# Defunct Functions in Package surveillance

`surveillance-defunct.Rd`

The functions listed here are no longer part of surveillance.

## Usage

```
## Removed in surveillance 1.17.0
compMatrix.writeTable(compMatrix)
correct53to52(disProgObj, firstweek = 1)
enlargeData(disProgObj, range = 1:156, times = 1)
makePlot(outputpath, data = "k1", method = "rki1",
name, disease, range = 157:339)
readData(abb, week53to52=TRUE, sysPath=TRUE)
test(data = c("k1", "m5"), range = 157:339)
testSim(p = 0.99, r = 0.01, length = 400, A = 1, alpha = 1,
beta = 0, phi = 0, frequency = 1, state = NULL, K,
range = 200:400)
toFileDisProg(disProgObj, toFile)
## Removed in surveillance 1.18.0
algo.hhh(disProgObj, control=list(
lambda=TRUE, neighbours=FALSE, linear=FALSE, nseason=0,
negbin=c("none", "single", "multiple"),
proportion=c("none", "single", "multiple"), lag.range=NULL
), thetastart=NULL, verbose=TRUE)
algo.hhh.grid(disProgObj, control=list(
lambda=TRUE, neighbours=FALSE, linear=FALSE, nseason=0,
negbin=c("none", "single", "multiple"),
proportion=c("none", "single", "multiple"), lag.range=NULL
), thetastartMatrix, maxTime=1800, verbose=FALSE)
create.grid(disProgObj, control, params=list(
epidemic=c(0.1, 0.9, 5), endemic=c(-0.5, 0.5, 3),
negbin=c(0.3, 12, 10)
))
## Removed in surveillance 1.20.0
qlomax(p, scale, shape)
## Removed in surveillance 1.22.0
inside.gpc.poly(x, y = NULL, polyregion, mode.checked = FALSE)
# S3 method for class 'gpc.poly'
intersectPolyCircle(object, center, radius, npoly = 32,
useGEOS = FALSE, ...)
# S3 method for class 'gpc.poly'
scale(x, center = c(0,0), scale = c(1,1))
## Removed in surveillance 1.24.0
algo.twins(disProgObj, control=list(
burnin=1000, filter=10, sampleSize=2500,
noOfHarmonics=1, alpha_xi=10, beta_xi=10,
psiRWSigma=0.25, alpha_psi=1, beta_psi=0.1,
nu_trend=FALSE, logFile="twins.log"))
# S3 method for class 'atwins'
plot(x, which=c(1,4,6,7), ask=TRUE, ...)
```

## Details

The trivial function `compMatrix.writeTable`

is no longer used
(it did nothing more than generating an `xtable`

of its input).

The ancient test function `makePlot`

is no longer used,
nor are functions `readData`

(the datasets are still available
via `data(m1)`

etc) and `correct53to52`

/
`enlargeData`

(which both only worked for old `"disProg"`

objects with non-matrix elements). `enlargeData`

is still
exemplified in the old `vignette("surveillance")`

.
`test`

calls of outbreak detection algorithms applied to the old
SurvStat datasets can be found in `vignette("surveillance")`

,
and `testSim`

is provided as an example
in `help("sim.pointSource")`

.

Functions related to the old `"disProg"`

class are no longer needed. The effect of `toFileDisProg`

could
still be achieved via `write.table`

of
`as.data.frame(disProg2sts(disProgObj))[c("epoch", "observed", "state")]`

.

`algo.hhh`

was an early implementation of the HHH regression
framework for multivariate time series of infectious disease counts.
An improved and considerably extended implementation is provided by
the `hhh4`

function since 2012.

A `qlomax`

function is provided in package VGAM.

Long unused methods for `"gpc.poly"`

objects have been removed;
the corresponding package gpclib has been unmaintained on CRAN.

The experimental and since unused `algo.twins`

implementation of
Held et al. (2006) has been removed; it is archived at
https://codeberg.org/EE-hub/twins.