fitRMU: Adjust incomplete timeseries with various constraints.
In phenology: Tools to Manage a Parametric Function that Describes Phenology and More
fitRMU R Documentation
Adjust incomplete timeseries with various constraints.
Description
The data must be a data.frame with the first column being years
and two columns for each beach: the average and the se for the estimate.
The correspondence between mean, se and density for each rookery are given in the RMU.names data.frame.
This data.frame must have a column named mean, another named se and a third named density. If
no sd column exists, no sd will be considered for the series and if no density column exists, it
will be considered as being "dnorm" (Gaussian distribution).
The aggregated number of nests and its confidence interval can be obtained using CI.RMU().
The names of beach columns must not begin by T_, SD_, a0_, a1_ or a2_ and cannot be r.
A RMU is the acronyme for Regional Managment Unit. See:
Wallace, B.P., DiMatteo, A.D., Hurley, B.J., Finkbeiner, E.M., Bolten, A.B.,
Chaloupka, M.Y., Hutchinson, B.J., Abreu-Grobois, F.A., Amorocho, D., Bjorndal, K.A.,
Bourjea, J., Bowen, B.W., Dueñas, R.B., Casale, P., Choudhury, B.C., Costa, A.,
Dutton, P.H., Fallabrino, A., Girard, A., Girondot, M., Godfrey, M.H., Hamann, M.,
López-Mendilaharsu, M., Marcovaldi, M.A., Mortimer, J.A., Musick, J.A., Nel, R.,
Seminoff, J.A., Troëng, S., Witherington, B., Mast, R.B., 2010. Regional
management units for marine turtles: a novel framework for prioritizing
conservation and research across multiple scales. PLoS One 5, e15465.
Variance for each value is additive based on both the observed SE (in the RMU.data
object) and a value.
The value is a global constant when model.SD is "global-constant".
The value is proportional to the observed number of nests when model.SD is
"global-proportional" with aSD_*observed+SD_ with aSD_ and SD_ being fitted
values. This value is fixed to zero when model.SD is "Zero".
The value is dependent on the rookery when model.SD is equal to
"Rookery-constant" or "Rookery-proportional" with a similar formula as previously
described for "global".
if method is NULL, it will simply return the names of required parameters.
Usage
fitRMU(
RMU.data = stop("data parameter must be provided"),
years.byrow = TRUE,
RMU.names = NULL,
model.trend = "Constant",
model.rookeries = "Constant",
model.SD = "Global-constant",
parameters = NULL,
fixed.parameters = NULL,
SE = NULL,
method = c("Nelder-Mead", "BFGS"),
control = list(trace = 1),
itnmax = c(1500, 1500),
cptmax.optim = 100,
limit.cpt.optim = 1e-05,
hessian = TRUE,
replicate.CI = 1000,
colname.year = "Year",
maxL = 1e+09
)
Arguments
RMU.data
A data.frame with a column Year (the name is defined in colname.year) and one to three columns per rookery defined in RMU.names
years.byrow
If TRUE, the RMU.data data.frame is organized with years in rows
RMU.names
A dataframe with one to three columns indicating name of columns for mean, standard deviation, and distribution for roockeris
model.trend
Can be Constant, Exponential or Year-specific
model.rookeries
Description temporal change in rookeries proportion. It be Constant, First-order or Second-order
model.SD
Can be Zero, Global-constant, Global-proportional or Rookery-constant. See description.
parameters
Parameters to fit
fixed.parameters
Parameters that are fixed
SE
Parameters SE for example from fitRMU_MHmcmc()
method
Methods to be used by optim()
control
List of controls for optim()
itnmax
A vector with maximum iterations for each method.
cptmax.optim
How many times optim can be ran when likelihood is better.
limit.cpt.optim
Limit to consider that likelihood is better.
hessian
If TRUE, the hessian matrix is calculated and then the standard error of parameters.
replicate.CI
Number of replicates to estimate CI of proportion for each rookery
colname.year
Name of the column to be used as time index
maxL
If an error is produced during the estimation of likelihood, replace -Ln L by this value
Details
fitRMU is used to estimate missing information when several linked values are observed along a timeseries
Value
Return a list with the results from optim and synthesis for proportions and numbers
Author(s)
Marc Girondot marc.girondot@gmail.com
See Also
Other Fill gaps in RMU:
CI.RMU(),
fitRMU_MHmcmc_p(),
fitRMU_MHmcmc(),
logLik.fitRMU(),
plot.fitRMU()
Examples
## Not run:
library("phenology")
RMU.names.AtlanticW <- data.frame(mean=c("Yalimapo.French.Guiana",
"Galibi.Suriname",
"Irakumpapy.French.Guiana"),
se=c("se_Yalimapo.French.Guiana",
"se_Galibi.Suriname",
"se_Irakumpapy.French.Guiana"),
density=c("density_Yalimapo.French.Guiana",
"density_Galibi.Suriname",
"density_Irakumpapy.French.Guiana"))
data.AtlanticW <- data.frame(Year=c(1990:2000),
Yalimapo.French.Guiana=c(2076, 2765, 2890, 2678, NA,
6542, 5678, 1243, NA, 1566, 1566),
se_Yalimapo.French.Guiana=c(123.2, 27.7, 62.5, 126, NA,
230, 129, 167, NA, 145, 20),
density_Yalimapo.French.Guiana=rep("dnorm", 11),
Galibi.Suriname=c(276, 275, 290, NA, 267,
542, 678, NA, 243, 156, 123),
se_Galibi.Suriname=c(22.3, 34.2, 23.2, NA, 23.2,
4.3, 2.3, NA, 10.3, 10.1, 8.9),
density_Galibi.Suriname=rep("dnorm", 11),
Irakumpapy.French.Guiana=c(1076, 1765, 1390, 1678, NA,
3542, 2678, 243, NA, 566, 566),
se_Irakumpapy.French.Guiana=c(23.2, 29.7, 22.5, 226, NA,
130, 29, 67, NA, 15, 20),
density_Irakumpapy.French.Guiana=rep("dnorm", 11)
)
cst <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Constant",
model.SD="Zero")
cst <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Constant",
model.SD="Zero",
control=list(trace=1, REPORT=100, maxit=500, parscale = c(3000, -0.2, 0.6)))
cst <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Constant",
model.SD="Zero", method=c("Nelder-Mead","BFGS"),
control = list(trace = 0, REPORT = 100, maxit = 500,
parscale = c(3000, -0.2, 0.6)))
expo <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Exponential",
model.SD="Zero", method=c("Nelder-Mead","BFGS"),
control = list(trace = 0, REPORT = 100, maxit = 500,
parscale = c(6000, -0.05, -0.25, 0.6)))
YS <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Year-specific", method=c("Nelder-Mead","BFGS"),
model.SD="Zero")
YS1 <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Year-specific", method=c("Nelder-Mead","BFGS"),
model.SD="Zero", model.rookeries="First-order")
YS1_cst <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Year-specific",
model.SD="Constant", model.rookeries="First-order",
parameters=YS1$par, method=c("Nelder-Mead","BFGS"))
YS2 <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Year-specific",
model.SD="Zero", model.rookeries="Second-order",
parameters=YS1$par, method=c("Nelder-Mead","BFGS"))
YS2_cst <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Year-specific",
model.SD="Constant", model.rookeries="Second-order",
parameters=YS1_cst$par, method=c("Nelder-Mead","BFGS"))
compare_AIC(Constant=cst, Exponential=expo,
YearSpecific=YS)
compare_AIC(YearSpecific_ProportionsFirstOrder_Zero=YS1,
YearSpecific_ProportionsFirstOrder_Constant=YS1_cst)
compare_AIC(YearSpecific_ProportionsConstant=YS,
YearSpecific_ProportionsFirstOrder=YS1,
YearSpecific_ProportionsSecondOrder=YS2)
compare_AIC(YearSpecific_ProportionsFirstOrder=YS1_cst,
YearSpecific_ProportionsSecondOrder=YS2_cst)
# Example of different types of plots
plot(cst, main="Use of different beaches along the time", what="total",
ylim=c(0, 4000))
plot(cst, main="Use of different beaches along the time", what = "proportions",
replicate.CI=0)
plot(cst, main="Use of different beaches along the time", what = "numbers",
aggregate="model", ylim=c(0, 4000), replicate.CI=0)
plot(cst, main="Use of different beaches along the time", what = "numbers",
aggregate="both", ylim=c(0, 11000), replicate.CI=0)
plot(expo, main="Use of different beaches along the time", what="total")
plot(YS2_cst, main="Use of different beaches along the time", what="total")
plot(YS1, main="Use of different beaches along the time")
plot(YS1_cst, main="Use of different beaches along the time")
plot(YS1_cst, main="Use of different beaches along the time", what="numbers")
# Gamma distribution should be used for MCMC outputs
RMU.names.AtlanticW <- data.frame(mean=c("Yalimapo.French.Guiana",
"Galibi.Suriname",
"Irakumpapy.French.Guiana"),
se=c("se_Yalimapo.French.Guiana",
"se_Galibi.Suriname",
"se_Irakumpapy.French.Guiana"),
density=c("density_Yalimapo.French.Guiana",
"density_Galibi.Suriname",
"density_Irakumpapy.French.Guiana"),
stringsAsFactors = FALSE)
data.AtlanticW <- data.frame(Year=c(1990:2000),
Yalimapo.French.Guiana=c(2076, 2765, 2890, 2678, NA,
6542, 5678, 1243, NA, 1566, 1566),
se_Yalimapo.French.Guiana=c(123.2, 27.7, 62.5, 126, NA,
230, 129, 167, NA, 145, 20),
density_Yalimapo.French.Guiana=rep("dgamma", 11),
Galibi.Suriname=c(276, 275, 290, NA, 267,
542, 678, NA, 243, 156, 123),
se_Galibi.Suriname=c(22.3, 34.2, 23.2, NA, 23.2,
4.3, 2.3, NA, 10.3, 10.1, 8.9),
density_Galibi.Suriname=rep("dgamma", 11),
Irakumpapy.French.Guiana=c(1076, 1765, 1390, 1678, NA,
3542, 2678, 243, NA, 566, 566),
se_Irakumpapy.French.Guiana=c(23.2, 29.7, 22.5, 226, NA,
130, 29, 67, NA, 15, 20),
density_Irakumpapy.French.Guiana=rep("dgamma", 11), stringsAsFactors = FALSE
)
cst <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Constant",
model.SD="Zero")
## End(Not run)
phenology documentation built on Oct. 16, 2023, 9:06 a.m.
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| fitRMU | R Documentation |
Adjust incomplete timeseries with various constraints.
Description
The data must be a data.frame with the first column being years
and two columns for each beach: the average and the se for the estimate.
The correspondence between mean, se and density for each rookery are given in the RMU.names data.frame.
This data.frame must have a column named mean, another named se and a third named density. If
no sd column exists, no sd will be considered for the series and if no density column exists, it
will be considered as being "dnorm" (Gaussian distribution).
The aggregated number of nests and its confidence interval can be obtained using CI.RMU().
The names of beach columns must not begin by T_, SD_, a0_, a1_ or a2_ and cannot be r.
A RMU is the acronyme for Regional Managment Unit. See:
Wallace, B.P., DiMatteo, A.D., Hurley, B.J., Finkbeiner, E.M., Bolten, A.B.,
Chaloupka, M.Y., Hutchinson, B.J., Abreu-Grobois, F.A., Amorocho, D., Bjorndal, K.A.,
Bourjea, J., Bowen, B.W., Dueñas, R.B., Casale, P., Choudhury, B.C., Costa, A.,
Dutton, P.H., Fallabrino, A., Girard, A., Girondot, M., Godfrey, M.H., Hamann, M.,
López-Mendilaharsu, M., Marcovaldi, M.A., Mortimer, J.A., Musick, J.A., Nel, R.,
Seminoff, J.A., Troëng, S., Witherington, B., Mast, R.B., 2010. Regional
management units for marine turtles: a novel framework for prioritizing
conservation and research across multiple scales. PLoS One 5, e15465.
Variance for each value is additive based on both the observed SE (in the RMU.data
object) and a value.
The value is a global constant when model.SD is "global-constant".
The value is proportional to the observed number of nests when model.SD is
"global-proportional" with aSD_*observed+SD_ with aSD_ and SD_ being fitted
values. This value is fixed to zero when model.SD is "Zero".
The value is dependent on the rookery when model.SD is equal to
"Rookery-constant" or "Rookery-proportional" with a similar formula as previously
described for "global".
if method is NULL, it will simply return the names of required parameters.
Usage
fitRMU(
RMU.data = stop("data parameter must be provided"),
years.byrow = TRUE,
RMU.names = NULL,
model.trend = "Constant",
model.rookeries = "Constant",
model.SD = "Global-constant",
parameters = NULL,
fixed.parameters = NULL,
SE = NULL,
method = c("Nelder-Mead", "BFGS"),
control = list(trace = 1),
itnmax = c(1500, 1500),
cptmax.optim = 100,
limit.cpt.optim = 1e-05,
hessian = TRUE,
replicate.CI = 1000,
colname.year = "Year",
maxL = 1e+09
)
Arguments
RMU.data |
A data.frame with a column Year (the name is defined in colname.year) and one to three columns per rookery defined in RMU.names |
years.byrow |
If TRUE, the RMU.data data.frame is organized with years in rows |
RMU.names |
A dataframe with one to three columns indicating name of columns for mean, standard deviation, and distribution for roockeris |
model.trend |
Can be Constant, Exponential or Year-specific |
model.rookeries |
Description temporal change in rookeries proportion. It be Constant, First-order or Second-order |
model.SD |
Can be Zero, Global-constant, Global-proportional or Rookery-constant. See description. |
parameters |
Parameters to fit |
fixed.parameters |
Parameters that are fixed |
SE |
Parameters SE for example from fitRMU_MHmcmc() |
method |
Methods to be used by optim() |
control |
List of controls for optim() |
itnmax |
A vector with maximum iterations for each method. |
cptmax.optim |
How many times optim can be ran when likelihood is better. |
limit.cpt.optim |
Limit to consider that likelihood is better. |
hessian |
If TRUE, the hessian matrix is calculated and then the standard error of parameters. |
replicate.CI |
Number of replicates to estimate CI of proportion for each rookery |
colname.year |
Name of the column to be used as time index |
maxL |
If an error is produced during the estimation of likelihood, replace -Ln L by this value |
Details
fitRMU is used to estimate missing information when several linked values are observed along a timeseries
Value
Return a list with the results from optim and synthesis for proportions and numbers
Author(s)
Marc Girondot marc.girondot@gmail.com
See Also
Other Fill gaps in RMU:
CI.RMU(),
fitRMU_MHmcmc_p(),
fitRMU_MHmcmc(),
logLik.fitRMU(),
plot.fitRMU()
Examples
## Not run:
library("phenology")
RMU.names.AtlanticW <- data.frame(mean=c("Yalimapo.French.Guiana",
"Galibi.Suriname",
"Irakumpapy.French.Guiana"),
se=c("se_Yalimapo.French.Guiana",
"se_Galibi.Suriname",
"se_Irakumpapy.French.Guiana"),
density=c("density_Yalimapo.French.Guiana",
"density_Galibi.Suriname",
"density_Irakumpapy.French.Guiana"))
data.AtlanticW <- data.frame(Year=c(1990:2000),
Yalimapo.French.Guiana=c(2076, 2765, 2890, 2678, NA,
6542, 5678, 1243, NA, 1566, 1566),
se_Yalimapo.French.Guiana=c(123.2, 27.7, 62.5, 126, NA,
230, 129, 167, NA, 145, 20),
density_Yalimapo.French.Guiana=rep("dnorm", 11),
Galibi.Suriname=c(276, 275, 290, NA, 267,
542, 678, NA, 243, 156, 123),
se_Galibi.Suriname=c(22.3, 34.2, 23.2, NA, 23.2,
4.3, 2.3, NA, 10.3, 10.1, 8.9),
density_Galibi.Suriname=rep("dnorm", 11),
Irakumpapy.French.Guiana=c(1076, 1765, 1390, 1678, NA,
3542, 2678, 243, NA, 566, 566),
se_Irakumpapy.French.Guiana=c(23.2, 29.7, 22.5, 226, NA,
130, 29, 67, NA, 15, 20),
density_Irakumpapy.French.Guiana=rep("dnorm", 11)
)
cst <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Constant",
model.SD="Zero")
cst <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Constant",
model.SD="Zero",
control=list(trace=1, REPORT=100, maxit=500, parscale = c(3000, -0.2, 0.6)))
cst <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Constant",
model.SD="Zero", method=c("Nelder-Mead","BFGS"),
control = list(trace = 0, REPORT = 100, maxit = 500,
parscale = c(3000, -0.2, 0.6)))
expo <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Exponential",
model.SD="Zero", method=c("Nelder-Mead","BFGS"),
control = list(trace = 0, REPORT = 100, maxit = 500,
parscale = c(6000, -0.05, -0.25, 0.6)))
YS <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Year-specific", method=c("Nelder-Mead","BFGS"),
model.SD="Zero")
YS1 <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Year-specific", method=c("Nelder-Mead","BFGS"),
model.SD="Zero", model.rookeries="First-order")
YS1_cst <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Year-specific",
model.SD="Constant", model.rookeries="First-order",
parameters=YS1$par, method=c("Nelder-Mead","BFGS"))
YS2 <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Year-specific",
model.SD="Zero", model.rookeries="Second-order",
parameters=YS1$par, method=c("Nelder-Mead","BFGS"))
YS2_cst <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Year-specific",
model.SD="Constant", model.rookeries="Second-order",
parameters=YS1_cst$par, method=c("Nelder-Mead","BFGS"))
compare_AIC(Constant=cst, Exponential=expo,
YearSpecific=YS)
compare_AIC(YearSpecific_ProportionsFirstOrder_Zero=YS1,
YearSpecific_ProportionsFirstOrder_Constant=YS1_cst)
compare_AIC(YearSpecific_ProportionsConstant=YS,
YearSpecific_ProportionsFirstOrder=YS1,
YearSpecific_ProportionsSecondOrder=YS2)
compare_AIC(YearSpecific_ProportionsFirstOrder=YS1_cst,
YearSpecific_ProportionsSecondOrder=YS2_cst)
# Example of different types of plots
plot(cst, main="Use of different beaches along the time", what="total",
ylim=c(0, 4000))
plot(cst, main="Use of different beaches along the time", what = "proportions",
replicate.CI=0)
plot(cst, main="Use of different beaches along the time", what = "numbers",
aggregate="model", ylim=c(0, 4000), replicate.CI=0)
plot(cst, main="Use of different beaches along the time", what = "numbers",
aggregate="both", ylim=c(0, 11000), replicate.CI=0)
plot(expo, main="Use of different beaches along the time", what="total")
plot(YS2_cst, main="Use of different beaches along the time", what="total")
plot(YS1, main="Use of different beaches along the time")
plot(YS1_cst, main="Use of different beaches along the time")
plot(YS1_cst, main="Use of different beaches along the time", what="numbers")
# Gamma distribution should be used for MCMC outputs
RMU.names.AtlanticW <- data.frame(mean=c("Yalimapo.French.Guiana",
"Galibi.Suriname",
"Irakumpapy.French.Guiana"),
se=c("se_Yalimapo.French.Guiana",
"se_Galibi.Suriname",
"se_Irakumpapy.French.Guiana"),
density=c("density_Yalimapo.French.Guiana",
"density_Galibi.Suriname",
"density_Irakumpapy.French.Guiana"),
stringsAsFactors = FALSE)
data.AtlanticW <- data.frame(Year=c(1990:2000),
Yalimapo.French.Guiana=c(2076, 2765, 2890, 2678, NA,
6542, 5678, 1243, NA, 1566, 1566),
se_Yalimapo.French.Guiana=c(123.2, 27.7, 62.5, 126, NA,
230, 129, 167, NA, 145, 20),
density_Yalimapo.French.Guiana=rep("dgamma", 11),
Galibi.Suriname=c(276, 275, 290, NA, 267,
542, 678, NA, 243, 156, 123),
se_Galibi.Suriname=c(22.3, 34.2, 23.2, NA, 23.2,
4.3, 2.3, NA, 10.3, 10.1, 8.9),
density_Galibi.Suriname=rep("dgamma", 11),
Irakumpapy.French.Guiana=c(1076, 1765, 1390, 1678, NA,
3542, 2678, 243, NA, 566, 566),
se_Irakumpapy.French.Guiana=c(23.2, 29.7, 22.5, 226, NA,
130, 29, 67, NA, 15, 20),
density_Irakumpapy.French.Guiana=rep("dgamma", 11), stringsAsFactors = FALSE
)
cst <- fitRMU(RMU.data=data.AtlanticW, RMU.names=RMU.names.AtlanticW,
colname.year="Year", model.trend="Constant",
model.SD="Zero")
## End(Not run)
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