Last updated on 2024-08-16 01:48:31 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.23.0 | 53.64 | 430.67 | 484.31 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.23.0 | 35.72 | 296.72 | 332.44 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 1.23.0 | 795.91 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.23.0 | 823.96 | OK | |||
| r-devel-windows-x86_64 | 1.23.0 | 60.00 | 344.00 | 404.00 | NOTE | --no-vignettes |
| r-patched-linux-x86_64 | 1.23.0 | 60.61 | 408.99 | 469.60 | NOTE | |
| r-release-linux-x86_64 | 1.23.0 | 53.57 | 414.43 | 468.00 | NOTE | |
| r-release-macos-arm64 | 1.23.0 | 239.00 | NOTE | |||
| r-release-macos-x86_64 | 1.23.0 | 357.00 | NOTE | |||
| r-release-windows-x86_64 | 1.23.0 | 61.00 | 330.00 | 391.00 | NOTE | --no-vignettes |
| r-oldrel-macos-arm64 | 1.23.0 | 241.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.23.0 | 557.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.23.0 | 77.00 | 317.00 | 394.00 | ERROR | --no-vignettes |
Version: 1.23.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘INLA’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.23.0
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
epidata.Rd: Matrix-class
knox.Rd: truehist
permutationTest.Rd: truehist
twinstim_epitest.Rd: truehist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.23.0
Check: installed package size
Result: NOTE
installed size is 6.8Mb
sub-directories of 1Mb or more:
R 1.7Mb
doc 2.3Mb
help 1.0Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.23.0
Flags: --no-vignettes
Check: installed package size
Result: NOTE
installed size is 7.5Mb
sub-directories of 1Mb or more:
R 1.7Mb
doc 2.3Mb
help 1.0Mb
libs 1.1Mb
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 1.23.0
Flags: --no-vignettes
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
epidata.Rd: Matrix-class
knox.Rd: truehist
permutationTest.Rd: truehist
twinstim_epitest.Rd: truehist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavor: r-devel-windows-x86_64
Version: 1.23.0
Flags: --no-vignettes
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: 'INLA'
Flavor: r-oldrel-windows-x86_64
Version: 1.23.0
Flags: --no-vignettes
Check: examples
Result: ERROR
Running examples in 'surveillance-Ex.R' failed
The error most likely occurred in:
> ### Name: hhh4
> ### Title: Fitting HHH Models with Random Effects and Neighbourhood
> ### Structure
> ### Aliases: hhh4
> ### Keywords: ts regression
>
> ### ** Examples
>
> ######################
> ## Univariate examples
> ######################
>
> ### weekly counts of salmonella agona cases, UK, 1990-1995
>
> data("salmonella.agona")
> ## convert old "disProg" to new "sts" data class
> salmonella <- disProg2sts(salmonella.agona)
> salmonella
-- An object of class sts --
freq: 52
start: 1990 1
dim(observed): 312 1
Head of observed:
observed1
[1,] 1
> plot(salmonella)
>
> ## generate formula for an (endemic) time trend and seasonality
> f.end <- addSeason2formula(f = ~1 + t, S = 1, period = 52)
> f.end
~1 + t + sin(2 * pi * t/52) + cos(2 * pi * t/52)
> ## specify a simple autoregressive negative binomial model
> model1 <- list(ar = list(f = ~1), end = list(f = f.end), family = "NegBin1")
> ## fit this model to the data
> res <- hhh4(salmonella, model1)
> ## summarize the model fit
> summary(res, idx2Exp=1, amplitudeShift=TRUE, maxEV=TRUE)
Call:
hhh4(stsObj = salmonella, control = model1)
Coefficients:
Estimate Std. Error
exp(ar.1) 0.2678139 0.0596124
end.1 0.7697737 0.1240722
end.t -0.0007282 0.0006345
end.A(2 * pi * t/52) 0.5841434 0.0810975
end.s(2 * pi * t/52) -2.6961872 0.0303381
overdisp 0.1905914 0.0467357
Epidemic dominant eigenvalue: 0.27
Log-likelihood: -620.23
AIC: 1252.46
BIC: 1274.9
Number of units: 1
Number of time points: 311
> plot(res)
> plot(res, type = "season", components = "end")
>
>
> ### weekly counts of meningococcal infections, Germany, 2001-2006
>
> data("influMen")
> fluMen <- disProg2sts(influMen)
> meningo <- fluMen[, "meningococcus"]
> meningo
-- An object of class sts --
freq: 52
start: 2001 1
dim(observed): 312 1
Head of observed:
meningococcus
[1,] 4
> plot(meningo)
>
> ## again a simple autoregressive NegBin model with endemic seasonality
> meningoFit <- hhh4(stsObj = meningo, control = list(
+ ar = list(f = ~1),
+ end = list(f = addSeason2formula(f = ~1, S = 1, period = 52)),
+ family = "NegBin1"
+ ))
>
> summary(meningoFit, idx2Exp=TRUE, amplitudeShift=TRUE, maxEV=TRUE)
Call:
hhh4(stsObj = meningo, control = list(ar = list(f = ~1), end = list(f = addSeason2formula(f = ~1,
S = 1, period = 52)), family = "NegBin1"))
Coefficients:
Estimate Std. Error
exp(ar.1) 0.16471 0.05513
exp(end.1) 8.05551 0.55271
end.A(2 * pi * t/52) 0.43158 0.03793
end.s(2 * pi * t/52) 0.65109 0.04841
overdisp 0.04917 0.01168
Epidemic dominant eigenvalue: 0.16
Log-likelihood: -845.61
AIC: 1701.23
BIC: 1719.93
Number of units: 1
Number of time points: 311
> plot(meningoFit)
> plot(meningoFit, type = "season", components = "end")
>
>
> ########################
> ## Multivariate examples
> ########################
>
> ### bivariate analysis of influenza and meningococcal infections
> ### (see Paul et al, 2008)
>
> plot(fluMen, same.scale = FALSE)
>
> ## Fit a negative binomial model with
> ## - autoregressive component: disease-specific intercepts
> ## - neighbour-driven component: only transmission from flu to men
> ## - endemic component: S=3 and S=1 sine/cosine pairs for flu and men, respectively
> ## - disease-specific overdispersion
>
> WfluMen <- neighbourhood(fluMen)
> WfluMen["meningococcus","influenza"] <- 0
> WfluMen
influenza meningococcus
influenza 0 1
meningococcus 0 0
> f.end_fluMen <- addSeason2formula(f = ~ -1 + fe(1, which = c(TRUE, TRUE)),
+ S = c(3, 1), period = 52)
> f.end_fluMen
~-1 + fe(1, which = c(TRUE, TRUE)) + fe(sin(2 * pi * t/52), which = c(TRUE,
TRUE)) + fe(cos(2 * pi * t/52), which = c(TRUE, TRUE)) +
fe(sin(4 * pi * t/52), which = c(TRUE, FALSE)) + fe(cos(4 *
pi * t/52), which = c(TRUE, FALSE)) + fe(sin(6 * pi * t/52),
which = c(TRUE, FALSE)) + fe(cos(6 * pi * t/52), which = c(TRUE,
FALSE))
> fluMenFit <- hhh4(fluMen, control = list(
+ ar = list(f = ~ -1 + fe(1, unitSpecific = TRUE)),
+ ne = list(f = ~ 1, weights = WfluMen),
+ end = list(f = f.end_fluMen),
+ family = "NegBinM"))
Execution halted
Flavor: r-oldrel-windows-x86_64