Thanks all for suggestions. I now have a nice plot showing the temperature of 6 different sites, each site distinguished by different coloured points, using nested ifelse. My apologies I thought I could change the type to "l" and the same arguments would be applied to line graph, with 6 different lines for each site...? I wanted to try lines as I think they might show the trends more clearly. I have just found the plottrix package manual and will try that to achieve this, and look at ggplot too.
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