reworking articles

Carly Lovas · Carly Lovas · commit 36b2279e9c7e · 2026-05-19T14:02:57.000-04:00
diff --git a/README.Rmd b/README.Rmd
@@ -1,5 +1,5 @@
 ---
-output: github_document
+output: rmarkdown::html_vignette
 ---
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
diff --git a/README.html b/README.html
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -12,7 +12,3 @@ navbar:
           href: articles/data_cleaning_functions.html
         - text: Plotting Functions
           href: articles/plotting_functions.html
-articles:
-  - title: "Articles"
-    contents:
-      - plotting_functions
diff --git a/data/examples/catch.csv b/data/examples/catch.csv
@@ -0,0 +1,4 @@
+﻿estimate_status,year,coast,region,state,common_name,sci_name,harvest_a_b1_numbers,pse_harvest_a_b1_numbers,harvest_a_b1_weight_lb,pse_harvest_a_b1_weight,released_alive_b2_numbers,released_alive_b2_lower_95_percent_confidence_limit,released_alive_b2_upper_95_percent_confidence_limit,total_catch_a_b1_b2_numbers,total_catch_a_b1_b2_lower_95_percent_confidence_limit,total_catch_a_b1_b2_upper_95_percent_confidence_limit,total_catch_pse,comname
+Final,2024,Atlantic Coast,Mid Atlantic,Delaware,"rudderfish, banded",Seriola zonata,0,0,0,0,23,0,56,23,0,56,73.9,banded rudderfish
+Final,2024,Atlantic Coast,Mid Atlantic,Delaware,"shark, dogfish, spiny",Squalus acanthias,0,0,0,0,35430,6611,64249,35430,6611,64249,41.5,spiny dogfish
+Final,2024,Atlantic Coast,Mid Atlantic,Delaware,"bass, black sea",Centropristis striata,105763,28.8,130995,28.1,1008441,290955,1725926,1114203,395720,1832686,32.9,black sea bass
diff --git a/data/examples/directedtrips.csv b/data/examples/directedtrips.csv
@@ -0,0 +1,4 @@
+﻿year,wave,st,sub_reg,mode_fx,area_x,species,Trips,SE,PSE,state,mode,area
+2018,1,10,5,3,1,striped bass,23379.878595590002,8886.434611,38,DE,Shore,State Territorial Seas (Ocean<=3 mi excluding Inland)
+2018,1,10,5,3,5,striped bass,169377.66509117998,40817.09488360292,24.1,DE,Shore,Inland
+2018,1,10,5,7,1,striped bass,44944.56538431001,38431.207502274716,85.5,DE,Private & Rental,State Territorial Seas (Ocean<=3 mi excluding Inland)
diff --git a/data/examples/landings.csv b/data/examples/landings.csv
@@ -0,0 +1,4 @@
+﻿year,portnm,state,species_name,land,live,value,confidential,comname,lat,long,state_full,council
+1996,ADDISON,ME,"clam, quahog, ocean",26418,217965,98152,NA,"ocean clam, quahog",44.61882,-67.74445,Maine,New England
+1996,ADDISON,ME,"lobster, american",355359,355359,1178910,NA,american lobster,44.61882,-67.74445,Maine,New England
+1996,ADDISON,ME,"scallop, sea",9704,80837,66560,NA,sea scallop,44.61882,-67.74445,Maine,New England
diff --git a/data/examples/nefsc.csv b/data/examples/nefsc.csv
@@ -0,0 +1,4 @@
+﻿id,svspp,comname,year,est_month,est_day,season,lat,lon,est_towdate,total_biomass_kg
+1.97003E+12,23,winter skate,1970,3,0,Spring,41.58333,-69.46667,3/12/70 8:00,3.128
+1.97003E+12,28,thorny skate,1970,3,0,Spring,41.58333,-69.46667,3/12/70 8:45,0.9
+1.97003E+12,73,atlantic cod,1970,3,0,Spring,41.58333,-69.46667,3/12/70 8:45,8.91
diff --git a/data/examples/obs.csv b/data/examples/obs.csv
@@ -0,0 +1,4 @@
+﻿year,negear,comname,targspec1,targspec2,targspec3,lat,lon,hailwt,live_wt,kept,decade
+1989,50,MONKFISH (GOOSEFISH),5260,0,0,40.91,-70.83083,25,25,Kept,1980
+1989,50,BUTTERFISH,5260,0,0,40.91,-70.83083,25,25,Kept,1980
+1989,50,"FLOUNDER, YELLOWTAIL",5260,0,0,40.91,-70.83083,100,100,Discarded,1980
diff --git a/data/examples/permits.csv b/data/examples/permits.csv
@@ -0,0 +1,4 @@
+﻿ap_year,ap_num,vp_num,pport,ppst,permit,target,category,lat,long,state_full,council
+1996,227829,221741,GLOUCESTER,MA,lobster_1,lobster,commercial,42.6153595,-70.662461,Massachusetts,New England
+1996,227830,127133,GLOUCESTER,MA,lobster_1,lobster,commercial,42.6153595,-70.662461,Massachusetts,New England
+1996,227831,231461,RYE,NH,lobster_1,lobster,commercial,43.0120186,-70.771943,New Hampshire,New England
diff --git a/data/examples/vtr.csv b/data/examples/vtr.csv
@@ -0,0 +1,4 @@
+﻿year,trip_type,lat,lon,species_name,port_name,state_abb,state_full,kept,discarded
+1996,COMMERCIAL,41.67694,-69.59028,"FLOUNDER, WINTER / BLACKBACK",CHATHAM,MA,Massachusetts,350,0
+1996,COMMERCIAL,42.54417,-70.5375,COD,GLOUCESTER,MA,Massachusetts,850,0
+1996,COMMERCIAL,41.37472,-71.57028,"FLOUNDER, WINTER / BLACKBACK",POINT JUDITH,RI,Rhode Island,72,0
diff --git a/inst/static-articles/data_cleaning_functions.html b/inst/static-articles/data_cleaning_functions.html
diff --git a/vignettes/_quarto.yaml b/vignettes/_quarto.yaml
@@ -0,0 +1,3 @@
+project:
+  render:
+  - '*.qmd'
diff --git a/vignettes/data_cleaning_functions.html b/vignettes/data_cleaning_functions.html
diff --git a/vignettes/data_cleaning_functions.qmd b/vignettes/data_cleaning_functions.qmd
@@ -0,0 +1,195 @@
+---
+title: "Accessing and cleaning federal fisheries data"
+author: "Carly Lovas"
+format:
+  html:
+    title-block-banner: "#236192"
+    grid: 
+      body-width: 1500px
+      sidebar-width: 450px
+      margin-width: 450px
+    toc: true
+    self-contained: true
+execute: 
+  echo: false
+  warning: false
+  message: false
+  error: true
+  comment: ""
+  fig-align: center
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{data_cleaning_functions}
+  %\VignetteEngine{quarto::html}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r}
+#| label: setup
+#| message: false
+#| warning: false
+#| echo: false
+
+library(tidyverse)
+library(here)
+library(species.shifts)
+
+# box_path <- "/Users/clovas/Library/CloudStorage/Box-Box/MAFMC-25 Data/"
+```
+
+## About
+
+This package contains various functions for accessing (pulling) and cleaning federal fisheries dependent and independent data. Many of these data sets are confidential and require a formal data request submission to the appropriate governing body. Information regarding metadata and access for most of these data sets can be accessed via [inPort](https://www.fisheries.noaa.gov/inport/), see below:
+
+> InPort is the authoritative metadata repository and data inventory platform for NOAA Fisheries and the National Ocean Service. The system supports documentation of datasets and provides tools to facilitate data discovery, public access, and responsible stewardship of scientific data within these line offices.
+
+As such, using `species.shifts` will require access to this data in order to use the cleaning and plotting functions. It is *strongly* recommended that this data be stored locally in a centralized repository. Please refer to the package `README` more information on recommended work flows.
+
+## Data sets
+
+The functions in this package correspond to six federal fisheries data sets, each with its own respective `pull_()` function.
+
+[NOAA Fisheries Vessel Trip Reports](https://www.fisheries.noaa.gov/inport/item/11489)
+
+[NEFSC Observer at Sea](https://www.fisheries.noaa.gov/inport/item/24111)
+
+[NEFSC Spring-Fall Bottom Trawl Survey](https://www.fisheries.noaa.gov/inport/item/22557)
+
+[GARFO Permits Data](https://apps-garfo.fisheries.noaa.gov/permits/)
+
+[GARFO Dealer Reported Landings](https://www.fisheries.noaa.gov/contact/greater-atlantic-regional-fisheries-office)
+
+[NOAA Fisheries Marine Recreational Information Program](https://www.fisheries.noaa.gov/insight/marine-recreational-information-program)
+
+------------------------------------------------------------------------
+
+### Vessel trip reports
+
+`vtr <- pull_vtr(proj_path = my_path)`
+
+```{r}
+#| label: vtr
+#| message: false
+#| warning: false
+#| echo: false
+
+# my_path <- paste0(box_path, "Confidential/VTR and Dealer/")
+# knitr::kable(species.shifts::pull_vtr(proj_path = my_path) |>
+#                select(!sub_trip_id) |> 
+#                head(n = 3))
+
+knitr::kable(read.csv(here::here("data","examples","vtr.csv")))
+```
+
+\*Trip ID information removed from demo to maintain confidentiality.
+
+### Fisheries Observer
+
+`observer <- pull_observer(proj_path = my_path)`
+
+```{r}
+#| label: observer
+#| message: false
+#| warning: false
+#| echo: false
+#|
+# my_path <- paste0(box_path, "Confidential/Observer/DR25-200_Mills_Allyn.xlsx")
+# knitr::kable(species.shifts::pull_observer(proj_path = my_path) |>
+#                ungroup() |>
+#                select(!link3) |>
+#                head(n = 3))
+
+knitr::kable(read.csv(here::here("data","examples","obs.csv")))
+```
+
+\*Trip ID information removed from demo to maintain confidentiality.
+
+### NEFSC Bottom Trawl
+
+`nefsc <- pull_nefsc(proj_path = my_path)`
+
+```{r}
+#| warning: false
+# my_path <- paste0(box_path, "Non-confidential/NEFSC Trawl/survdat_lw.rds")
+# knitr::kable(species.shifts::pull_nefsc(proj_path = my_path) |>
+#   head(n = 3))
+
+knitr::kable(read.csv(here::here("data","examples","nefsc.csv")))
+```
+
+### GARFO Federal Permits
+
+`permits <- pull_permits(proj_path = my_path)`
+
+```{r}
+#| label: permits
+#| message: false
+#| warning: false
+#| echo: false
+
+# knitr::kable(readr::read_csv(
+#   here::here("vignettes","permits_data.csv")
+# ) |>
+#   head(n = 3))
+
+knitr::kable(read.csv(here::here("data","examples","permits.csv")))
+```
+
+### GARFO Dealer-reported landings
+
+`landings <- pull_landings(proj_path = my_path)`
+
+```{r}
+#| label: landings
+#| message: false
+#| warning: false
+#| echo: false
+
+my_path <- paste0(box_path, "Confidential/VTR and Dealer/Dealer Data 2025.xlsx")
+knitr::kable(species.shifts::pull_garfo_landings(proj_path = my_path, sheet = 1, skip = 9) |>
+               filter(is.na(confidential)) |>
+               head(n = 3))
+```
+
+### Marine Recreational Information Program
+
+#### Directed trips
+
+`mrip_directed_trips <- pull_mrip_directed_trips()`
+
+```{r}
+#| label: mrip directed trips
+#| message: false
+#| warning: false
+#| echo: false
+
+# knitr::kable(readr::read_csv(
+#   here::here("vignettes","mrip_example.csv")
+# ) |>
+#   head(n = 3))
+
+knitr::kable(read.csv(here::here("data","examples","directedtrips.csv")))
+
+```
+
+#### Catch estimates
+
+`mrip_catch <- pull_mrip_catch()`
+
+```{r}
+#| label: mrip catch estimates
+#| message: false
+#| warning: false
+#| echo: false
+
+# my_path <- paste0(box_path, "Non-confidential/ACCSP/Catch_Estimates.csv")
+# knitr::kable(species.shifts::pull_mrip_catch(proj_path = my_path) |> head(n = 3))
+
+knitr::kable(read.csv(here::here("data","examples","catch.csv")))
+
+
+```
+
+## Plotting
+
+Once the data has been pulled and saved to the local environment, each data set has a respective `plot_()` or `map_()` function. More about those functions [here](https://carlylovas.github.io/species.shifts/articles/plotting_functions.html).
