There are some environmental factors in habitat such as several soil properties and topography, then what is the appopriate analysis methos to compress it become several habitat types?
You need to explain more clearly what you are asking when you say--"what is the appopriate analysis methos to compress it become several habitat types?"
i want to group several environmental factors and determine it as representative of habitat types. should I use PCA? and How can I know the spatial distribution? or should I mapping the all enviromental factors? then do overlay? How can I do overlay in R? the environmental data is distributed in quadrats in a plot.
You could consider using k-means clustering followed by SIMPER to explore the factors contributing to the differences between the assigned clusters. PCA could then be utilized to visualize the clustering
The first thing, is this habitat protected (conservation nal) or is held by man?.
If the first one, you will study the relationship between soil-climate and (vegetation / foun), you can started with an exhaustive inventory in case of rare species.
If it's the second, you will study it on the Agroforestry plan.
First you have to take into account the number of habitat variables you have. Then you can use different multivariate tools. I suggest you look for the PRIMER program. This rpeogram is available at: http://www.primer-e.com/. Although it has been widely used in studies of Marian biodiversity, it has a group of very useful grouping tools.