Eelgrass community trophic relationships (ETR) data exploration

Here I will conduct exploratory analysis of 2018 eelgrass community data

Load data

Load biomass/abundace data, stable isotope, and fatty acid data

Biomass and oceanography

Stable Isotope - preliminary

Fatty Acid

Biomarker metadata

Complie biomass data

Merge all the different biomass data types into one data frame

Data exploration

Biomass

## Warning: Removed 5 rows containing missing values (geom_errorbar).

Particulate Organic Matter

summaries by site

## Warning: Removed 1 rows containing missing values (geom_errorbar).

## Warning: Removed 1 rows containing missing values (geom_errorbar).

Oceanography

Stable Isotopes

SI data prep

Merge species with si values

SI Plots

## Warning: Removed 23 rows containing missing values (geom_point).

## Warning: Removed 23 rows containing missing values (geom_point).

Fatty acids

The ultimate goal will be to look at some basic nmds plots of all species. Then overlay some depended variables like site and sea otter treatment.

Examine FAs

What FAs do we have here.

##  [1] "a.C17.0" "a.C18.0" "a.C19.0" "C14.0"   "C15.0"   "C16.0"   "C16.1w" 
##  [8] "C16.1w5" "C16.1w7" "C16.1w9" "C16.2w"  "C16.2w3" "C16.2w6" "C16.3w3"
## [15] "C16.4w"  "C16.4w3" "C17.0"   "C17.1w"  "C17.1w9" "C18.0"   "C18.1w" 
## [22] "C18.1w7" "C18.1w9" "C18.2w"  "C18.2w3" "C18.2w6" "C18.3w"  "C18.3w3"
## [29] "C18.3w6" "C18.4w"  "C18.4w2" "C18.4w3" "C19.1w"  "C20.0"   "C20.1w" 
## [36] "C20.1w7" "C20.1w9" "C20.2w"  "C20.2w3" "C20.2w6" "C20.3w3" "C20.3w6"
## [43] "C20.4w"  "C20.4w3" "C20.4w6" "C20.5w3" "C21.0"   "C22.0"   "C22.1w" 
## [50] "C22.1w9" "C22.2w"  "C22.2w2" "C22.2w3" "C22.2w6" "C22.3w"  "C22.4w3"
## [57] "C22.4w6" "C22.5w3" "C22.6w3" "C23.0"   "C24.0"   "i.C15.0" "i.C16.0"
## [64] "i.C17.0" "i.C18.0"

First will will have to prep that data with some manipulations and transformations and standardizations.

Transformations and standardizations

Subsets

I will use and arcsine sqrt transformation

NMDS

NMDS calculations

FA vectors

NMDS plots

Data prep. Build dataframe from metaMDS output fo easy plotting

Plots