| Version: | 0.2 |
| Date: | 2018-10-14 |
| Title: | Temperature Response |
| Depends: | R (≥ 3.1.0) |
| Description: | Fits temperature response models to rate measurements taken at different temperatures. Etienne Low-Decarie,Tobias G. Boatman, Noah Bennett,Will Passfield,Antonio Gavalas-Olea,Philipp Siegel, Richard J. Geider (2017) <doi:10.1002/ece3.3576> . |
| License: | GPL-3 |
| URL: | https://github.com/low-decarie/temperatureresponse |
| RoxygenNote: | 6.0.1 |
| LazyData: | true |
| Imports: | graphics, stats, broom, dplyr, rootSolve, minpack.lm, AICcmodavg, numDeriv |
| NeedsCompilation: | no |
| Packaged: | 2018-10-30 01:20:11 UTC; LowDecarie |
| Author: | Etienne Low-Decarie [aut, cre] |
| Maintainer: | Etienne Low-Decarie <etienne.decarie@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2018-10-30 15:50:07 UTC |
Temperature response of the growth rate of Emiliania_huxleyi
Description
A data set containing the temperature response of the growth rate of Emiliania_huxleyi
Usage
Emiliania_huxleyi
Format
A data frame with 39 rows and 3 variables:
- temp
temperature
- rate
growth rate
...
Source
amend_output
Description
Helper function that add terms to the broom output of fit
Usage
amend_output(output, fit, f_equ, temp, rate, try_test, augment, return_fit)
Arguments
output |
broom output of fit |
fit |
the model output of the fitting process |
f_equ |
equation with fitted parameters |
temp |
temperature values of measurements |
rate |
rate that changes with temperature |
try_test |
did the model fitting succeed or produce an error? |
augment |
add columns to the original dataset such as predictions, residuals and cluster assignments using package::broom (T/F)? |
return_fit |
return the model object (T/F)? |
Value
a data frame of, depending on augment argument, if FALSE, parameters, if TRUE, data with predicted values
Equation 10
Description
Equation from Thomas et al. (2014)
Usage
equ10(temp, rate, augment = F, return_fit = F)
Arguments
temp |
temperature (in Celsius) |
rate |
rate measurement |
augment |
logical wether the dataset with fits should be returned instead of the parameter values |
return_fit |
logical wether the model fit object should be returned |
Value
a data frame of, depending on augment argument, if FALSE, parameters, if TRUE, data with predicted values
Examples
## Not run:
output <- with(Emiliania_huxleyi, equ10(temp=temp, rate=rate))
## End(Not run)
Equation 11
Description
Equation in Montagnes et al. 2008
Usage
equ11(temp, rate, augment = F, return_fit = F)
Arguments
temp |
temperature (in Celsius) |
rate |
rate measurement |
augment |
logical wether the dataset with fits should be returned instead of the parameter values |
return_fit |
logical wether the model fit object should be returned |
Value
depends on augment: if false, fitting parameters or fitted data
Examples
## Not run:
output <- with(Emiliania_huxleyi, equ11(temp=temp, rate=rate))
## End(Not run)
Equation 12
Description
Equation in Montagnes et al (2008) citing Flinn (1991)
Usage
equ12(temp, rate, augment = F, return_fit = F)
Arguments
temp |
temperature (in Celsius) |
rate |
rate measurement |
augment |
logical wether the dataset with fits should be returned instead of the parameter values |
return_fit |
logical wether the model fit object should be returned |
Value
depends on augment: if false, fitting parameters or fitted data
Examples
output <- with(Emiliania_huxleyi, equ12(temp=temp, rate=rate))
Equation 13
Description
Equation in Ratkowsky et al. (1983)
Usage
equ13(temp, rate, augment = F, return_fit = F)
Arguments
temp |
temperature (in Celsius) |
rate |
rate measurement |
augment |
logical wether the dataset with fits should be returned instead of the parameter values |
return_fit |
logical wether the model fit object should be returned |
Value
depends on augment: if false, fitting parameters or fitted data
Examples
output <- with(Emiliania_huxleyi, equ14(temp=temp, rate=rate))
Equation 14
Description
Equation from Kamykowski (1985)
Usage
equ14(temp, rate, augment = F, return_fit = F)
Arguments
temp |
temperature (in Celsius) |
rate |
rate measurement |
augment |
logical wether the dataset with fits should be returned instead of the parameter values |
return_fit |
logical wether the model fit object should be returned |
Value
a data frame of, depending on augment argument, if FALSE, parameters, if TRUE, data with predicted values
Equation 15
Description
New equation (based on sine)
Usage
equ15(temp, rate, augment = F, return_fit = F)
Arguments
temp |
temperature (in Celsius) |
rate |
rate measurement |
augment |
logical wether the dataset with fits should be returned instead of the parameter values |
return_fit |
logical wether the model fit object should be returned |
Value
a data frame of, depending on augment argument, if FALSE, parameters, if TRUE, data with predicted values
Examples
output <- with(Emiliania_huxleyi, equ15(temp=temp, rate=rate))
Equation 16
Description
Equation from "A Key Marine Diazotroph in a Changing Ocean: The Interacting Effects of Temperature, CO2 and Light on the Growth of Trichodesmium erythraeum IMS101". Challenging to fit to many datasets. Does not fit to example dataset.
Usage
equ16(temp, rate, augment = F, return_fit = F)
Arguments
temp |
temperature (in Celsius) |
rate |
rate measurement |
augment |
logical wether the dataset with fits should be returned instead of the parameter values |
return_fit |
logical wether the model fit object should be returned |
Value
a data frame of, depending on augment argument, if FALSE, parameters, if TRUE, data with predicted values
Examples
output <- with(Emiliania_huxleyi, equ16(temp=temp, rate=rate))
Equation 4
Description
Equation 4 is model H in Li & Dickie (1987) citing Hinshelwood (1947)
Usage
equ4(temp, rate, augment = F, return_fit = F)
Arguments
temp |
temperature (in Celsius) |
rate |
rate measurement |
augment |
logical wether the dataset with fits should be returned instead of the parameter values |
return_fit |
logical wether the model fit object should be returned |
Value
a data frame of, depending on augment argument, if FALSE, parameters, if TRUE, data with predicted values
Examples
output <- with(Emiliania_huxleyi, equ4(temp=temp, rate=rate))
Equation 5
Description
Equation 5 is model J from Li & Dickie (1987) citing Johnson et al. (1942) Does not currently work
Usage
equ5(temp, rate, augment = F, return_fit = F)
Arguments
temp |
temperature (in Celsius) |
rate |
rate measurement |
augment |
logical wether the dataset with fits should be returned instead of the parameter values |
return_fit |
logical wether the model fit object should be returned |
Value
a data frame of, depending on augment argument, if FALSE, parameters, if TRUE, data with predicted values
Examples
output <- with(Emiliania_huxleyi, equ5(temp=temp, rate=rate))
Equation 6
Description
Equation 6
Usage
equ6(temp, rate, augment = F, return_fit = F)
Arguments
temp |
temperature (in Celsius) |
rate |
rate measurement |
augment |
logical wether the dataset with fits should be returned instead of the parameter values |
return_fit |
logical wether the model fit object should be returned |
Value
a data frame of, depending on augment argument, if FALSE, parameters, if TRUE, data with predicted values
Examples
output <- with(Emiliania_huxleyi, equ6(temp=temp, rate=rate))
Equation 7
Description
Equation 7 from Montagnes et al (2008) citing Schoolfield et al. (1981)
Usage
equ7(temp, rate, augment = F, return_fit = F)
Arguments
temp |
temperature (in Celsius) |
rate |
rate measurement |
augment |
logical wether the dataset with fits should be returned instead of the parameter values |
return_fit |
logical wether the model fit object should be returned |
Value
a data frame of, depending on augment argument, if FALSE, parameters, if TRUE, data with predicted values
Examples
output <- with(Emiliania_huxleyi, equ7(temp=temp, rate=rate))
Equation 8
Description
Equation in Li & Dickie (1987) citing Stoermer & Ladewski (1976): a*exp(-0.5*((temp-tref)/b)^2)
Usage
equ8(temp, rate, augment = F, plot_profile = F, return_fit = F)
Arguments
temp |
temperature (in celsius or Kelvin) |
rate |
rate measurement |
augment |
logical wether the dataset with fits should be returned instead of the parameter values |
plot_profile |
logical should the model fitting profile be plotted |
return_fit |
logical wether the model fit object should be returned |
Value
depends on augment: if false, fitting parameters or fitted data
Examples
output <- with(Emiliania_huxleyi, equ8(temp=temp, rate=rate))
Equation 9
Description
Equation from Montagnes et al. 2008
Usage
equ9(temp, rate, augment = F, return_fit = F)
Arguments
temp |
temperature (in Celsius) |
rate |
rate measurement |
augment |
logical wether the dataset with fits should be returned instead of the parameter values |
return_fit |
logical wether the model fit object should be returned |
Value
a data frame of, depending on augment argument, if FALSE, parameters, if TRUE, data with predicted values
Examples
output <- with(Emiliania_huxleyi, equ9(temp=temp, rate=rate))
Fit model list
Description
Fits list of models (all models in package by default)
Usage
fitmodellist(temp, rate, augment = F, return_fit = F,
models = paste0("equ", 4:15))
Arguments
temp |
temperature (in Celsius) |
rate |
rate measurement (for example growth rate, but could also be abundance) |
augment |
logical wether the dataset with fits should be returned instead of the parameter values |
return_fit |
logical should the model object be returned |
models |
list of strings of equations to be fit such as paste0("equ",4:15) |
Value
a data frame of, depending on augment argument, if FALSE, parameters, if TRUE, data with predicted values
Examples
output <- with(Emiliania_huxleyi, fitmodellist(temp=temp, rate=rate))