xs
X-value of the last (rightmost) point in the subincrement
- areaY
Area between subsequent subincrements
- areaC
Area between subincrement and top of shell
- p1y
Y-value of the first (leftmost) point in the subincrement
- p2y
Y-value of the last (rightmost) point in the subincrement
- shell_height
Height of shell during deposition of the subincrement
- firstl
Row number in IncG of first (leftmost) data point belonging to the subincrement
- lastl
Row number in IncG of last (rightmost) data point belonging to the subincrement
- av_thickness
Average thickness during deposition of the subincrement
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Matrix containing data calculated for each growth band.
Description
A dataset containing specific parameters calculated for all interpolated subincrements from the Crassostrea gigas #1 oyster used as an example in de Winter (2017) sorted per increment.
Usage
data(subincr_matrix4)
Format
A data frame with 1291 rows and 15 variables:
- Age
age (in days) of the subincrement
- p1xs
X-value of the first (leftmost) point in the subincrement
- p2xs
X-value of the last (rightmost) point in the subincrement
- areaY
Area between subsequent subincrements
- areaC
Area between subincrement and top of shell
- p1y
Y-value of the first (leftmost) point in the subincrement
- p2y
Y-value of the last (rightmost) point in the subincrement
- shell_height
Height of shell during deposition of the subincrement
- firstl
Row number in IncG of first (leftmost) data point belonging to the subincrement
- lastl
Row number in IncG of last (rightmost) data point belonging to the subincrement
- av_thickness
Average thickness during deposition of the subincrement
- W_ellipse
Length of the short axis of the base ellipse of the oyster during deposition of the subincrement
- L_ellipse_acc
Length of the long axis of the base ellipse of the oyster during deposition of the subincrement projected on the X-axis
- a_ellipse
Half the length of the long axis of the base ellipse of the oyster during deposition of the subincrement
- b_ellipse
Half the length of the short axis of the base ellipse of the oyster during deposition of the subincrement
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Matrix containing data calculated for each growth band.
Description
A dataset containing specific parameters calculated for all interpolated subincrements from the Crassostrea gigas #1 oyster used as an example in de Winter (2017) sorted per increment.
Usage
data(subincr_matrix5)
Format
A data frame with 1291 rows and 17 variables:
- Age
age (in days) of the subincrement
- p1xs
X-value of the first (leftmost) point in the subincrement
- p2xs
X-value of the last (rightmost) point in the subincrement
- areaY
Area between subsequent subincrements
- areaC
Area between subincrement and top of shell
- p1y
Y-value of the first (leftmost) point in the subincrement
- p2y
Y-value of the last (rightmost) point in the subincrement
- shell_height
Height of shell during deposition of the subincrement
- firstl
Row number in IncG of first (leftmost) data point belonging to the subincrement
- lastl
Row number in IncG of last (rightmost) data point belonging to the subincrement
- av_thickness
Average thickness during deposition of the subincrement
- W_ellipse
Length of the short axis of the base ellipse of the oyster during deposition of the subincrement
- L_ellipse_acc
Length of the long axis of the base ellipse of the oyster during deposition of the subincrement projected on the X-axis
- a_ellipse
Half the length of the long axis of the base ellipse of the oyster during deposition of the subincrement
- b_ellipse
Half the length of the short axis of the base ellipse of the oyster during deposition of the subincrement
- VolI
Volume between subsequent subincrements
- VolC
Volume between subincrement and top of shell
Source
https://doi.org/10.5194/gmd-2017-137-supplement
Matrix containing data calculated for each growth band.
Description
A dataset containing specific parameters calculated for all interpolated subincrements from the Crassostrea gigas #1 oyster used as an example in de Winter (2017) sorted per increment.
Usage
data(subincr_matrix6)
Format
A data frame with 1291 rows and 20 variables:
- Age
age (in days) of the subincrement
- p1xs
X-value of the first (leftmost) point in the subincrement
- p2xs
X-value of the last (rightmost) point in the subincrement
- areaY
Area between subsequent subincrements
- areaC
Area between subincrement and top of shell
- p1y
Y-value of the first (leftmost) point in the subincrement
- p2y
Y-value of the last (rightmost) point in the subincrement
- shell_height
Height of shell during deposition of the subincrement
- firstl
Row number in IncG of first (leftmost) data point belonging to the subincrement
- lastl
Row number in IncG of last (rightmost) data point belonging to the subincrement
- av_thickness
Average thickness during deposition of the subincrement
- W_ellipse
Length of the short axis of the base ellipse of the oyster during deposition of the subincrement
- L_ellipse_acc
Length of the long axis of the base ellipse of the oyster during deposition of the subincrement projected on the X-axis
- a_ellipse
Half the length of the long axis of the base ellipse of the oyster during deposition of the subincrement
- b_ellipse
Half the length of the short axis of the base ellipse of the oyster during deposition of the subincrement
- VolI
Volume between subsequent subincrements
- VolC
Volume between subincrement and top of shell
- WeightI
Mass of shell material between subsequent subincrements
- Growth_rate
Mass of shell material accumulated per day
- WeightC
Mass of shell material between subincrement and top of shell