add selectivities rmd and html

data-raw/create_selectivities.R

@@ -0,0 +1,109 @@
+#' Find all groundfish species length data caught by groundfish fleets.
+#'
+#' Pick trips identified as groundfish to find species lengths.
+#' Use to estimate selectivity
+
+
+# pull groundfish data
+lbstotons <- 2204.62
+boundaryBoxes <- c(0,23:29)
+gfData <- readRDS(here::here("data/NEGroundfishDataCAMS.rds"))
+gf <- gfData$neus |>
+  dplyr::mutate(Year = as.integer(Year)) |>
+  dplyr::mutate(InsideLANDED = InsideLANDED/lbstotons)
+
+if(0) {
+  # attempts to join tables with GARFO
+  channel <- dbutils::connect_to_database("NEFSC_USERS","abeet")
+
+  sql1 <- "select distinct CAMSID, VTR_IMGID
+  from CAMS_GARFO.CAMS_SUBTRIP
+  where YEAR >= 1996
+  and VTR_IMGID IS NOT NULL"
+  subtrip <- DBI::dbGetQuery(channel,sql1)
+
+  # this table is a list of camsid and original vtr ids
+  saveRDS(subtrip,here::here("data-raw/subtrip.rds"))
+}
+
+subtrip <- readRDS(here::here("data-raw/subtrip.rds")) |>
+  dplyr::as_tibble()
+
+#select trips
+trips <- gf |>
+  dplyr::distinct(TRIPID) |>
+  dplyr::pull()
+
+camstrips <- subtrip |>
+  dplyr::filter(VTR_IMGID %in% trips) |>
+  dplyr::pull(CAMSID)
+
+# now pull lengths
+if(0) {
+  sqlLengths <- "select CAMSID, NESPP3, LENGTH, NUMLEN
+  from CAMS_GARFO.cams_cflen_aa
+  where YEAR >= 1996"
+
+  lengths <- DBI::dbGetQuery(channel,sqlLengths) |>
+    dplyr::as_tibble()
+}
+
+lengths <- readRDS(here::here("data-raw/gflengths.rds"))
+
+# filter trips based on GF trips
+gflengths <- lengths |>
+  dplyr::filter(CAMSID %in% camstrips) |>
+  dplyr::mutate(NESPP3 = as.double(NESPP3))
+
+gfcodes <- c("RED", "WHK", "COD" ,"HAD" ,"POL", "WTF", "WIF", "HAL", "PLA", "YTF" ,"WPF" ,"WOL", "OPT")
+
+atlantisGroups <- readr::read_csv("https://raw.githubusercontent.com/NEFSC/READ-EDAB-neusAtlantis/dev_branch/data-raw/data/Atlantis_2_0_groups_svspp_nespp3.csv")
+gfgroups <- atlantisGroups |>
+  dplyr::filter(Code %in% gfcodes)
+
+
+allgflengths <- gflengths |>
+  dplyr::left_join(gfgroups,by = "NESPP3") |>
+  dplyr::filter(Code %in% gfcodes)
+
+replicatelengths <- allgflengths |>
+  tidyr::uncount(NUMLEN)
+
+# over all fleets.
+# to do this by fleet we 'd need to filter out tripid's
+# plot histogram of lengths
+replicatelengths |>
+  ggplot2::ggplot() +
+  ggplot2::geom_histogram(ggplot2::aes(x=LENGTH)) +
+  ggplot2::facet_wrap(~Code,scale = "free_x") +
+  ggplot2::ylab("Number of fish") +
+  ggplot2::xlab("length (cm)")
+
+# plot prob curve by species
+replicatelengths |>
+  dplyr::select(Code,LENGTH) |>
+  dplyr::arrange(Code,LENGTH) |>
+  dplyr::group_by(Code) |>
+  dplyr::mutate(prob = (1:dplyr::n())/dplyr::n()) |>
+  ggplot2::ggplot(ggplot2::aes(x=LENGTH,y=prob)) +
+  ggplot2::geom_line() +
+  ggplot2::geom_point(size = 0.5) +
+  ggplot2::facet_wrap(~Code,scale = "free_x") +
+  ggplot2::ylab("Probability") +
+  ggplot2::xlab("length (cm)")
+
+# plot all on same figure
+p <- replicatelengths |>
+  dplyr::select(Code,LENGTH) |>
+  dplyr::arrange(Code,LENGTH) |>
+  dplyr::group_by(Code) |>
+  dplyr::mutate(prob = (1:dplyr::n())/dplyr::n()) |>
+  ggplot2::ggplot(ggplot2::aes(x=LENGTH,y=prob, col=Code)) +
+  ggplot2::geom_line() +
+  ggplot2::geom_point(size = 0.5) +
+  ggplot2::ylab("Probability") +
+  ggplot2::xlab("length (cm)")
+
+plotly::ggplotly(p)
+
+

vignettes/groundfishSelectivity.Rmd

@@ -39,16 +39,130 @@ Non target species
 -   Ocean Pout (OPT)
 -   Atlantic Wolffish (WOL)
 
-```{r groundfishdata, echo = F}
-# CONVERT TO METRIC TONS
+```{r groundselectivity, echo = F,eval=T, message=F}
+# pull groundfish data
 lbstotons <- 2204.62
 boundaryBoxes <- c(0,23:29)
-gfData <- readRDS(here::here("data/NEGroundfishDataCAMS.rds")) 
-gf <- gfData$neus |> 
-  dplyr::mutate(Year = as.integer(Year)) |> 
+# species of interest
+gfcodes <- c("RED", "WHK", "COD" ,"HAD" ,"POL", "WTF", "WIF", "HAL", "PLA", "YTF" ,"WPF" ,"WOL", "OPT")
+
+gfData <- readRDS(here::here("data/NEGroundfishDataCAMS.rds"))
+gf <- gfData$neus |>
+  dplyr::mutate(Year = as.integer(Year)) |>
   dplyr::mutate(InsideLANDED = InsideLANDED/lbstotons)
 
-speciesCodes <- c("COD","HAD","YTF","POL","PLA","WTF","WHK","WIF","RED","HAL","WPF","OPT","WOL")
+# reads in CAMS tables
+if(0) {
+  # attempts to join tables with GARFO
+  channel <- dbutils::connect_to_database("NEFSC_USERS","abeet")
+
+  sql1 <- "select distinct CAMSID, VTR_IMGID
+  from CAMS_GARFO.CAMS_SUBTRIP
+  where YEAR >= 1996
+  and VTR_IMGID IS NOT NULL"
+  subtrip <- DBI::dbGetQuery(channel,sql1)
+
+  # this table is a list of camsid and original vtr ids
+  saveRDS(subtrip,here::here("data-raw/subtrip.rds"))
+}
+
+subtrip <- readRDS(here::here("data-raw/subtrip.rds")) |>
+  dplyr::as_tibble()
+
+# distinct trips in gf data
+trips <- gf |>
+  dplyr::distinct(TRIPID) |>
+  dplyr::pull()
+
+# identify corresponding cams trip id based on gf trips
+camstrips <- subtrip |>
+  dplyr::filter(VTR_IMGID %in% trips) |>
+  dplyr::pull(CAMSID)
+
+# now pull lengths of species caught 
+if(0) {
+  sqlLengths <- "select CAMSID, NESPP3, LENGTH, NUMLEN
+  from CAMS_GARFO.cams_cflen_aa
+  where YEAR >= 1996"
+
+  lengths <- DBI::dbGetQuery(channel,sqlLengths) |>
+    dplyr::as_tibble()
+}
+
+lengths <- readRDS(here::here("data-raw/gflengths.rds"))
+
+# filter trips based on GF trips
+gflengths <- lengths |>
+  dplyr::filter(CAMSID %in% camstrips) |>
+  dplyr::mutate(NESPP3 = as.double(NESPP3))
+
+# reads in atlantis groups file to find nespp3 codes
+atlantisGroups <- readr::read_csv("https://raw.githubusercontent.com/NEFSC/READ-EDAB-neusAtlantis/dev_branch/data-raw/data/Atlantis_2_0_groups_svspp_nespp3.csv",show_col_types = FALSE)
+gfgroups <- atlantisGroups |>
+  dplyr::filter(Code %in% gfcodes)
+
+## join by nespp3
+allgflengths <- gflengths |>
+  dplyr::left_join(gfgroups,by = "NESPP3") |>
+  dplyr::filter(Code %in% gfcodes)
+
+# replicate rows based on NUMLEN field
+# eg LENGTH = 46 , NUMLE = 6. 6 fish caught of length 46
+replicatelengths <- allgflengths |>
+  tidyr::uncount(NUMLEN)
+```
+
+## Histogram of lengths
+
+Number of fish over all designated groundfish fleets
+
+```{r sel1,echo = F, eval = T}
+
+# Plot over all fleets.
+# to do this by fleet we 'd need to filter out tripid's specific to designated fleets
+# plot histogram of lengths
+replicatelengths |>
+  ggplot2::ggplot() +
+  ggplot2::geom_histogram(ggplot2::aes(x=LENGTH),bins=25) +
+  ggplot2::facet_wrap(~Code,scale = "free_x") +
+  ggplot2::ylab("Number of fish") +
+  ggplot2::xlab("length (cm)")
+```
+
+## Probability curves
+
+```{r sel2, echo=F, eval=T}
+# plot prob curve by species
+replicatelengths |>
+  dplyr::select(Code,LENGTH) |>
+  dplyr::arrange(Code,LENGTH) |>
+  dplyr::group_by(Code) |>
+  dplyr::mutate(prob = (1:dplyr::n())/dplyr::n()) |>
+  ggplot2::ggplot(ggplot2::aes(x=LENGTH,y=prob)) +
+  ggplot2::geom_line() +
+  ggplot2::geom_point(size = 0.5) +
+  ggplot2::facet_wrap(~Code,scale = "free_x") +
+  ggplot2::ylab("Probability") +
+  ggplot2::xlab("length (cm)")
+```
+
+## Probability curves stacked
+
+```{r sel3 ,echo=F,eval=T}
+# plot all on same figure
+p <- replicatelengths |>
+  dplyr::select(Code,LENGTH) |>
+  dplyr::arrange(Code,LENGTH) |>
+  dplyr::group_by(Code) |>
+  dplyr::mutate(prob = (1:dplyr::n())/dplyr::n()) |>
+  ggplot2::ggplot(ggplot2::aes(x=LENGTH,y=prob, col=Code)) +
+  ggplot2::geom_line() +
+  ggplot2::geom_point(size = 0.5) +
+  ggplot2::ylab("Probability") +
+  ggplot2::xlab("length (cm)")
+
+plotly::ggplotly(p)
+
+```
 
-timeRange <- range(gf$Year)
 ```