Centroid exploration
LGCarlson
10/3/2019
Data loading and cleaning
Create plot theme.
LGCtheme <- theme(strip.background = element_blank(),
panel.grid = element_blank(),
axis.title = element_text(size = 13),
axis.text = element_text(size = 12),
legend.text = element_text(size = 12),
strip.text = element_text(size = 12, color = "black"))Build full trawl dataset.
trawl.data<-survdat %>%
dplyr::select(ID, EST_YEAR,SEASON, STRATUM, DECDEG_BEGLAT,DECDEG_BEGLON,
SVSPP, COMNAME, CATCHSEX,BIOMASS, AVGDEPTH, ABUNDANCE, LENGTH, NUMLEN) %>%
filter(STRATUM >= 01010 & STRATUM <= 01760) %>%
filter(STRATUM!=1310 & STRATUM!=1320 & STRATUM!=1330 & STRATUM!=1350 &
STRATUM!=1410 & STRATUM!=1420 & STRATUM!=1490) %>%
filter(SEASON == "SPRING" | SEASON == "FALL") %>%
filter(EST_YEAR >= 1970 & EST_YEAR < 2018) %>%
mutate(BIOMASS = ifelse(is.na(BIOMASS) == TRUE & ABUNDANCE > 0,0.01, BIOMASS)) %>%
mutate(BIOMASS = ifelse(BIOMASS == 0 & ABUNDANCE > 0,0.01, BIOMASS)) %>%
mutate(ABUNDANCE = ifelse(is.na(ABUNDANCE) == TRUE & BIOMASS > 0, 1, ABUNDANCE)) %>%
mutate(ABUNDANCE = ifelse(ABUNDANCE == 0 & BIOMASS > 0, 1, ABUNDANCE)) %>%
filter(!is.na(BIOMASS),
!is.na(ABUNDANCE))Create template containing unique tow IDs.
template<-trawl.data %>%
distinct(ID, .keep_all = TRUE) %>%
dplyr::select(ID, EST_YEAR, SEASON, STRATUM,DECDEG_BEGLAT,DECDEG_BEGLON,AVGDEPTH)Create a dataframe to add common names by SVSPP code.
COMNAMEdata<-trawl.data %>%
dplyr::select(SVSPP, COMNAME) %>%
distinct(SVSPP, .keep_all = TRUE)Select only species of interest (has adjacent vtr data).
species_of_interest<-COMNAMEdata %>%
filter(COMNAME == "ATLANTIC COD" | COMNAME == "ATLANTIC HALIBUT" | COMNAME == "ATLANTIC MACKEREL" |
COMNAME == "BLACK SEA BASS" | COMNAME == "RED HAKE" | COMNAME == "SILVER HAKE" |
COMNAME == "SUMMER FLOUNDER" | COMNAME == "YELLOWTAIL FLOUNDER" | COMNAME == "ATLANTIC HERRING")Biomass species-1 year-1 * Sum total biomass by species in each year.
biomass.spp.year<-trawl.data %>%
dplyr::group_by(SVSPP, EST_YEAR) %>%
summarize(ANNUAL_SPECIES_BIOMASS = sum(BIOMASS)) Biomass species-1 tow-1 * Sum total biomass by species in each tow. * Add “template” metadata for each tow. * Add annual species biomass column. * Will use this dataframe to calculate center of biomass later on
biomass.spp<-trawl.data %>%
group_by(ID, SVSPP) %>%
summarize(SPECIES_BIOMASS = sum(BIOMASS), SPECIES_ABUNDANCE = sum(ABUNDANCE)) %>%
right_join(template, by = "ID") %>%
left_join(biomass.spp.year, by = c("EST_YEAR", "SVSPP"))Center of biomass calculation (trawl)
Calculate center of species biomass for each year.
centerofbiomass<-biomass.spp %>%
filter(!is.na(SPECIES_BIOMASS),
!is.na(ANNUAL_SPECIES_BIOMASS)) %>%
mutate(weightedLAT = (SPECIES_BIOMASS/ANNUAL_SPECIES_BIOMASS)*DECDEG_BEGLAT) %>%
mutate(weightedLON = (SPECIES_BIOMASS/ANNUAL_SPECIES_BIOMASS)*DECDEG_BEGLON) %>%
group_by(SVSPP,EST_YEAR) %>%
summarise(CENTER_LAT = sum(weightedLAT, na.rm = TRUE), CENTER_LON = sum(weightedLON, na.rm = TRUE)) %>%
filter(!is.na(CENTER_LAT),
!is.na(CENTER_LON)) %>%
left_join(COMNAMEdata, by = "SVSPP")Filter only centroid data for species of interest.
soi_center<-centerofbiomass %>%
semi_join(species_of_interest, by = "SVSPP") %>%
dplyr::rename("year" = "EST_YEAR", "mean.lat" = "CENTER_LAT", "mean.long" = "CENTER_LON", "nice.spp.name" = "COMNAME") %>%
mutate(nice.spp.name = tolower(nice.spp.name)) %>%
mutate(nice.spp.name = snakecase::to_sentence_case(nice.spp.name)) %>%
mutate(centroidtype = "trawl")VTR vs trawl centroid
Latitude
Plot latitude centroid of trawl survey vs vtr.
Grey line represents model of best fit when centroid type (VTR vs trawl) is not considered.
| species | lhs | estimate | std.error | statistic | p.value |
|---|---|---|---|---|---|
| Atlantic cod | vtr - trawl | -24.358 | 19.970 | -1.220 | 0.230 |
| Atlantic halibut | vtr - trawl | -11.439 | 32.309 | -0.354 | 0.725 |
| Atlantic herring | vtr - trawl | 152.600 | 35.243 | 4.330 | 0.000 |
| Atlantic mackerel | vtr - trawl | -114.723 | 96.957 | -1.183 | 0.244 |
| Black sea bass | vtr - trawl | 139.913 | 35.631 | 3.927 | 0.000 |
| Red hake | vtr - trawl | -11.565 | 26.565 | -0.435 | 0.666 |
| Silver hake | vtr - trawl | -19.144 | 36.722 | -0.521 | 0.605 |
| Summer flounder | vtr - trawl | -19.483 | 40.087 | -0.486 | 0.630 |
| Yellowtail flounder | vtr - trawl | 14.980 | 22.551 | 0.664 | 0.511 |
Longitude
Plot longitude centroid of trawl survey vs vtr.
Grey line represents model of best fit when centroid type (VTR vs trawl) is not considered.
| species | lhs | estimate | std.error | statistic | p.value |
|---|---|---|---|---|---|
| Atlantic cod | vtr - trawl | 60.643 | 63.543 | 0.954 | 0.346 |
| Atlantic halibut | vtr - trawl | 78.666 | 38.325 | 2.053 | 0.047 |
| Atlantic herring | vtr - trawl | 126.709 | 52.028 | 2.435 | 0.020 |
| Atlantic mackerel | vtr - trawl | -182.235 | 167.550 | -1.088 | 0.284 |
| Black sea bass | vtr - trawl | 115.916 | 37.015 | 3.132 | 0.003 |
| Red hake | vtr - trawl | 108.106 | 47.107 | 2.295 | 0.028 |
| Silver hake | vtr - trawl | -61.832 | 55.044 | -1.123 | 0.269 |
| Summer flounder | vtr - trawl | 26.307 | 56.454 | 0.466 | 0.644 |
| Yellowtail flounder | vtr - trawl | -61.915 | 77.347 | -0.800 | 0.429 |
VTR Centroid spatial
Mapped centroid points over time/ biomass over time
Consider full time series
Latitude
Longitude
Distance between centroid and VTR
State VTR Centroids
Top states by species
Multiple comparisons: state slope by species
Latitude
Atlantic cod
tablelist[["Atlantic cod"]]| lhs | estimate | statistic | p.value |
|---|---|---|---|
| Maine - New Hampshire | -17.949 | -1.011 | 0.850 |
| Massachusetts - Maine | -22.534 | -1.270 | 0.710 |
| Massachusetts - New Hampshire | -40.484 | -2.281 | 0.161 |
| New York - Maine | 42.982 | 2.422 | 0.119 |
| New York - Massachusetts | 65.517 | 3.692 | 0.003 |
| New York - New Hampshire | 25.033 | 1.411 | 0.623 |
| New York - Rhode Island | -46.453 | -2.618 | 0.076 |
| Rhode Island - Maine | 89.435 | 5.039 | 0.000 |
| Rhode Island - Massachusetts | 111.969 | 6.309 | 0.000 |
| Rhode Island - New Hampshire | 71.485 | 4.028 | 0.001 |
Atlantic halibut
tablelist[["Atlantic halibut"]]| lhs | estimate | statistic | p.value |
|---|---|---|---|
| Maine - New Hampshire | -15.367 | -0.488 | 0.988 |
| Massachusetts - Maine | -72.486 | -2.303 | 0.155 |
| Massachusetts - New Hampshire | -87.853 | -2.791 | 0.050 |
| New York - Maine | -13.100 | -0.377 | 0.996 |
| New York - Massachusetts | 59.386 | 1.710 | 0.433 |
| New York - New Hampshire | -28.467 | -0.820 | 0.924 |
| New York - Rhode Island | -5.727 | -0.165 | 1.000 |
| Rhode Island - Maine | -7.373 | -0.234 | 0.999 |
| Rhode Island - Massachusetts | 65.112 | 2.068 | 0.243 |
| Rhode Island - New Hampshire | -22.740 | -0.722 | 0.951 |
Atlantic herring
tablelist[["Atlantic herring"]]| lhs | estimate | statistic | p.value |
|---|---|---|---|
| Maine - New Hampshire | 69.795 | 1.509 | 0.559 |
| Massachusetts - Maine | 7.752 | 0.168 | 1.000 |
| Massachusetts - New Hampshire | 77.546 | 1.677 | 0.453 |
| New Jersey - Maine | -60.041 | -1.298 | 0.693 |
| New Jersey - Massachusetts | -67.792 | -1.466 | 0.587 |
| New Jersey - New Hampshire | 9.754 | 0.211 | 1.000 |
| New Jersey - Rhode Island | 46.595 | 1.007 | 0.851 |
| Rhode Island - Maine | -106.636 | -2.306 | 0.153 |
| Rhode Island - Massachusetts | -114.388 | -2.473 | 0.106 |
| Rhode Island - New Hampshire | -36.841 | -0.797 | 0.931 |
Atlantic mackerel
tablelist[["Atlantic mackerel"]]| lhs | estimate | statistic | p.value |
|---|---|---|---|
| Massachusetts - Maine | 65.153 | 0.791 | 0.933 |
| New Jersey - Maine | -63.250 | -0.768 | 0.939 |
| New Jersey - Massachusetts | -128.403 | -1.559 | 0.527 |
| New Jersey - New York | -37.297 | -0.453 | 0.991 |
| New Jersey - Rhode Island | 35.433 | 0.430 | 0.993 |
| New York - Maine | -25.954 | -0.315 | 0.998 |
| New York - Massachusetts | -91.107 | -1.106 | 0.803 |
| New York - Rhode Island | 72.729 | 0.883 | 0.902 |
| Rhode Island - Maine | -98.683 | -1.198 | 0.752 |
| Rhode Island - Massachusetts | -163.836 | -1.989 | 0.280 |
Black sea bass
tablelist[["Black sea bass"]]| lhs | estimate | statistic | p.value |
|---|---|---|---|
| Maryland - New Jersey | 38.893 | 1.252 | 0.721 |
| Maryland - New York | 15.384 | 0.495 | 0.988 |
| Maryland - North Carolina | 117.410 | 3.778 | 0.003 |
| New Jersey - New York | -23.510 | -0.757 | 0.942 |
| North Carolina - New Jersey | -78.516 | -2.527 | 0.094 |
| North Carolina - New York | -102.026 | -3.283 | 0.012 |
| Virginia - Maryland | -105.034 | -3.380 | 0.009 |
| Virginia - New Jersey | -66.141 | -2.128 | 0.217 |
| Virginia - New York | -89.651 | -2.885 | 0.038 |
| Virginia - North Carolina | 12.375 | 0.398 | 0.995 |
Red hake
tablelist[["Red hake"]]| lhs | estimate | statistic | p.value |
|---|---|---|---|
| Connecticut - Massachusetts | -84.512 | -4.406 | 0.000 |
| Connecticut - New Jersey | 5.763 | 0.300 | 0.998 |
| Connecticut - New York | 25.454 | 1.327 | 0.675 |
| Connecticut - Rhode Island | 22.257 | 1.160 | 0.774 |
| New Jersey - Massachusetts | -90.276 | -4.707 | 0.000 |
| New Jersey - New York | 19.690 | 1.027 | 0.842 |
| New Jersey - Rhode Island | 16.493 | 0.860 | 0.911 |
| New York - Massachusetts | -109.966 | -5.733 | 0.000 |
| New York - Rhode Island | -3.197 | -0.167 | 1.000 |
| Rhode Island - Massachusetts | -106.769 | -5.566 | 0.000 |
Silver hake
tablelist[["Silver hake"]]| lhs | estimate | statistic | p.value |
|---|---|---|---|
| Connecticut - Massachusetts | -76.518 | -3.057 | 0.024 |
| Connecticut - New Jersey | 27.958 | 1.117 | 0.797 |
| Connecticut - New York | 7.999 | 0.320 | 0.998 |
| Connecticut - Rhode Island | 7.466 | 0.298 | 0.998 |
| New Jersey - Massachusetts | -104.476 | -4.174 | 0.001 |
| New Jersey - New York | -19.960 | -0.797 | 0.931 |
| New Jersey - Rhode Island | -20.493 | -0.819 | 0.924 |
| New York - Massachusetts | -84.517 | -3.377 | 0.009 |
| New York - Rhode Island | -0.533 | -0.021 | 1.000 |
| Rhode Island - Massachusetts | -83.984 | -3.356 | 0.010 |
Summer flounder
tablelist[["Summer flounder"]]| lhs | estimate | statistic | p.value |
|---|---|---|---|
| New Jersey - New York | -31.110 | -0.986 | 0.861 |
| New Jersey - Rhode Island | -58.657 | -1.860 | 0.347 |
| New York - Rhode Island | -27.547 | -0.873 | 0.906 |
| North Carolina - New Jersey | -307.044 | -9.735 | 0.000 |
| North Carolina - New York | -338.154 | -10.721 | 0.000 |
| North Carolina - Rhode Island | -365.701 | -11.595 | 0.000 |
| Virginia - New Jersey | -199.472 | -6.324 | 0.000 |
| Virginia - New York | -230.582 | -7.311 | 0.000 |
| Virginia - North Carolina | 107.572 | 3.411 | 0.008 |
| Virginia - Rhode Island | -258.129 | -8.184 | 0.000 |
Yellowtail flounder
tablelist[["Yellowtail flounder"]]| lhs | estimate | statistic | p.value |
|---|---|---|---|
| Connecticut - Massachusetts | 60.845 | 4.503 | 0.000 |
| Connecticut - New Hampshire | 12.628 | 0.935 | 0.883 |
| Connecticut - New York | 42.403 | 3.138 | 0.019 |
| Connecticut - Rhode Island | 18.016 | 1.333 | 0.671 |
| Massachusetts - New Hampshire | -48.218 | -3.569 | 0.005 |
| New York - Massachusetts | 18.443 | 1.365 | 0.651 |
| New York - New Hampshire | -29.775 | -2.204 | 0.188 |
| New York - Rhode Island | -24.387 | -1.805 | 0.377 |
| Rhode Island - Massachusetts | 42.830 | 3.170 | 0.017 |
| Rhode Island - New Hampshire | -5.388 | -0.399 | 0.995 |
Top species by state
