Partial Least square regression model (PLS) for Budle Bay meadow
I am investigating if climatic variables (max temp, rainfall, and solar radiation) are influencing seagrass percent cover. This example is for one meadow. I am using a partial least square regression model to investigate this.
###make this example reproducible
set.seed(1)
### pls model
model1 <- plsr(budle_bay_pls_$cover~budle_bay_pls_$`sunshine 01`+budle_bay_pls_$`sunshine 03`+budle_bay_pls_$`sunshine 06`+budle_bay_pls_$`sunshine 09`+budle_bay_pls_$`sunshine 12`+budle_bay_pls_$`max temp 01`+budle_bay_pls_$`max temp 03`+budle_bay_pls_$`max temp 06`+budle_bay_pls_$`max temp 09`+budle_bay_pls_$`max temp 12`+budle_bay_pls_$`rainfall 01`+budle_bay_pls_$`rainfall 03`+budle_bay_pls_$`rainfall 06`+budle_bay_pls_$`rainfall 09`+budle_bay_pls_$rainfall12, data=budle_bay_pls_, scale=TRUE, validation="CV")
summary(model1)
Data: X dimension: 10 15
Y dimension: 10 1
Fit method: kernelpls
Number of components considered: 8
VALIDATION: RMSEP
Cross-validated using 10 leave-one-out segments.
(Intercept) 1 comps 2 comps 3 comps 4 comps 5 comps 6 comps 7 comps 8 comps
CV 18.02 19.79 19.85 18.55 16.57 16.48 17.19 17.37 17.14
adjCV 18.02 19.25 19.09 17.85 15.83 15.73 16.33 16.49 16.26
TRAINING: % variance explained
1 comps 2 comps 3 comps 4 comps 5 comps 6 comps 7 comps 8 comps
X 19.67 41.83 56.42 65.25 75.83 84.03 95.79 98.53
budle_bay_pls_$cover 61.94 81.26 88.81 95.79 97.59 99.43 99.83 99.98
I understand from these graphs that 4 components can make a strong model. However, I want to know which components they are, and I am not sure how to do that. I have played around with the order I have written the code and that does not seem to change anything.
My thoughts are to make a graph like the one below however this is for a PCA analysis and not a PLS analysis. Therefore, when I try follow a method to make a graph like this it does not work.
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