Use trawlData

Using trawlData is really simple. Just remember that the main point of the package is to have standardized data sets available to you, but to not limit what you can do with them. Thus, you can almost forget about all the functions, and just remember that 2 simple categories of data sets:

1. raw.__
2. clean.__

Where the __ represents a region name. Regions include

ai	Aleutian Islands
ebs	Eastern Bering Sea
gmex	Gulf of Mexico
goa	Gulf of Alaska
newf	Newfoundland
neus	Northeast US
sa	'South Atlantic' (Southeast US)
sgulf	Southern Gulf of St. Lawrence
shelf	Scotian Shelf
wcann	West Coast US (annual survey)
wctri	West Coast US (triennial survey)

There are also data sets for species taxonomy (spp.key), gridded depth (depth), gridded surface temperatures (sst, sst.ann, sst.mu), gridded bottom temperatures (soda, soda.annMax, soda.annMean, soda.annMean.mu).

Currently, some plotting functions are also being developed. A fun one right now is to plot a picture of a species given it's scientific name ... see ?sppImg!

Note: There is currently a problem with the function to read in the raw data when using the latest version of data.table; if you want this functionality, please do

remove.packages("data.table")
library(devtools)
install_version("data.table", "1.9.4")

Below is a quick tour of some of the functions and data sets in the package:

# load package
library(trawlData)

# both raw & clean data + taxonomy already in workspace
data(raw.newf) # raw Newfoundland
data(clean.ebs) # clean Eastern Berring Sea
data(spp.key) # the species key

# check documentation
?raw.sa
?clean.wctri

# easy function to read in from source data
my.goa <- read.trawl(reg="goa") # same as raw.goa

# functions for cleaning raw data
# a specific order for calling these functions!
clean.names(my.goa, reg="goa") # note it affects my.goa directly!
clean.format(my.goa, reg="goa")
clean.columns(my.goa, reg="goa")
my.goa <- clean.tax(my.goa, reg="goa") # only clean.__ function that doesn't change data.table in place!
clean.trimRow(my.goa, reg="goa") # doesn't drop rows, just adds suggestive keep.row column

# somewhat confusingly, clean.trimCol actually
# reduces information in your data set!
# (it drops columns)
skinny.goa <- copy(clean.goa)
clean.trimCol(skinny.goa, reg="goa")

# these functions are documented
?clean.trimCol # you will see the options for which columns to keep (or not)!

# check which data sets are available
data(package="trawlData")