[R] Temporal clustering of factors

[Bert Gunter]

Post to R-sig-ecology  , not here.

-- Bert

On Thu, Aug 15, 2013 at 2:20 AM, Chris McOwen
<Chris.McOwen at unep-wcmc.org> wrote:
> Dear list,
>
> I have 50 sites where information was recorded over a 45 year time period. The recorded data could take one of four forms: Fishing effort, Environmental, Both or Inconclusive.
>
> What i am aiming to do is cluster sites based on their similarity through time, essentially i view this as being similar to making a phylogeny, where instead of a genetic sequence i have a sequence of factors.
>
> I was thinking of using Gower distance to create a dissimilarity matrix and go from there but i don't think this captures what i am looking for?
>
> Any suggestions would be gratefully received.
>
>
> For space i have restricted the sample data to 4 sites
>
> temporal_sites <- structure(list(Year = c(1959L, 1960L, 1961L, 1962L, 1963L, 1964L,
> 1965L, 1966L, 1967L, 1968L, 1969L, 1970L, 1971L, 1972L, 1973L,
> 1974L, 1975L, 1976L, 1977L, 1978L, 1979L, 1980L, 1981L, 1982L,
> 1983L, 1984L, 1985L, 1986L, 1987L, 1988L, 1989L, 1990L, 1991L,
> 1992L, 1993L, 1994L, 1995L, 1996L, 1997L, 1998L, 1999L, 2000L,
> 2001L, 2002L, 2003L, 2004L, 1959L, 1960L, 1961L, 1962L, 1963L,
> 1964L, 1965L, 1966L, 1967L, 1968L, 1969L, 1970L, 1971L, 1972L,
> 1973L, 1974L, 1975L, 1976L, 1977L, 1978L, 1979L, 1980L, 1981L,
> 1982L, 1983L, 1984L, 1985L, 1986L, 1987L, 1988L, 1989L, 1990L,
> 1991L, 1992L, 1993L, 1994L, 1995L, 1996L, 1997L, 1998L, 1999L,
> 2000L, 2001L, 2002L, 2003L, 2004L, 1959L, 1960L, 1961L, 1962L,
> 1963L, 1964L, 1965L, 1966L, 1967L, 1968L, 1969L, 1970L, 1971L,
> 1972L, 1973L, 1974L, 1975L, 1976L, 1977L, 1978L, 1979L, 1980L,
> 1981L, 1982L, 1983L, 1984L, 1985L, 1986L, 1987L, 1988L, 1989L,
> 1990L, 1991L, 1992L, 1993L, 1994L, 1995L, 1996L, 1997L, 1998L,
> 1999L, 2000L, 2001L, 2002L, 2003L, 2004L, 1959L, 1960L, 1961L,
> 1962L, 1963L, 1964L, 1965L, 1966L, 1967L, 1968L, 1969L, 1970L,
> 1971L, 1972L, 1973L, 1974L, 1975L, 1976L, 1977L, 1978L, 1979L,
> 1980L, 1981L, 1982L, 1983L, 1984L, 1985L, 1986L, 1987L, 1988L,
> 1989L, 1990L, 1991L, 1992L, 1993L, 1994L, 1995L, 1996L, 1997L,
> 1998L, 1999L, 2000L, 2001L, 2002L, 2003L, 2004L), Site = structure(c(1L,
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L,
> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L,
> 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
> 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
> 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
> 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
> 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
> 4L, 4L, 4L, 4L, 4L, 4L, 4L), .Label = c("A", "B", "C", "D"), class = "factor"),
>     Factor = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
>     2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 1L,
>     1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
>     3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
>     2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
>     2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L,
>     3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
>     2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
>     3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
>     3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
>     2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
>     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L,
>     3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label = c("Both",
>     "Environmental", "Fishing Effort"), class = "factor")), .Names = c("Year",
> "Site", "Factor"), class = "data.frame", row.names = c(NA, -184L
> ))
>
>
>
>         [[alternative HTML version deleted]]
>
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-- 

Bert Gunter
Genentech Nonclinical Biostatistics

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