Last updated on 2026-06-08 02:51:41 CEST.
| Package | ERROR | WARN | NOTE | OK |
|---|---|---|---|---|
| ecostatscale | 1 | 2 | 10 | |
| gauseR | 1 | 12 | ||
| multispatialCCM | 2 | 11 | ||
| partitionBEFsp | 2 | 11 | ||
| pttstability | 1 | 12 |
Current CRAN status: ERROR: 1, NOTE: 2, OK: 10
Version: 1.1
Check: examples
Result: ERROR
Running examples in ‘ecostatscale-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ecostatscale
> ### Title: ecostatscale: Statistical Scaling Functions for Ecological
> ### Systems
> ### Aliases: ecostatscale
> ### Keywords: "_PACKAGE" internal
>
> ### ** Examples
>
> # simulate a time series:
> ?symdyn # one species one patch
symdyn package:ecostatscale R Documentation
_<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>e _<08>t_<08>i_<08>m_<08>e _<08>s_<08>e_<08>r_<08>i_<08>e_<08>s _<08>f_<08>o_<08>r _<08>a _<08>s_<08>i_<08>n_<08>g_<08>l_<08>e _<08>s_<08>p_<08>e_<08>c_<08>i_<08>e_<08>s _<08>i_<08>n _<08>a _<08>s_<08>i_<08>n_<08>g_<08>l_<08>e _<08>p_<08>a_<08>t_<08>c_<08>h
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Function for simulating dynamics from Eq.1 in the main text.
_<08>U_<08>s_<08>a_<08>g_<08>e:
symdyn(
r,
f,
d,
d_sd,
sf,
tmax,
stochd = TRUE,
stocht = TRUE,
as.matrix = FALSE,
oscillate_dist = FALSE
)
_<08>A_<08>r_<08>g_<08>u_<08>m_<08>e_<08>n_<08>t_<08>s:
r: per-capita growth rate (r in Eq.1)
f: the waiting time (or average waiting time) between
disturbance events (equal to 1/lambda in Eq.1)
d: mean size of disturbance function (mu in Eq.1)
d_sd: standard deviation of disturbance function (sigma in Eq.1)
sf: waiting time between sampling events
tmax: the time series length to be simulated
stochd: a logical variable, indicating whether disturbance size
should be stochastic - otherwise, all disturbances are of
magnitude d - defaults to TRUE
stocht: a logical variable, indicating whether waiting time between
disturbance events should be stochastic - otherwise, waiting
time is always f - defaults to TRUE
as.matrix: indicates whether results should be returned as matrix
(potentially faster for some applications) - defaults to
FALSE
oscillate_dist: a logical variable indicating whether the sign of the
disturbance should oscillate between positive and negative -
ignored if stochd==TRUE - defaults to FALSE
_<08>V_<08>a_<08>l_<08>u_<08>e:
a matrix or data.frame with columns for sampling times,
abundances, and number of disturbances for each time interval
_<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
# see xt2fun
> ?symdynN # multiple species or patches
symdynN package:ecostatscale R Documentation
_<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>e _<08>t_<08>i_<08>m_<08>e _<08>s_<08>e_<08>r_<08>i_<08>e_<08>s _<08>f_<08>o_<08>r _<08>N _<08>s_<08>p_<08>e_<08>c_<08>i_<08>e_<08>s _<08>o_<08>r _<08>p_<08>a_<08>t_<08>c_<08>h_<08>e_<08>s
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Function for simulating dynamics from Eq.2-3 in the main text.
_<08>U_<08>s_<08>a_<08>g_<08>e:
symdynN(
r,
amu,
asd,
f,
d,
d_sd,
d_cov,
N,
sf,
tmax,
stochd = TRUE,
stocht = TRUE,
as.matrix = FALSE,
amax = 0,
amin = -Inf,
Ifrac = NULL,
Iloss = NULL,
dffun = df0,
fullout = FALSE,
xstart = NULL,
Ksim = 1
)
_<08>A_<08>r_<08>g_<08>u_<08>m_<08>e_<08>n_<08>t_<08>s:
r: per-capita growth rate (r in Eq.2-3)
amu: the mean interaction strength
asd: standard deviation used to generate interaction strengths
f: the waiting time (or average waiting time) between
disturbance events (equal to 1/lambda in Eq.2-3)
d: mean size of disturbance function (mu in Eq.2-3)
d_sd: standard deviation of disturbance function (sigma in Eq.5)
d_cov: the covariance for generating disturbances
N: number of species or patches
sf: waiting time between sampling events
tmax: the time series length to be simulated
stochd: a logical variable, indicating whether disturbance size
should be stochastic - otherwise, all disturbances are of
magnitude d - defaults to TRUE
stocht: a logical variable, indicating whether waiting time between
disturbance events should be stochastic - otherwise, waiting
time is always f - defaults to TRUE
as.matrix: indicates whether results should be returned as matrix
(potentially faster for some applications) - defaults to
FALSE
amax: the maximum value allowed for interaction coefficients -
defaults to zero
amin: the minimum value allowed for interaction coefficients -
defaults to -Inf
Ifrac: dispersal rate (D in Eq. 2) - defaults to NULL (i.e. no
dispersal)
Iloss: loss rate from dispersal that falls outside of the patch -
defaults to NULL
dffun: the function handed to the ODE solver - should be df_col for
spatial simulations, and df0 for multi-species simulations -
defaults to df0
fullout: a logical, determining whether the full output or just a
summary is returned - defaults to fullout
xstart: optional vector of starting abundances - defaults to NULL
(i.e. no values)
Ksim: carrying capacities - defaults to 1
_<08>V_<08>a_<08>l_<08>u_<08>e:
a matrix or data.frame with columns for sampling times,
abundances, and number of disturbances for each time interval
_<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
### Example 1: 10 patches
r<-1 #rate of recovery
d<-(0) #mean size of disturbance (mu in text)
d_sd<-sqrt(0.1) #SD of disturbances (sigma in text)
f<-1 #average time between disturbances (1/lambda in text)
sf<-0.1 #sampling interval
tmax<-120 #maximum time for simulation
d_cov<-d_cov0<-(d_sd)^2/2 #covariance in disturbance size among patches
xtNpatches<-symdynN(r = r, amu=0, asd=0, f=f, d=d,
d_sd=d_sd, d_cov=d_cov, N=10,
sf=sf, tmax=tmax, Ifrac=0, dffun = df_col)
### Example 2: 30 species
r<-1 #rate of recovery
d<-(0) #mean size of disturbance (mu in text)
d_sd<-sqrt(0.1) #SD of disturbances (sigma in text)
f<-1 #average time between disturbances (1/lambda in text)
sf<-0.1 #sampling interval
tmax<-120 #maximum time for simulation
d_cov<-0 #covariance in disturbances among species
amu<-(-r/2) #average interaction coefficient
asd<-0.1 #standard deviation of interaction coefficient
xtNsp<-symdynN(r = r, amu=amu, asd=asd, f=f, d=d,
d_sd=d_sd, d_cov=d_cov, N=30,
sf=sf, tmax=tmax)
>
> # get unbiased parameter estimates:
> ?xt2fun
Warning in file(out, "wt") :
cannot open file '/tmp/RtmpEf6Gea/Rtxt4f0136fe9e97f': No space left on device
Error in file(out, "wt") : cannot open the connection
Calls: <Anonymous> -> print.help_files_with_topic -> <Anonymous> -> file
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘graphics’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Current CRAN status: ERROR: 1, OK: 12
Version: 1.3
Check: examples
Result: ERROR
Running examples in ‘gauseR-Ex.R’ failed
The error occurred in:
Fatal error: cannot create 'R_TempDir'
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: NOTE: 2, OK: 11
Version: 1.3
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Adam Clark <adam.tclark@gmail.com>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Adam",
family = "Clark",
role = c("aut", "cre"),
email = "adam.tclark@gmail.com")
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: NOTE: 2, OK: 11
Version: 1.0
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Adam Clark <adam.tclark@gmail.com>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: person(given = "Adam",
family = "Clark",
role = c("aut", "cre"),
email = "adam.tclark@gmail.com")
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: WARN: 1, OK: 12
Version: 1.4
Check: for missing documentation entries
Result: WARN
Fatal error: cannot create 'R_TempDir'
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.4
Check: for code/documentation mismatches
Result: WARN
Warning in file(open = "w+") :
cannot open file '/tmp/RtmpAhxOl1/Rfe4c5b9b2228b': No space left on device
Error in file(open = "w+") : cannot open the connection
Calls: <Anonymous> -> .try_quietly -> file
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc