Percent cover data from Jasper Ridge Biological Preserve serpentine grassland site

Description

A data set of percent cover of plant species in a plot from Jasper Ridge Biological Preserve serpentine grassland site. See Hallett et al (2014), Ecology for details. Subplot 3 from block 3 from the control treatment was used. Plot size was 1 m^2. Values are percents. Values occasionally sum across species to more than 100 because of overlapping plant canopies.

Usage

JRGdat

Format

A data frame with 28 rows and 27 columns. First column is the year of measurement, subsequent columns correspond to individual species, named in the column headers.

References

Hallett et al (2014) Biotic mechanisms of community stability shift along a precipitation gradient. Ecology 95, 1693-1700.

Aggregates a tsvreq_classic object across a set of timescales; also the constructor function for class vreq_classic_ag.

Description

All the components of a tsvreq_classic object can be aggregated across an arbitrary set of timescales, producing a new variance ratio equation - this function performs that aggregation. The function returns a vreq_classic_ag object, and is the constructor function of that class. The vreq_classic_ag class has slots com, comnull, vr, which are the same as a vreq object, but also has slot ts, which is the timescales over which aggregation was performed to get the object. The class inherits from vreq, which inherits from list.

Usage

aggts(obj, ts)

Arguments

Details

Before aggregation is performed, the argument 'ts' is intersected with the canonical Fourier timescales greater than or equal to the Nyquist timescale, and the resulting timescales are then reflected about the Nyquist timescale. This is to account for the symmetry of Fourier transforms about the Nyquist frequency. The 'ts' slot of the output object shows the intersected, reflected timescales that were actually used for aggregation. See the examples.

Value

aggts returns an object of class vreq_classic_ag. Slots are:

Author(s)

Shaopeng Wang, shaopeng.wang@pku.edu.cn; Lei Zhao, lei.zhao@cau.edu.cn; Daniel Reuman, reuman@ku.edu

References

Zhao et al, (In prep) Decomposition of the variance ratio illuminates timescale-specific population and community variability.

See Also

tsvreq_classic, vreq_classic_ag_methods, browseVignettes("tsvr")

Examples

X<-matrix(runif(10*100),10,100)
h<-tsvreq_classic(X)
res1<-aggts(h,h$ts[h$ts>=4]) 
res2<-aggts(h,h$ts[h$ts>=4 | h$ts<=4/3]) 
#res1 and res2 produce the same result 
#because of Fourier symmetry around the 
#Nyquist timescale - see Details 

Calculate the cospectrum between all pairs of time series

Description

This function is used to calculate the cospectra between pairs of time series, including each time series with itself. These are based on simple ffts without smoothing.

Usage

cospect(X)

Arguments

Value

cospect return a list with elements

Author(s)

Lei Zhao, lei.zhao@cau.edu.cn; Daniel Reuman, reuman@ku.edu

Examples

X<-matrix(runif(200,1,100), 10, 20)
ans<-cospect(X)

Calculates various measures of population and community variability

Description

Calculates various measures of population and community variability

Usage

cv2(X, type)

Arguments

Value

cv2 returns the value of population or community variability.

Author(s)

Lei Zhao, lei.zhao@cau.edu.cn; Daniel Reuman, reuman@ku.edu; Shaopeng Wang, shaopeng.wang@pku.edu.cn

References

Zhao et al, (In prep) Decomposition of the variance ratio illuminates timescale-specific population and community variability.

See Also

vreq_classic, vreq_LdM, cv2f, browseVignettes("tsvr")

Examples

X<-matrix(runif(200,1,100), 10, 20)
ans<-cv2(X, type="com")

Compute a frequency-specific version of CVcom or CVcomip

Description

Compute a frequency-specific version of CVcom or CVcomip.

Usage

cv2f(X, type)

Arguments

Value

cv2f returns an object of type list consisting of

Author(s)

Shaopeng Wang, shaopeng.wang@pku.edu.cn; Lei Zhao, lei.zhao@cau.edu.cn; Daniel Reuman, reuman@ku.edu

References

Zhao et al, (In prep) Decomposition of the variance ratio illuminates timescale-specific population and community variability.

See Also

tsvreq_classic, cv2, browseVignettes("tsvr")

Examples

X<-matrix(runif(200,1,100), 10, 20) 
ans<-cv2f(X, type="com")

Error check a data matrix.

Description

Error check a data matrix.

Usage

errcheck_data(X, calledby)

Arguments

Value

errcheck_data returns nothing but throws and error if the inputs do not meet the requirements

Author(s)

Daniel Reuman, reuman@ku.edu

Error check inputs for the creator function for the tsvreq class.

Description

Error check inputs for the creator function for the tsvreq class.

Usage

errcheck_tsvreq(ts, com, comnull, tsvr, wts)

Arguments

Value

errcheck_tsvreq returns nothing but throws and error if the inputs do not meet the requirements of a tsvreq object

Author(s)

Daniel Reuman, reuman@ku.edu

Error check inputs for the creator function for the vreq class.

Description

Error check inputs for the creator function for the vreq class.

Usage

errcheck_vreq(com, comnull, vr)

Arguments

Value

errcheck_vreq returns nothing but throws and error if the inputs do not meet the requirements of a vreq object

Author(s)

Daniel Reuman, reuman@ku.edu

Print method for summary_tsvr class

Description

Print method for summary_tsvr class

Usage

## S3 method for class 'summary_tsvr'
print(x, ...)

Arguments

Value

print.summary_tsvr is called for its effect of printing to the screen.

Author(s)

Daniel Reuman, reuman@ku.edu

See Also

vreq_methods, vreq_classic_methods, vreq_LdM_methods, vreq_classic_ag_methods, tsvreq_methods, tsvreq_classic_methods, browseVignettes("tsvr")

Examples

res<-vreq(2,1,2)
summary(res)

Set and get methods for classes in the tsvr package

Description

Set and get methods for classes in the tsvr package. There are methods for each slot of each class, named set_* and get_* for * the slot name. Below are listed function specs for the generics and the default methods.

Usage

set_ts(obj, newval)

## Default S3 method:
set_ts(obj, newval)

set_tsvr(obj, newval)

## Default S3 method:
set_tsvr(obj, newval)

set_wts(obj, newval)

## Default S3 method:
set_wts(obj, newval)

get_ts(obj)

## Default S3 method:
get_ts(obj)

get_tsvr(obj)

## Default S3 method:
get_tsvr(obj)

get_wts(obj)

## Default S3 method:
get_wts(obj)

set_com(obj, newval)

## Default S3 method:
set_com(obj, newval)

set_comnull(obj, newval)

## Default S3 method:
set_comnull(obj, newval)

set_vr(obj, newval)

## Default S3 method:
set_vr(obj, newval)

get_com(obj)

## Default S3 method:
get_com(obj)

get_comnull(obj)

## Default S3 method:
get_comnull(obj)

get_vr(obj)

## Default S3 method:
get_vr(obj)

Arguments

Details

There are methods for S3 classes defined in the package. See documentation for the generator functions for these classes (which in all cases have the same name as the class) for lists of slots for each class.

Value

set_* methods throw an error - setting of individual slots is not allowed, as it breaks consistency with the other slots. get_* just returns the value in question.

Author(s)

Daniel Reuman, reuman@ku.edu

See Also

vreq

Examples

res<-vreq(com=2,comnull=1,vr=2)
get_com(res)

Creator function for the tsvreq S3 class

Description

The tsvreq (timescale-specific variance ratio equation) class is for storing functional equations based on a timescale-specific variance ratio. This is a general class from which other classes inherit (only tsvreq_classic at this point). tsvreq inherits from the list class.

Usage

tsvreq(ts, com, comnull, tsvr, wts)

Arguments

Value

tsvreq returns an object of class tsvreq. Slots are:

Author(s)

Shaopeng Wang, shaopeng.wang@pku.edu.cn; Lei Zhao, lei.zhao@cau.edu.cn; Daniel Reuman, reuman@ku.edu

See Also

tsvreq_methods, tsvreq_classic, vreq, browseVignettes("tsvr")

Examples

res<-tsvreq(ts=1:10,com=2*c(1:10),comnull=1:10,tsvr=rep(2,10),wts=rep(3,10))

Creator function for the tsvreq_classic S3 class

Description

The tsvreq_classic (timescale-specific variance ratio equation, classic variance ratio) class is for storing functional equations based on a timescale specific version of the classic variance ratio. Inherits from tsvreq, which inherits from list.

Usage

tsvreq_classic(X)

Arguments

Value

tsvreq_classic returns a tsvreq_classic object. Slots are:

Author(s)

Daniel Reuman, reuman@ku.edu

References

Zhao et al, (In prep) Decomposition of the variance ratio illuminates timescale-specific population and community variability.

See Also

tsvreq_classic_methods, tsvreq, vreq_classic, browseVignettes("tsvr")

Examples

X<-matrix(runif(10*100),10,100)
res<-tsvreq_classic(X)

Basic methods for the tsvreq_classic class

Description

Set, get, summary, print and plot methods for the tsvreq_classic class.

Usage

## S3 method for class 'tsvreq_classic'
summary(object, ...)

## S3 method for class 'tsvreq_classic'
print(x, ...)

## S3 method for class 'tsvreq_classic'
plot(x, filename = NA, ...)

## S3 method for class 'tsvreq_classic'
set_ts(obj, newval)

## S3 method for class 'tsvreq_classic'
set_com(obj, newval)

## S3 method for class 'tsvreq_classic'
set_comnull(obj, newval)

## S3 method for class 'tsvreq_classic'
set_tsvr(obj, newval)

## S3 method for class 'tsvreq_classic'
set_wts(obj, newval)

## S3 method for class 'tsvreq_classic'
get_ts(obj)

## S3 method for class 'tsvreq_classic'
get_com(obj)

## S3 method for class 'tsvreq_classic'
get_comnull(obj)

## S3 method for class 'tsvreq_classic'
get_tsvr(obj)

## S3 method for class 'tsvreq_classic'
get_wts(obj)

Arguments

Value

summary.tsvreq_classic produces a summary of a tsvreq_classic object. Methods print.tsvreq_classic and plot.tsvreq_classic are also available. For tsvreq_classic objects, set_* and get_* methods are available for all slots (see the documentation for tsvreq_classic for a list). The set_* methods just throw an error, to prevent breaking the consistency between the slots of a tsvreq_classic object.

Author(s)

Daniel Reuman, reuman@ku.edu

References

Zhao et al, (In prep) Decomposition of the variance ratio illuminates timescale-specific population and community variability.

See Also

tsvreq_classic

Examples

X<-matrix(runif(10*100),10,100)
res<-tsvreq_classic(X)
get_ts(res)
print(res)
summary(res)
 

Basic methods for the tsvreq class

Description

Set, get, summary, print and plot methods for the tsvreq class.

Usage

## S3 method for class 'tsvreq'
summary(object, ...)

## S3 method for class 'tsvreq'
print(x, ...)

## S3 method for class 'tsvreq'
plot(x, filename = NA, ...)

## S3 method for class 'tsvreq'
set_ts(obj, newval)

## S3 method for class 'tsvreq'
set_com(obj, newval)

## S3 method for class 'tsvreq'
set_comnull(obj, newval)

## S3 method for class 'tsvreq'
set_tsvr(obj, newval)

## S3 method for class 'tsvreq'
set_wts(obj, newval)

## S3 method for class 'tsvreq'
get_ts(obj)

## S3 method for class 'tsvreq'
get_com(obj)

## S3 method for class 'tsvreq'
get_comnull(obj)

## S3 method for class 'tsvreq'
get_tsvr(obj)

## S3 method for class 'tsvreq'
get_wts(obj)

Arguments

Value

summary.tsvreq produces a summary of a tsvreq object. Methods print.tsvreq and plot.tsvreq are also available. For tsvreq objects, set_* and get_* methods are available for all slots (see the documentation for tsvreq for a list). The set_* methods just throw an error, to prevent breaking the consistency between the slots of a tsvreq object.

Author(s)

Daniel Reuman, reuman@ku.edu

See Also

tsvreq

Examples

res<-tsvreq(ts=1:10,com=2*c(1:10),comnull=1:10,tsvr=rep(2,10),wts=rep(3,10))
get_ts(res)
print(res)
summary(res)
plot(res)
 

Compute the classic or Loreau-de Mazancourt variance ratio

Description

This function is used to compute the classical or Loreau-de Mazancourt variance ratio for a community in a single plot.

Usage

vr(X, method = "classic")

Arguments

Value

vr returns the value of variance ratio

Author(s)

Lei Zhao, lei.zhao@cau.edu.cn; Daniel Reuman, reuman@ku.edu

References

Loreau & Mazancourt, Species Synchrony and Its Drivers: Neutral and Nonneutral Community Dynamics in Fluctuating Environments. 2008, Am. Nat. 172(2)

Zhao et al, (In prep) Decomposition of the variance ratio illuminates timescale-specific population and community variability.

Peterson, Stability of species and of community for the benthos of two lagoons. 1975, Ecology, 56, 958-965.

See Also

vrf, vreq, vreq_classic, vreq_LdM, browseVignettes("tsvr")

Examples

X<-matrix(runif(200,1,100), 10, 20)
vr(X, method="LdM")
vr(X, method="classic")

Creator function for the vreq S3 class

Description

The vreq (variance ratio equation) class is for storing equations based on a variance ratio, as in Wang S. & Loreau M. (2016) Biodiversity and ecosystem stability across scales in metacommunities, Ecol Lett, 19, 510-518. This is a general class from which other classes inherit (vreq_classic, vreq_LdM). vreq inherits from the list class.

Usage

vreq(com, comnull, vr)

Arguments

Value

vreq returns an object of class vreq. Slots are:

Author(s)

Shaopeng Wang, shaopeng.wang@pku.edu.cn; Lei Zhao, lei.zhao@cau.edu.cn; Daniel Reuman, reuman@ku.edu

References

Wang S. & Loreau M. (2016) Biodiversity and ecosystem stability across scales in metacommunities. Ecol Lett, 19, 510-518.

Zhao et al, (In prep) Decomposition of the variance ratio illuminates timescale-specific population and community variability.

Peterson, Stability of species and of community for the benthos of two lagoons. 1975, Ecology, 56, 958-965.

See Also

vreq_methods, vreq_classic, vreq_LdM, vreq_classic_ag_methods, browseVignettes("tsvr")

Examples

res<-vreq(com=2,comnull=1,vr=2)
  

Creator function of vreq_LdM S3 class

Description

The vreq_LdM (variance ratio equation, Loreau-de Mazancourt variance ratio) class is for storing equations based on the L-dM variance ratio. Inherits from the vreq class, which inherits from the list class.

Usage

vreq_LdM(X)

Arguments

Value

vreq_LdM returns a vreq_LdM object. Slots are:

Author(s)

Daniel Reuman, reuman@ku.edu

References

Loreau & Mazancourt, Species Synchrony and Its Drivers: Neutral and Nonneutral Community Dynamics in Fluctuating Environments. 2008, Am. Nat. 172(2)

See Also

vreq_LdM_methods, vreq_classic, vreq, browseVignettes("tsvr")

Examples

X<-matrix(runif(10*100),10,100)
res<-vreq_LdM(X)

Basic methods for the vreq_LdM class

Description

Set, get, summary, and print methods for the vreq_LdM class.

Usage

## S3 method for class 'vreq_LdM'
summary(object, ...)

## S3 method for class 'vreq_LdM'
print(x, ...)

## S3 method for class 'vreq_LdM'
set_com(obj, newval)

## S3 method for class 'vreq_LdM'
set_comnull(obj, newval)

## S3 method for class 'vreq_LdM'
set_vr(obj, newval)

## S3 method for class 'vreq_LdM'
get_com(obj)

## S3 method for class 'vreq_LdM'
get_comnull(obj)

## S3 method for class 'vreq_LdM'
get_vr(obj)

Arguments

Value

summary.vreq_LdM produces a summary of a vreq_LdM object. A print.vreq_LdM method is also available. For vreq_LdM objects, set_* and get_* methods are available for all slots (see the documentation for vreq_LdM for a list). The set_* methods just throw an error, to prevent breaking the consistency between the slots of a vreq_LdM object.

Author(s)

Daniel Reuman, reuman@ku.edu

References

Loreau & Mazancourt, Species Synchrony and Its Drivers: Neutral and Nonneutral Community Dynamics in Fluctuating Environments. 2008, Am. Nat. 172(2)

See Also

vreq_LdM

Examples

X<-matrix(runif(10*100),10,100)
res<-vreq_LdM(X)
print(res)
summary(res)
 

Creator function of vreq_classic S3 class

Description

The vreq_classic (variance ratio equation, classic variance ratio) class is for storing equations based on the classic variance ratio. Inherits from the vreq class, which inherits from the list class.

Usage

vreq_classic(X)

Arguments

Value

vreq_classic returns a vreq_classic object. Slots are:

Author(s)

Daniel Reuman, reuman@ku.edu

References

Peterson (1975) Stability of species and of community for the benthos of two lagoons. Ecology 56, 958-965.

See Also

vreq_classic_methods, vreq, vreq_LdM, vreq_classic_ag_methods, browseVignettes("tsvr")

Examples

X<-matrix(runif(10*100),10,100)
res<-vreq_classic(X)

Basic methods for the vreq_classic_ag class

Description

Set, get, summary, and print methods for the vreq_classic_ag class.

Usage

## S3 method for class 'vreq_classic_ag'
summary(object, ...)

## S3 method for class 'vreq_classic_ag'
print(x, ...)

## S3 method for class 'vreq_classic_ag'
set_com(obj, newval)

## S3 method for class 'vreq_classic_ag'
set_comnull(obj, newval)

## S3 method for class 'vreq_classic_ag'
set_vr(obj, newval)

## S3 method for class 'vreq_classic_ag'
set_ts(obj, newval)

## S3 method for class 'vreq_classic_ag'
get_com(obj)

## S3 method for class 'vreq_classic_ag'
get_comnull(obj)

## S3 method for class 'vreq_classic_ag'
get_vr(obj)

## S3 method for class 'vreq_classic_ag'
get_ts(obj)

Arguments

Value

summary.vreq_classic_ag produces a summary of a vreq_classic_ag object. A print.vreq_classic_ag method is also available. For vreq_classic_ag objects, set_* and get_* methods are available for all slots (see the documentation for aggts for a list). The set_* methods just throw an error, to prevent breaking the consistency between the slots of a vreq_classic_ag object.

Author(s)

Daniel Reuman, reuman@ku.edu

References

Zhao et al, (In prep) Decomposition of the variance ratio illuminates timescale-specific population and community variability.

See Also

aggts, tsvreq_classic, vreq_classic, vreq_LdM, vreq, browseVignettes("tsvr")

Examples

X<-matrix(runif(10*100),10,100)
h<-tsvreq_classic(X)
inp<-aggts(h,h$ts[h$ts>4])
print(inp)
summary(inp)
 

Basic methods for the vreq_classic class

Description

Set, get, summary, and print methods for the vreq_classic class.

Usage

## S3 method for class 'vreq_classic'
summary(object, ...)

## S3 method for class 'vreq_classic'
print(x, ...)

## S3 method for class 'vreq_classic'
set_com(obj, newval)

## S3 method for class 'vreq_classic'
set_comnull(obj, newval)

## S3 method for class 'vreq_classic'
set_vr(obj, newval)

## S3 method for class 'vreq_classic'
get_com(obj)

## S3 method for class 'vreq_classic'
get_comnull(obj)

## S3 method for class 'vreq_classic'
get_vr(obj)

Arguments

Value

summary.vreq_classic produces a summary of a vreq_classic object. A print.vreq_classic method is also available. For vreq_classic objects, set_* and get_* methods are available for all slots (see the documentation for vreq_classic for a list). The set_* methods just throw an error, to prevent breaking the consistency between the slots of a vreq_classic object.

Author(s)

Daniel Reuman, reuman@ku.edu

References

Peterson (1975) Stability of species and of community for the benthos of two lagoons. Ecology 56, 958-965.

See Also

vreq_classic

Examples

X<-matrix(runif(10*100),10,100)
res<-vreq_classic(X)
print(res)
summary(res)
 

Basic methods for the vreq class

Description

Set, get, summary, and print methods for the vreq class.

Usage

## S3 method for class 'vreq'
summary(object, ...)

## S3 method for class 'vreq'
print(x, ...)

## S3 method for class 'vreq'
set_com(obj, newval)

## S3 method for class 'vreq'
set_comnull(obj, newval)

## S3 method for class 'vreq'
set_vr(obj, newval)

## S3 method for class 'vreq'
get_com(obj)

## S3 method for class 'vreq'
get_comnull(obj)

## S3 method for class 'vreq'
get_vr(obj)

Arguments

Value

summary.vreq produces a summary of a vreq object. A print.vreq method is also available. For vreq objects, set_* and get_* methods are available for all slots (see the documentation for vreq for a list). The set_* methods just throw an error, to prevent breaking the consistency between the slots of a vreq object.

Author(s)

Daniel Reuman, reuman@ku.edu

See Also

vreq

Examples

res<-vreq(com=2,comnull=1,vr=2)
print(res)
 

Compute the frequency-specific variance ratio

Description

This function computes the frequency-specific variance ratio for a community in a single plot.

Usage

vrf(X)

Arguments

Value

vrf returns a list consisting of

Author(s)

Lei Zhao, lei.zhao@cau.edu.cn; Daniel Reuman, reuman@ku.edu

References

<Lei's paper>

See Also

vr

Examples

X<-matrix(runif(200,1,100), 10, 20)
ans<-vrf(X)

Compute the weights (wts)

Description

This function is used to compute weights (wts)

Usage

wts(X)

Arguments

Value

wts returns an object of class list consisting of

Author(s)

Lei Zhao, lei.zhao@cau.edu.cn; Daniel Reuman, reuman@ku.edu

References

<Lei paper>

Examples

X<-matrix(runif(200,1,100), 10, 20)
ans<-wts(X)