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
))




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