Functions for plotting fish distributions from AFSC survey data, location, depth, etc. with centroids. Instructions on how to use the functions are documented on the top of each file.
To use any of these functions you must start with the Get_DATA.R which will pull data from AFSC. You need to supply a password, username, species, and bins you wish to use.
Get_DATA.r
This function pulls RACE survey haul and length data for later analysis
survey 52=AI,98=EBS Shelf, 78=EBS Slope, and 47 = GOA
bins can either be specified as in bins=c(0,100,200,300,400) or as percentiles based on time series length composition frequency
with the number of divisions entered in bins e.g. bins=5 would be 5 percentiles.
Example use code below for EBS Pollock and with 5 percentile bins:
afsc_username=""
afsc_password=""
data_1<-Get_DATA(username=afsc_username,password=afsc_password,species=21720,survey = 98,bins = 5,FIG=T,yr=1982:2021)
You will also need to source the Get_TEMP.r file to set up temperatures for the data for many of the centroids by temperature plots.
Get_TEMP.r
Function calculates a timeseries of mean bottom temperature from the RACE surveys following Spencer (2006) for all surveys years
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2419.2008.00486.x/full
The Bering Sea is likely the only one that works as intended. May need some work for the other regions. I think that the GOA Stratum surveyed are not consistent across time
and therefore the mean temps across years are not going to be consistent in this treatment.
Uses data from the Get_DATA.r function
plotT=T plots temperatures over time
The temperature anomaly is based on the full timeseries average bottom temp.
"WARM" is > 0.5std from the mean, "COLD" is < 0.5std from the mean "MED" is between the two
Example:
Get_TEMP(data=data_1, plotT=T)
plot_centroid_num.r
Function for plotting RACE survey data for any species by temperature and depth (plotT=1) and specified length or by location (plotT=2)and specified length
This function takes data pulled using the get_DATA() function.
REG = T plots data by cold,med, and warm temperture regime, REF=F plots it by year
PATH = T plots a line between points ordered by year
ELLIP = T plots a modified Fox and Weisberg (2011)
method for calculating the ellipses (ELLIP=TRUE)with a confidence level set at p1.
colx = 1 is a yellow to brown color scheme friendly to B&W and colorbline colx=2 is a rainbow color scheme
Confidence intervals are based on 1.96*SE
Example plots:
plot_centroid_num(data=data_1,REG=T,plotT=1,PATH=F,ELLIP=F,p1=0.95,colx=1,thin=F)
plot_centroid_num(data=data_1,REG=T,plotT=2,PATH=F,ELLIP=F,p1=0.95,colx=1,thin=F)
plot_dist_num.r
Function for plotting data by temperature (plotT=1) or location (plotT=2)and specified length
Uses data from Get_DATA() function and requires the Get_TEMP() function
Plots individual bins specified when data was retrieved.
example plots:
plot_dist_num(data=data_1,bin=3,plotT=1)
plot_dist_num(data=data_1,bin=3,plotT=2)
plot_SEX_num.r
Function to plot RACE survey data centroids of temperature and depth (plotT=1) or location (plotT=2) by sex
Takes as input data retrieved using the Get_DATA() function, will plot all centroids by year and length bins
p1 indicates the area of confidence interval ellipse
Requires the Get_TEMP() function
Examples:
plot_SEX_num(data=data_1,plotT=2,p1=0.9)
plot_SEX_num(data=data_1,plotT=1,p1=0.9)
plot_year_num.r
Function to plot RACE survey data centroids of temperature and depth (plotT=1) or location (plotT=2) by year
Takes as input data retrieved using the Get_DATA() function, will plot all centroids by year and length bins
p1 indicates the area of confidence interval ellipse
Example:
plot_YEAR_num(data=data_1,plotT=1,REG=TRUE,PATH=TRUE,ELLIP=TRUE,p1=0.9,colx=1)
plot_YEAR_num(data=data_1,plotT=2,REG=TRUE,PATH=TRUE,ELLIP=TRUE,p1=0.9,colx=1)
Plotting_bins.r
Function for creating multiple PDFs of length bins as defined in the Get_DATA()
Function will plot into your working directory
Each PDF page will hold all years for each of the specified bins in the Get_DATA() function
Example:
Plotting_bins(datas=data_1)
Series of plots for doing boxplots by temperature, depth, and location
Plot_WC.r
Get_td(data=data_1)
Function which pulls the temperature data from the data file.
Get_Mean_td(data=data_1)
Function to calculate both mean shelf temperatures and mean temperature for the species at the different bins.
Plot_WC(data=data_1,plotT=1,depth=c(-250,0))
Function to plot boxplots of bins by depth and year temperature regine (warm, med, cold). Two possible plots, first is simply the boxplot by depth, the second includs lines in red grey and blue depicting shelf mean for warm, med, and cold years.
Depth sets the Y-axis of the plot.
Plot 1: Plot_WC(data=data_1,plotT=1,depth=c(-120,0))
Plot 2: Plot_WC(data=data_1,plotT=2)
Plot_LL(data=data_1,plotT=1)
Function to plot boxplots of bins by latitude and longlitude by annual temperature regine (warm, med, cold). Two possible plots, first is simply the boxplot by depth, the second includs lines in red grey and blue depicting shelf mean for warm, med, and cold years.
Plot_LL(data_1,plotT=1)
Plot_LL(data_1,plotT=2)
Plot of all 'Major' species locations by size classes in the AFSC bottom trawl surveys
You can click the species on and off using the legend. Each ball represents a size class by pentile for each species for each survey (1982-2017). Smaller bubbles are smaller size classes. The lines go through the mean of each size class for each species for all survey years and can also be toggled on or off.