Gleditsia_aquatica

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Seasonal patterns

A standard Water and Leith climate diagram for the mean values of precipitation and temperature extracted from the species presence points.

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The Walter and Leith diagram assumes that the growing season occurs when rainfall is over 100mm. A more refined method is to extract the values from a bucket model that keeps track of input to the soil profile through precipitation and reductions in soil moisture through evaptranspiration over the course of the year. This can be compared to changes in NDVI at the collection points.

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## Error: Not enough (non-NA) data to do anything meaningful

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## Error: invalid first argument

## Error: Not enough (non-NA) data to do anything meaningful

## Error: error in evaluating the argument 'object' in selecting a method for function 'predict': Error: object 'soilmod' not found

Comparison

In some cases NDVI will remain fairly constant, even when the balance model shows that soil water constant is lowered for part of the year. Providing SWC is above 50% of maximum levels the vegetation would not experience a great deal of hydric stress.

## Error: error in evaluating the argument 'y' in selecting a method for function 'plot': Error in predict(soilmod, newdata = data.frame(ind)) : 
##   error in evaluating the argument 'object' in selecting a method for function 'predict': Error: object 'soilmod' not found

## Error: error in evaluating the argument 'object' in selecting a method for function 'predict': Error: object 'ndvimod' not found

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Summary of the variable values at the collection points.

	Mode	NA’s
x	logical	0
y	logical	0
X	logical	0
Y	logical	0
elev	logical	0
anprec	logical	0
mtemp	logical	0
Trange	logical	0
saet	logical	0
msoil	logical	0

Niche space with relation to annual precipitation and mean annual temperature.

The following diagrams show kernel densities one two synthestic climate axes (total annual rainfall and mean annual temperature). If their are signs of multimodality this may indicate that the species has not fully explored its climate niche, or that there are disjunct populations with differing characteristics. The method will not show clear results for species with few collection points.

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## Error: arguments imply differing number of rows: 0, 1

Spatial clustering

The same analysis can be run to look at spatial clustering. The kernel densities are smoothed, so will only suggest multimodality if the points are very highly clustered.

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Finding spatial clusters

The significance of any spatial clusters can be checked using the silhouette width method. The width is calculated for values of k between 2 and 5. If any are higher than 0.52 the analysis will produce a diagram showing the clusters.

## Error: Number of clusters 'k' must be in {1,2, .., n-1}; hence n >= 2

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## [1] ""

Anosim

If there is evidence that the points fall into at least 2 groups, but fewer than 6 we can look at whether there is significant differences in variability between and within groups in the climatic conditions at the sites using Anosim. This is a sensitive test, as would be MANOVA, so there will often be significant differences. They should only be intepreted as important if R is much larger than 0.3.

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Gam model using simple environmental variables

For comparison we can fit a model using mean temperature, temperature range and annual precipitation.

## Error: cannot evaluate a model without absence and presence data that are
## not NA

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## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'modpres' not found

## Error: cannot evaluate a model without absence and presence data that are
## not NA

## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'eback' not found

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## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'modpres' not found

## Error: plot.new has not been called yet

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## Error: plot.new has not been called yet

## Error: Not enough (non-NA) data to do anything meaningful

## Error: error in evaluating the argument 'object' in selecting a method for function 'predict': Error: object 'testmod' not found

## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'e' not found

## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'modpres' not found

## Error: plot.new has not been called yet

## Error: plot.new has not been called yet

## Error: plot.new has not been called yet

## Error: Not enough (non-NA) data to do anything meaningful

## Error: error in evaluating the argument 'object' in selecting a method for function 'predict': Error: object 'testmod' not found

## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'e' not found

Bucket model GAM.

Now fit a gam using temperature range, mean temperature and the annual soil moisture dynamic as input.

## Error: cannot evaluate a model without absence and presence data that are
## not NA

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## Error: comparison (6) is possible only for atomic and list types

## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'modpres' not found

## Error: cannot evaluate a model without absence and presence data that are
## not NA

## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'eback' not found

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## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'modpres' not found

## Error: plot.new has not been called yet

## Error: plot.new has not been called yet

## Error: plot.new has not been called yet

## Error: plot.new has not been called yet

## Error: Not enough (non-NA) data to do anything meaningful

## Error: error in evaluating the argument 'object' in selecting a method for function 'predict': Error: object 'testmod' not found

## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'e' not found

## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'modpres' not found

## Error: plot.new has not been called yet

## Error: plot.new has not been called yet

## Error: plot.new has not been called yet

## Error: plot.new has not been called yet

## Error: Not enough (non-NA) data to do anything meaningful

## Error: error in evaluating the argument 'object' in selecting a method for function 'predict': Error: object 'testmod' not found

## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'e' not found

Random Forest

## Error: cannot evaluate a model without absence and presence data that are
## not NA

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## Error: comparison (6) is possible only for atomic and list types

## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'modpres' not found

## Error: cannot evaluate a model without absence and presence data that are
## not NA

## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'eback' not found

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## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'modpres' not found

## Error: plot.new has not been called yet

## Error: plot.new has not been called yet

## Error: plot.new has not been called yet

## Error: plot.new has not been called yet

## Error: missing values in object

## Error: error in evaluating the argument 'object' in selecting a method for function 'predict': Error: object 'testmod' not found

## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'e' not found

## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'modpres' not found

## Error: plot.new has not been called yet

## Error: plot.new has not been called yet

## Error: plot.new has not been called yet

## Error: plot.new has not been called yet

## Error: missing values in object

## Error: error in evaluating the argument 'object' in selecting a method for function 'predict': Error: object 'testmod' not found

## Error: error in evaluating the argument 'x' in selecting a method for function 'plot': Error: object 'e' not found