In HoldenJe/GLReportR: Templates for GL reports using R

knitr::opts_chunk$set(echo = FALSE, message = FALSE)
library(gfsR) # due to plyr namespace conflicts gfsR needs to be loaded before dplyr
library(glfishr)
library(httr)
library(jsonlite)
library(dplyr)

fn011 <- get_FN011(list(prj_cd = params$prj_cd))
fn121 <- get_FN121(list(prj_cd = params$prj_cd))
fn123 <- get_FN123(list(prj_cd = params$prj_cd))
fn123 <- append.spc.names(fn123)
fn125 <- get_FN125(list(prj_cd = params$prj_cd))

prj<- get_pt_projects(list(prj_cd = params$prj_cd))
prj_ldr <- paste(prj$PRJ_LDR.FIRST_NAME, 
                 prj$PRJ_LDR.LAST_NAME, sep =" ")
prj_abstract <- prj$ABSTRACT

n_nets <- nrow(fn121)
n_sites <- length(unique(fn121$SITE))
n_species <- length(unique(fn123$SPC))
mn_effdur <- round(mean(fn121$EFFDUR), 1)
min_effdur <- round(min(fn121$EFFDUR),1)
max_effdur <- round(max(fn121$EFFDUR), 1)
min_SIDEP <- round(min(fn121$SIDEP), 1)
max_SIDEP <- round(max(fn121$SIDEP), 1)
min_SITEM <- round(min(fn121$SITEM), 1)
max_SITEM <- round(max(fn121$SITEM), 1)

spc_sum <- fn123 |> group_by(SPC) |> 
  summarize(N = sum(CATCNT)) 
spc_sum <-  append.spc.names(spc_sum)
spc_sum <- arrange(spc_sum, desc(N))

PROJECT COMPLETION REPORT

Project Name: r fn011$PRJ_NM
Project Code: r params$prj_cd
Project Lead: r prj_ldr
Start Date: r fn011$PRJ_DATE0
End Date: r fn011$PRJ_DATE1

Abstract

r prj_abstract

Data Summary

The project had r n_nets net tows at r n_sites r ifelse(n_sites == 1, "location", "locations"). The average effort duration was r mn_effdur hours (range: r min_effdur - r max_effdur hours). Tows were conducted at site depths ranging from r min_SIDEP m to r max_SIDEP m and surface temperatures ranging from r min_SITEM$^\circ$C to r max_SITEM$^\circ$C.

There were r n_species species and r sum(fn123$CATCNT) fish caught over the duration of this project, r sum(fn123$BIOCNT) of which were bio sampled. The majority of species caught were r spc_sum$SPC_NM[1] (n=r spc_sum$N[1]), followed by r spc_sum$SPC_NM[2] (n=r spc_sum$N[2]) and r spc_sum$SPC_NM[3] (n=r spc_sum$N[3])

Project Map

library(leaflet)
fn121 <- fn121 |> mutate(maplabel = paste("SAM:", SAM, sep = " "))
leaflet(fn121) |> addTiles() |> addCircles(lat = ~DD_LAT, lng = ~DD_LON, popup = ~maplabel)

Species Catches

library(knitr)
library(kableExtra)

catch_sum <- fn123  |> 
  group_by(SPC_LAB) |> 
  summarize(CATCNT = sum(CATCNT, na.rm = T), BIOCNT = sum(BIOCNT)) |> 
  arrange(desc(CATCNT))

catch_sum[1:10,] |> 
  knitr::kable(caption = "Table 1. Top 10 species captured.",) |> 
   kable_paper(bootstrap_options = "striped", full_width = F)