R/reports.R
In usgs/nabatr: R Tools for Accessing and Manipulating North American Bat Monitoring Data
Defines functions
build_ma_doc
build_col_doc
build_sa_doc
Documented in
build_col_doc
build_ma_doc
build_sa_doc
#############################################################################
# _ _____ ____ __ ____
# / | / / | / __ )____ _/ /_/ __ \
# / |/ / /| | / __ / __ `/ __/ /_/ /
# / /| / ___ |/ /_/ / /_/ / /_/ _, _/
# /_/ |_/_/ |_/_____/\__,_/\__/_/ |_|
#
# R Tools for accessing and manipulating North American Bat Monitoring data
#
# Written by: Kyle Enns
#
# FILE DESCRIPTION: This file contains functions build NABat reports for
# stationary, mobile, and colony count data
#
# USGS DISCLAIMER: This software is in the public domain because it contains
# materials that originally came from the U.S. Geological Survey, an agency
# of the United States Department of Interior. For more information, see the
# [official USGS copyright policy]
# (https://www.usgs.gov/visual-id/credit_usgs.html#copyright/
# "official USGS # copyright policy")
#
# Although this software program has been used by the U.S. Geological Survey
# (USGS), no warranty, expressed or implied, is made by the USGS or the U.S.
# Government as to the accuracy and functioning of the program and related
# program material nor shall the fact of distribution constitute any such
# warranty, and no responsibility is assumed by the USGS in connection
# therewith.
#
# This software is provided "AS IS."
#############################################################################
#' @title Build Stationary Acoustic Report document in .docx file
#'
#' @description Using the outputs from get_projects(), get_sa_project_summary(),
#' get_as_bulk_wavs(), and get_observed_nights() this function will create a
#' report .docx file to an out_dir.
#'
#' @import mapview
#' @import officer
#' @import magrittr
#' @import maps
#' @import maptools
#' @import sp
#' @import flextable
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' See vignette: build_sa_report (Build Stationary Acoustic Report)
#' }
#'
#' @export
build_sa_doc = function(
out_dir,
file_name = 'sa_doc.docx',
project_df,
project_id,
sa_bulk_df,
sa_survey_df,
species_df,
selected_year,
nightly_observed_list = NULL,
date = format(Sys.time(), "%B %d, %Y"),
range_maps = TRUE){
message ('Enter Stationary Report Function')
# Clean the data
sa_bulk_df = sa_bulk_df %>%
clean_time_fields() %>%
add_observed_nights() %>%
add_start_end_nights()
# Add selected year as 1st year
message ('Setup for temp directories')
if (is.null(selected_year)){
selected_year = unique(format(as.Date(sa_bulk_df$recording_time),
'%Y'))[1]
}
# Setup temps directory to store intermediate files
if (dir.exists(paste0(out_dir, '/temps/'))==FALSE){
dir.create(paste0(out_dir, '/temps/'))
}
if (dir.exists(paste0(out_dir, '/temps/range_maps/'))==FALSE){
dir.create(paste0(out_dir, '/temps/range_maps/'))
}
# Set Save figures boolean
save_figures = TRUE
message ('Getting nightly data')
# If nightly_observed_list isn't put in through variable
if (is.null(nightly_observed_list)){
nightly_observed_list = get_observed_nights(sa_bulk_df)
}
# Getting Manipulated data for species counts at GRTS cells
auto_nights_df = nightly_observed_list$auto_nightly_df
manual_nights_df = nightly_observed_list$manual_nightly_df
all_species_totals_l_l = get_all_species_counts_long(auto_nights_df,
manual_nights_df, fil = TRUE)
manual_species_grts_df_w = get_species_counts_wide(manual_nights_df)$species_grts_df
auto_species_grts_df_w = get_species_counts_wide(auto_nights_df)$species_grts_df
manual_species_totals_l = get_species_counts_long(manual_nights_df, filter=TRUE)
auto_species_totals_l = get_species_counts_long(auto_nights_df, filter=TRUE)
message ('Setting project specific variables')
# Set Variables
sa_logo_img_ = system.file("templates", "nabat_logo.png", package = "nabatr")
sa_circle_logo_ = system.file('templates', 'NABat_Circle_color.jpg',
package = 'nabatr')
sa_proj_id = project_id
sa_project_row_df = subset(project_df, project_df$project_id == sa_proj_id)
sa_title = sa_project_row_df$project_name
sa_organization = sa_project_row_df$organization
sa_this_project_description = sa_project_row_df$project_description
message ('Getting example text')
# Get the example text to put into the report
sa_examples = get_sa_examples()
message ('Build results text')
# Build the results text for Stationary acoustic report
sa_results = get_sa_results(sa_bulk_df, selected_year, species_df)
message ('Build table 1')
# sa_table_1
sa_table_1 = build_sa_table_1(sa_bulk_df, project_id, project_df,
species_df, selected_year)
message ('Build table 2')
# sa table 2
sa_table_2 = build_sa_table_2(sa_bulk_df, selected_year, species_df)
message ('Build figure 1')
# Figure 1 (map)
sa_figure_1 = build_sa_figure_1(sa_bulk_df, out_dir, project_df,
project_id, sa_survey_df, selected_year, save_figures)
message('Build figure 2')
# Figure 2a/2b
sa_figure_2 = build_sa_figure_2(sa_bulk_df, out_dir, species_df,
selected_year, auto_species_grts_df_w, manual_species_grts_df_w,
save_figures)
message('Build figure 3')
# Figure 3
sa_figure_3 = build_sa_figure_3(sa_bulk_df, out_dir, species_df,
selected_year, save_figures)
if (range_maps){
message ('Build range maps')
# build range maps
maps_data = get_sa_range_maps(sa_bulk_df, project_df, project_id,
all_species_totals_l_l, species_df, out_dir, range_maps)
}
message('Build final.docx document')
##### BUILD DOCUMENT
# Fonts
bold_face_map = shortcuts$fp_bold(font.size = 12)
bold_face = shortcuts$fp_bold(font.size = 16)
date_font = fp_text(color = 'black', font.family =
'Cambria', font.size = 12)
par_style = fp_par(text.align = "center")
example_font = fp_text(color = "#bfbfbf", font.size = 12,
bold = FALSE, italic = FALSE, underlined = FALSE,
font.family = "Cambria", vertical.align = "baseline",
shading.color = "transparent")
fig6_font = fp_text(color = "black", font.size = 10,
font.family = "Cambria")
message ('Begin .docx build')
sa_doc = read_docx() %>%
body_add_fpar(fpar(ftext('Stationary Acoustic Report',
prop = bold_face), fp_p = par_style ), style = 'centered') %>%
body_add_fpar(fpar(ftext(paste0(selected_year, ' Data'),
prop = date_font), fp_p = par_style ), style = 'centered') %>%
body_add_par(value = "", style = "centered") %>%
body_add_fpar(fpar(ftext(sa_title, prop = bold_face),
fp_p = par_style ), style = 'centered') %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = sa_organization, style = "centered") %>%
body_add_par(value = date, style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_img(src = sa_circle_logo_, width = 2.5, height = 2.5,
style= 'centered') %>%
# Add summary data for project and GRTS cells
body_add_par(value = "", style = "centered") %>%
body_add_break() %>%
# Project Description
body_add_par(value = "Project Description",
style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = sa_this_project_description,
style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(sa_examples$sa_ex_description,
prop = example_font)), style = 'Normal') %>%
body_add_break() %>%
# Methods
body_add_par(value = "Methods", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = "Site Selection", style = "heading 2") %>%
body_add_par(value = sa_examples$sa_methods_1, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = "Data Collection", style = "heading 2") %>%
body_add_par(value = sa_examples$sa_methods_2, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = "Call Processing/Species Identification",
style = "heading 2") %>%
body_add_par(value = sa_examples$sa_methods_3, style = "Normal") %>%
body_add_break() %>%
# Results
body_add_par(value = "Results", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = sa_results, style = "Normal") %>%
body_add_break() %>%
# Summary
body_add_par(value = "Summary", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(sa_examples$sa_summary_1,
prop = example_font)), style = 'Normal') %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(sa_examples$sa_summary_2,
prop = example_font)), style = 'Normal') %>%
body_add_break() %>%
# Table 1
body_add_par(value = sa_table_1$description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_flextable(sa_table_1$table, align='left') %>%
body_add_break() %>%
# Table 2
body_add_par(value = sa_table_2$description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_flextable(sa_table_2$table, align='left') %>%
body_add_break() %>%
# Figure 1
body_add_par(value = sa_figure_1$description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_img(src = sa_figure_1$file, width = 5.7,
height = 4, style= 'centered') %>%
body_add_break() %>%
# Figure 2a
body_add_par(value = sa_figure_2$description_a, style = "Normal") %>%
slip_in_img(src = sa_figure_2$file_a, width = 6.5, height = 5) %>%
body_add_break() %>%
# Figure 2b
body_add_par(value = sa_figure_2$description_b, style = "Normal") %>%
slip_in_img(src = sa_figure_2$file_b, width = 6.5, height = 5) %>%
body_add_break() %>%
# Figure 3
body_add_par(value = sa_figure_3$description, style = "Normal") %>%
slip_in_img(src = sa_figure_3$file, width = 6.5, height = 5) %>%
body_add_break()
message('Adding species range maps to .docx')
# Add species range maps
if (range_maps){
map_c = 0
fig_count = 3
for (range_m in maps_data$maps_range_files){
map_c = map_c + 1
fig_count = fig_count + 1
grts_m = maps_data$maps_grts_files[map_c]
spc_range_name = str_split(str_split(sub('\\.png$', '', range_m),
'range_maps/')[[1]][2], '_range')[[1]][1]
spc_grts_name = str_split(str_split(sub('\\.png$', '', grts_m),
'range_maps/')[[1]][2], '_grts')[[1]][1]
fig_a_name = paste0('Figure ', as.character(fig_count), 'a. ')
fig_b_name = paste0('Figure ', as.character(fig_count), 'b. ')
descr_fig5 = paste0(fig_a_name,"Species range map for ", spc_range_name, ".")
descr_fig6 = paste0(fig_b_name,"Map of NABat GRTS cells surveyed in ",selected_year," with species range map overlayed (",
spc_range_name,"). Green cells indicate the presence of ",spc_range_name," was confirmed exclusively through
manual vetting, blue cells indicate the presence of ",spc_range_name," was confirmed exclusively through
automated identification software, and orange cells indicate the presence of ",spc_range_name," was confirmed
using both automated identification software and manual vetting. Transparent
cells indicated that ",spc_range_name," was not detected at those locations.")
# Add the maps to the doc
sa_doc = sa_doc %>%
body_add_fpar(fpar(ftext(paste0('Species: ',spc_range_name),
prop = bold_face_map), fp_p = par_style ), style = 'Normal') %>%
body_add_fpar(fpar(ftext(descr_fig5, prop = fig6_font)),
style = 'Normal') %>%
slip_in_img(src = range_m, width = 5.7, height = 4) %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(descr_fig6, prop = fig6_font)),
style = 'Normal') %>%
body_add_par(value = "", style = "Normal") %>%
slip_in_img(src = grts_m, width = 5.7, height = 4) %>%
body_add_break()
}
}
# Literature Cited
sa_doc = sa_doc %>%
body_add_par(value = "Literature Cited", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = sa_examples$sa_lit_cited, style = "Normal")
return (sa_doc)
}
#' @title Build Report document in .docx file for Colony Count Data
#'
#' @description Using the outputs from get_projects(),
#' get_project_surveys(), get_colony_bulk_counts(),
#' and () this function will create a report .docx file to an out_dir.
#'
#' @import mapview
#' @import officer
#' @import magrittr
#' @import maps
#' @import maptools
#' @import sp
#' @import flextable
#' @import lubridate
#' @import ggplot2
#'
#' @examples
#'
#' \dontrun{
#' See vignette: build_cc_report (Build Colony Count Report)
#' }
#'
#' @export
build_col_doc = function(
out_dir,
file_name = 'cc_doc.docx',
project_df = NULL,
project_id,
cc_bulk_df = NULL,
date = format(Sys.time(), "%B %d, %Y")){
if (dir.exists(paste0(out_dir, '/temps/')) == FALSE){
dir.create(paste0(out_dir, '/temps/'))
}
message('Get front page info')
# Get front page info
cc_logo_img_ = system.file("templates", "nabat_logo.png",
package = "nabatr")
cc_circle_logo_ = system.file('templates', 'NABat_Circle_color.jpg',
package = 'nabatr')
cc_proj_id = project_id
cc_project_row_df = subset(project_df, project_df$project_id == cc_proj_id)
cc_title = cc_project_row_df$project_name
cc_organization = cc_project_row_df$organization
cc_description = cc_project_row_df$project_description
message ('Get Examples')
# Get Colony Count Examples
cc_examples = get_cc_examples()
message ('Get Results')
# Get Colony Count results
cc_results = get_cc_results(cc_bulk_df)
message ('Build table 1')
# Build Colony Count table 1
cc_table_1 = build_cc_table_1(cc_bulk_df, TRUE)
message('Build table 2')
# Build Colony Count table 2
cc_table_2 = build_cc_table_2(cc_bulk_df)
message ('Build figure 1')
# Build Colony Count figure 1
cc_figure_1 = build_cc_figure_1(cc_bulk_df, out_dir, TRUE)
message ('Add Fonts')
# Add fonts
bold_face = shortcuts$fp_bold(font.size = 16)
par_style = fp_par(text.align = "center")
example_font = fp_text(color = "#bfbfbf", font.size = 12, bold = FALSE,
italic = FALSE, underlined = FALSE, font.family = "Cambria",
vertical.align = "baseline", shading.color = "transparent")
message ('Begin Colony Count .docx build')
# Build Colony Count document
cc_doc = read_docx() %>%
body_add_fpar(fpar(ftext('Colony Count Report', prop = bold_face),
fp_p = par_style ), style = 'centered') %>%
body_add_par(value = "", style = "centered") %>%
body_add_fpar(fpar(ftext(cc_title, prop = bold_face), fp_p = par_style ),
style = 'centered') %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = cc_organization, style = "centered") %>%
body_add_par(value = date, style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_img(src = cc_circle_logo_, width = 2.5, height = 2.5,
style = 'centered') %>%
body_add_break() %>%
# Project Description
body_add_par(value = "Project Description", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = cc_description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(cc_examples$description, prop = example_font)),
style = 'Normal') %>%
body_add_break() %>%
# Methods
body_add_par(value = "Methods", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(cc_examples$methods_1, prop = example_font)),
style = 'Normal') %>%
body_add_break() %>%
# Results
body_add_par(value = "Results", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = cc_results, style = "Normal") %>%
body_add_break() %>%
body_end_section_continuous() %>%
# Table 1
body_add_par(value = cc_table_1$description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_flextable(cc_table_1$table, align='left') %>%
body_end_section_landscape() %>%
# Table 2
body_add_par(value = cc_table_2$description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_flextable(cc_table_2$table, align='left') %>%
body_end_section_continuous()
# Figure 1
count = 0
if (length(cc_figure_1$file) > 1){
for(file in cc_figure_1$file){
count = count + 1
cc_doc = cc_doc %>%
body_add_par(value = cc_figure_1$description[count], style = "Normal") %>%
slip_in_img(src = file, width = 7.5, height = 5.5)
}
}else{
cc_doc = cc_doc %>%
body_add_par(value = cc_figure_1$description, style = "Normal") %>%
slip_in_img(src = cc_figure_1$file, width = 7.5, height = 5.5)
}
cc_doc = cc_doc %>%
body_end_section_landscape() %>%
# Literature Cited
body_add_par(value = "Literature Cited", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = cc_examples$lit_cited, style = "Normal")
return (cc_doc)
}
#' @title Build Mobile Acoustic Report document in .docx file
#'
#' @description Using the outputs from get_projects(),
#' get_ma_project_summary(), get_ma_bulk_wavs(),
#' and get_observed_nights() this function will create
#' a report .docx file to an out_dir.
#'
#' @import mapview
#' @import officer
#' @import magrittr
#' @import maps
#' @import maptools
#' @import sp
#' @import flextable
#' @import leaflet
#' @import rmarkdown
#' @import htmlwidgets
#' @import htmltools
#'
#' @examples
#'
#' \dontrun{
#' See vignette: build_ma_report (Build Mobile Acoustic Report)
#' }
#'
#'
#' @export
build_ma_doc = function(
out_dir,
file_name = 'ma_doc.docx',
project_df,
project_id,
ma_bulk_df,
species_df,
year,
nightly_observed_list,
date = format(Sys.time(), "%B %d, %Y")){
message ('Enter Stationary Report Function')
# Clean the data
ma_bulk_df = ma_bulk_df %>%
clean_time_fields() %>%
add_observed_nights()
# Setup temps directory to store intermediate files
if (dir.exists(paste0(out_dir, '/temps/'))==FALSE){
dir.create(paste0(out_dir, '/temps/'))
}
if (dir.exists(paste0(out_dir, '/temps/range_maps/'))==FALSE){
dir.create(paste0(out_dir, '/temps/range_maps/'))
}
logo_img_ = system.file("templates", "nabat_logo.png",
package = "nabatr")
circle_logo_ = system.file('templates', 'NABat_Circle_color.jpg',
package = 'nabatr')
proj_id = project_id
project_row_df = subset(project_df,
project_df$project_id == proj_id)
ma_title = project_row_df$project_name
ma_organization = project_row_df$organization
ma_description = project_row_df$project_description
message ('build results')
# Build results text
ma_results = get_ma_results(ma_bulk_df, species_df, year)
message ('build examples')
# get example text for mobile acoustic report
ma_examples = get_ma_examples()
message ('build table 1')
# Build table 1
ma_table_1 = build_ma_table_1(ma_bulk_df, project_id,
project_df, species_df, year)
message ('build table 2')
# Build table 2
ma_table_2 = build_ma_table_2(ma_bulk_df, species_df, year)
message ('build table 3')
# Build table 3
ma_table_3 = build_ma_table_3(ma_bulk_df, nightly_observed_list,
species_df, year)
message ('build figure 1 (map)')
# Build figure 1
ma_figure_1 = build_ma_figure_1(ma_bulk_df, project_id,
project_df, year)
# Save out map to import into officer word doc builder later
map_out_ = paste0(out_dir, '/temps/intermediate_map.png')
message ('Saving map out')
mapshot(ma_figure_1$map, file = map_out_)
message ('build figure 2')
# Build figure 2a/2b
ma_figure_2 = build_ma_figure_2(ma_bulk_df, species_df, year)
# Export to a file to be used to upload into the .docx
fig2a_f = paste0(out_dir, "/temps/fig2a.png")
plotly::export(ma_figure_2$figure_a, file = fig2a_f)
# Export to a file to be used to upload into the .docx
fig2b_f = paste0(out_dir, "/temps/fig2b.png")
plotly::export(ma_figure_2$figure_b, file = fig2b_f)
message ('build figure 3')
# Build Figure 3
ma_figure_3 = build_ma_figure_3(ma_bulk_df, species_df, year)
# Export to a file to be used to upload into the .docx
fig3_f = paste0(out_dir, "/temps/fig3.png")
suppressWarnings(plotly::export(ma_figure_3$figure, file = fig3_f))
bold_face = shortcuts$fp_bold(font.size = 16)
date_font = fp_text(color = 'black', font.family = 'Cambria',
font.size = 12)
par_style = fp_par(text.align = "center")
example_font = fp_text(color = "#bfbfbf", font.size = 12,
bold = FALSE, italic = FALSE, underlined = FALSE,
font.family = "Cambria", vertical.align = "baseline",
shading.color = "transparent")
message ('Build mobile acoustic .docx')
ma_doc = read_docx() %>%
body_add_fpar(fpar(ftext('Mobile Acoustic Report', prop = bold_face),
fp_p = par_style ), style = 'centered') %>%
body_add_fpar(fpar(ftext(paste0(year, ' Data'), prop = date_font),
fp_p = par_style ), style = 'centered') %>%
body_add_par(value = "", style = "centered") %>%
body_add_fpar(fpar(ftext(ma_title, prop = bold_face), fp_p = par_style ),
style = 'centered') %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = ma_organization, style = "centered") %>%
body_add_par(value = date, style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_img(src = circle_logo_, width = 2.5, height = 2.5,
style= 'centered') %>%
body_add_break() %>%
# Project Description
body_add_par(value = "Project Description", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = ma_description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(ma_examples$ma_ex_description,
prop = example_font)), style = 'Normal') %>%
body_add_break() %>%
# Methods
body_add_par(value = "Methods", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = "Site Selection", style = "heading 2") %>%
body_add_par(value = ma_examples$ma_methods_1, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = "Data Collection", style = "heading 2") %>%
body_add_par(value = ma_examples$ma_methods_2, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = "Call Processing/Species Identification",
style = "heading 2") %>%
body_add_par(value = ma_examples$ma_methods_3, style = "Normal") %>%
body_add_break() %>%
# Results
body_add_par(value = "Results", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = ma_results, style = "Normal") %>%
body_add_break() %>%
# Summary
body_add_par(value = "Summary", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(ma_examples$ma_summary_1, prop = example_font)),
style = 'Normal') %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(ma_examples$ma_summary_2, prop = example_font)),
style = 'Normal') %>%
body_add_break() %>%
# Table 1
body_add_par(value = ma_table_1$description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_flextable(ma_table_1$table, align='left') %>%
body_add_break() %>%
# Table 2
body_add_par(value = ma_table_2$description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_flextable(ma_table_2$table, align='left') %>%
body_add_break() %>%
body_end_section_continuous()
# Add table 3a/b
auto_ids = unique(ma_bulk_df$auto_id[!is.na(ma_bulk_df$auto_id)])
if (length(auto_ids) > 0){
ma_doc = ma_doc %>%
# Table 3a
body_add_par(value = ma_table_3$description_a, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_flextable(ma_table_3$table_a, align='left') %>%
body_add_break()
}
man_ids = unique(ma_bulk_df$manual_id[!is.na(ma_bulk_df$manual_id)])
if (length(man_ids) > 0){
ma_doc = ma_doc %>%
# Table 3b
body_add_par(value = ma_table_3$description_b, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_flextable(ma_table_3$table_b, align='left') %>%
body_add_break()
}
ma_doc = ma_doc %>%
# Figure 1
body_add_par(value = ma_figure_1$description, style = "Normal") %>%
body_add_img(src = map_out_, width = 8, height = 6, style= 'centered') %>%
# Figure 2a
body_add_par(value = ma_figure_2$description_a, style = "Normal") %>%
slip_in_img(src = fig2a_f, width = 7, height = 5) %>%
body_add_break() %>%
# Figure 2b
body_add_par(value = ma_figure_2$description_b, style = "Normal") %>%
slip_in_img(src = fig2b_f, width = 7, height = 5) %>%
body_add_break() %>%
# Figure 3
body_add_par(value = ma_figure_3$description, style = "Normal") %>%
slip_in_img(src = fig3_f, width = 7, height = 5) %>%
body_end_section_landscape() %>%
# Literature Cited
body_add_par(value = "Literature Cited", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = ma_examples$ma_lit_cited, style = "Normal")
return (ma_doc)
}
usgs/nabatr documentation built on Jan. 28, 2024, 7:10 a.m.
R Package Documentation
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Defines functions build_ma_doc build_col_doc build_sa_doc
Documented in build_col_doc build_ma_doc build_sa_doc
#############################################################################
# _ _____ ____ __ ____
# / | / / | / __ )____ _/ /_/ __ \
# / |/ / /| | / __ / __ `/ __/ /_/ /
# / /| / ___ |/ /_/ / /_/ / /_/ _, _/
# /_/ |_/_/ |_/_____/\__,_/\__/_/ |_|
#
# R Tools for accessing and manipulating North American Bat Monitoring data
#
# Written by: Kyle Enns
#
# FILE DESCRIPTION: This file contains functions build NABat reports for
# stationary, mobile, and colony count data
#
# USGS DISCLAIMER: This software is in the public domain because it contains
# materials that originally came from the U.S. Geological Survey, an agency
# of the United States Department of Interior. For more information, see the
# [official USGS copyright policy]
# (https://www.usgs.gov/visual-id/credit_usgs.html#copyright/
# "official USGS # copyright policy")
#
# Although this software program has been used by the U.S. Geological Survey
# (USGS), no warranty, expressed or implied, is made by the USGS or the U.S.
# Government as to the accuracy and functioning of the program and related
# program material nor shall the fact of distribution constitute any such
# warranty, and no responsibility is assumed by the USGS in connection
# therewith.
#
# This software is provided "AS IS."
#############################################################################
#' @title Build Stationary Acoustic Report document in .docx file
#'
#' @description Using the outputs from get_projects(), get_sa_project_summary(),
#' get_as_bulk_wavs(), and get_observed_nights() this function will create a
#' report .docx file to an out_dir.
#'
#' @import mapview
#' @import officer
#' @import magrittr
#' @import maps
#' @import maptools
#' @import sp
#' @import flextable
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' See vignette: build_sa_report (Build Stationary Acoustic Report)
#' }
#'
#' @export
build_sa_doc = function(
out_dir,
file_name = 'sa_doc.docx',
project_df,
project_id,
sa_bulk_df,
sa_survey_df,
species_df,
selected_year,
nightly_observed_list = NULL,
date = format(Sys.time(), "%B %d, %Y"),
range_maps = TRUE){
message ('Enter Stationary Report Function')
# Clean the data
sa_bulk_df = sa_bulk_df %>%
clean_time_fields() %>%
add_observed_nights() %>%
add_start_end_nights()
# Add selected year as 1st year
message ('Setup for temp directories')
if (is.null(selected_year)){
selected_year = unique(format(as.Date(sa_bulk_df$recording_time),
'%Y'))[1]
}
# Setup temps directory to store intermediate files
if (dir.exists(paste0(out_dir, '/temps/'))==FALSE){
dir.create(paste0(out_dir, '/temps/'))
}
if (dir.exists(paste0(out_dir, '/temps/range_maps/'))==FALSE){
dir.create(paste0(out_dir, '/temps/range_maps/'))
}
# Set Save figures boolean
save_figures = TRUE
message ('Getting nightly data')
# If nightly_observed_list isn't put in through variable
if (is.null(nightly_observed_list)){
nightly_observed_list = get_observed_nights(sa_bulk_df)
}
# Getting Manipulated data for species counts at GRTS cells
auto_nights_df = nightly_observed_list$auto_nightly_df
manual_nights_df = nightly_observed_list$manual_nightly_df
all_species_totals_l_l = get_all_species_counts_long(auto_nights_df,
manual_nights_df, fil = TRUE)
manual_species_grts_df_w = get_species_counts_wide(manual_nights_df)$species_grts_df
auto_species_grts_df_w = get_species_counts_wide(auto_nights_df)$species_grts_df
manual_species_totals_l = get_species_counts_long(manual_nights_df, filter=TRUE)
auto_species_totals_l = get_species_counts_long(auto_nights_df, filter=TRUE)
message ('Setting project specific variables')
# Set Variables
sa_logo_img_ = system.file("templates", "nabat_logo.png", package = "nabatr")
sa_circle_logo_ = system.file('templates', 'NABat_Circle_color.jpg',
package = 'nabatr')
sa_proj_id = project_id
sa_project_row_df = subset(project_df, project_df$project_id == sa_proj_id)
sa_title = sa_project_row_df$project_name
sa_organization = sa_project_row_df$organization
sa_this_project_description = sa_project_row_df$project_description
message ('Getting example text')
# Get the example text to put into the report
sa_examples = get_sa_examples()
message ('Build results text')
# Build the results text for Stationary acoustic report
sa_results = get_sa_results(sa_bulk_df, selected_year, species_df)
message ('Build table 1')
# sa_table_1
sa_table_1 = build_sa_table_1(sa_bulk_df, project_id, project_df,
species_df, selected_year)
message ('Build table 2')
# sa table 2
sa_table_2 = build_sa_table_2(sa_bulk_df, selected_year, species_df)
message ('Build figure 1')
# Figure 1 (map)
sa_figure_1 = build_sa_figure_1(sa_bulk_df, out_dir, project_df,
project_id, sa_survey_df, selected_year, save_figures)
message('Build figure 2')
# Figure 2a/2b
sa_figure_2 = build_sa_figure_2(sa_bulk_df, out_dir, species_df,
selected_year, auto_species_grts_df_w, manual_species_grts_df_w,
save_figures)
message('Build figure 3')
# Figure 3
sa_figure_3 = build_sa_figure_3(sa_bulk_df, out_dir, species_df,
selected_year, save_figures)
if (range_maps){
message ('Build range maps')
# build range maps
maps_data = get_sa_range_maps(sa_bulk_df, project_df, project_id,
all_species_totals_l_l, species_df, out_dir, range_maps)
}
message('Build final.docx document')
##### BUILD DOCUMENT
# Fonts
bold_face_map = shortcuts$fp_bold(font.size = 12)
bold_face = shortcuts$fp_bold(font.size = 16)
date_font = fp_text(color = 'black', font.family =
'Cambria', font.size = 12)
par_style = fp_par(text.align = "center")
example_font = fp_text(color = "#bfbfbf", font.size = 12,
bold = FALSE, italic = FALSE, underlined = FALSE,
font.family = "Cambria", vertical.align = "baseline",
shading.color = "transparent")
fig6_font = fp_text(color = "black", font.size = 10,
font.family = "Cambria")
message ('Begin .docx build')
sa_doc = read_docx() %>%
body_add_fpar(fpar(ftext('Stationary Acoustic Report',
prop = bold_face), fp_p = par_style ), style = 'centered') %>%
body_add_fpar(fpar(ftext(paste0(selected_year, ' Data'),
prop = date_font), fp_p = par_style ), style = 'centered') %>%
body_add_par(value = "", style = "centered") %>%
body_add_fpar(fpar(ftext(sa_title, prop = bold_face),
fp_p = par_style ), style = 'centered') %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = sa_organization, style = "centered") %>%
body_add_par(value = date, style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_img(src = sa_circle_logo_, width = 2.5, height = 2.5,
style= 'centered') %>%
# Add summary data for project and GRTS cells
body_add_par(value = "", style = "centered") %>%
body_add_break() %>%
# Project Description
body_add_par(value = "Project Description",
style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = sa_this_project_description,
style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(sa_examples$sa_ex_description,
prop = example_font)), style = 'Normal') %>%
body_add_break() %>%
# Methods
body_add_par(value = "Methods", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = "Site Selection", style = "heading 2") %>%
body_add_par(value = sa_examples$sa_methods_1, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = "Data Collection", style = "heading 2") %>%
body_add_par(value = sa_examples$sa_methods_2, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = "Call Processing/Species Identification",
style = "heading 2") %>%
body_add_par(value = sa_examples$sa_methods_3, style = "Normal") %>%
body_add_break() %>%
# Results
body_add_par(value = "Results", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = sa_results, style = "Normal") %>%
body_add_break() %>%
# Summary
body_add_par(value = "Summary", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(sa_examples$sa_summary_1,
prop = example_font)), style = 'Normal') %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(sa_examples$sa_summary_2,
prop = example_font)), style = 'Normal') %>%
body_add_break() %>%
# Table 1
body_add_par(value = sa_table_1$description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_flextable(sa_table_1$table, align='left') %>%
body_add_break() %>%
# Table 2
body_add_par(value = sa_table_2$description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_flextable(sa_table_2$table, align='left') %>%
body_add_break() %>%
# Figure 1
body_add_par(value = sa_figure_1$description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_img(src = sa_figure_1$file, width = 5.7,
height = 4, style= 'centered') %>%
body_add_break() %>%
# Figure 2a
body_add_par(value = sa_figure_2$description_a, style = "Normal") %>%
slip_in_img(src = sa_figure_2$file_a, width = 6.5, height = 5) %>%
body_add_break() %>%
# Figure 2b
body_add_par(value = sa_figure_2$description_b, style = "Normal") %>%
slip_in_img(src = sa_figure_2$file_b, width = 6.5, height = 5) %>%
body_add_break() %>%
# Figure 3
body_add_par(value = sa_figure_3$description, style = "Normal") %>%
slip_in_img(src = sa_figure_3$file, width = 6.5, height = 5) %>%
body_add_break()
message('Adding species range maps to .docx')
# Add species range maps
if (range_maps){
map_c = 0
fig_count = 3
for (range_m in maps_data$maps_range_files){
map_c = map_c + 1
fig_count = fig_count + 1
grts_m = maps_data$maps_grts_files[map_c]
spc_range_name = str_split(str_split(sub('\\.png$', '', range_m),
'range_maps/')[[1]][2], '_range')[[1]][1]
spc_grts_name = str_split(str_split(sub('\\.png$', '', grts_m),
'range_maps/')[[1]][2], '_grts')[[1]][1]
fig_a_name = paste0('Figure ', as.character(fig_count), 'a. ')
fig_b_name = paste0('Figure ', as.character(fig_count), 'b. ')
descr_fig5 = paste0(fig_a_name,"Species range map for ", spc_range_name, ".")
descr_fig6 = paste0(fig_b_name,"Map of NABat GRTS cells surveyed in ",selected_year," with species range map overlayed (",
spc_range_name,"). Green cells indicate the presence of ",spc_range_name," was confirmed exclusively through
manual vetting, blue cells indicate the presence of ",spc_range_name," was confirmed exclusively through
automated identification software, and orange cells indicate the presence of ",spc_range_name," was confirmed
using both automated identification software and manual vetting. Transparent
cells indicated that ",spc_range_name," was not detected at those locations.")
# Add the maps to the doc
sa_doc = sa_doc %>%
body_add_fpar(fpar(ftext(paste0('Species: ',spc_range_name),
prop = bold_face_map), fp_p = par_style ), style = 'Normal') %>%
body_add_fpar(fpar(ftext(descr_fig5, prop = fig6_font)),
style = 'Normal') %>%
slip_in_img(src = range_m, width = 5.7, height = 4) %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(descr_fig6, prop = fig6_font)),
style = 'Normal') %>%
body_add_par(value = "", style = "Normal") %>%
slip_in_img(src = grts_m, width = 5.7, height = 4) %>%
body_add_break()
}
}
# Literature Cited
sa_doc = sa_doc %>%
body_add_par(value = "Literature Cited", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = sa_examples$sa_lit_cited, style = "Normal")
return (sa_doc)
}
#' @title Build Report document in .docx file for Colony Count Data
#'
#' @description Using the outputs from get_projects(),
#' get_project_surveys(), get_colony_bulk_counts(),
#' and () this function will create a report .docx file to an out_dir.
#'
#' @import mapview
#' @import officer
#' @import magrittr
#' @import maps
#' @import maptools
#' @import sp
#' @import flextable
#' @import lubridate
#' @import ggplot2
#'
#' @examples
#'
#' \dontrun{
#' See vignette: build_cc_report (Build Colony Count Report)
#' }
#'
#' @export
build_col_doc = function(
out_dir,
file_name = 'cc_doc.docx',
project_df = NULL,
project_id,
cc_bulk_df = NULL,
date = format(Sys.time(), "%B %d, %Y")){
if (dir.exists(paste0(out_dir, '/temps/')) == FALSE){
dir.create(paste0(out_dir, '/temps/'))
}
message('Get front page info')
# Get front page info
cc_logo_img_ = system.file("templates", "nabat_logo.png",
package = "nabatr")
cc_circle_logo_ = system.file('templates', 'NABat_Circle_color.jpg',
package = 'nabatr')
cc_proj_id = project_id
cc_project_row_df = subset(project_df, project_df$project_id == cc_proj_id)
cc_title = cc_project_row_df$project_name
cc_organization = cc_project_row_df$organization
cc_description = cc_project_row_df$project_description
message ('Get Examples')
# Get Colony Count Examples
cc_examples = get_cc_examples()
message ('Get Results')
# Get Colony Count results
cc_results = get_cc_results(cc_bulk_df)
message ('Build table 1')
# Build Colony Count table 1
cc_table_1 = build_cc_table_1(cc_bulk_df, TRUE)
message('Build table 2')
# Build Colony Count table 2
cc_table_2 = build_cc_table_2(cc_bulk_df)
message ('Build figure 1')
# Build Colony Count figure 1
cc_figure_1 = build_cc_figure_1(cc_bulk_df, out_dir, TRUE)
message ('Add Fonts')
# Add fonts
bold_face = shortcuts$fp_bold(font.size = 16)
par_style = fp_par(text.align = "center")
example_font = fp_text(color = "#bfbfbf", font.size = 12, bold = FALSE,
italic = FALSE, underlined = FALSE, font.family = "Cambria",
vertical.align = "baseline", shading.color = "transparent")
message ('Begin Colony Count .docx build')
# Build Colony Count document
cc_doc = read_docx() %>%
body_add_fpar(fpar(ftext('Colony Count Report', prop = bold_face),
fp_p = par_style ), style = 'centered') %>%
body_add_par(value = "", style = "centered") %>%
body_add_fpar(fpar(ftext(cc_title, prop = bold_face), fp_p = par_style ),
style = 'centered') %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = cc_organization, style = "centered") %>%
body_add_par(value = date, style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_img(src = cc_circle_logo_, width = 2.5, height = 2.5,
style = 'centered') %>%
body_add_break() %>%
# Project Description
body_add_par(value = "Project Description", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = cc_description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(cc_examples$description, prop = example_font)),
style = 'Normal') %>%
body_add_break() %>%
# Methods
body_add_par(value = "Methods", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(cc_examples$methods_1, prop = example_font)),
style = 'Normal') %>%
body_add_break() %>%
# Results
body_add_par(value = "Results", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = cc_results, style = "Normal") %>%
body_add_break() %>%
body_end_section_continuous() %>%
# Table 1
body_add_par(value = cc_table_1$description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_flextable(cc_table_1$table, align='left') %>%
body_end_section_landscape() %>%
# Table 2
body_add_par(value = cc_table_2$description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_flextable(cc_table_2$table, align='left') %>%
body_end_section_continuous()
# Figure 1
count = 0
if (length(cc_figure_1$file) > 1){
for(file in cc_figure_1$file){
count = count + 1
cc_doc = cc_doc %>%
body_add_par(value = cc_figure_1$description[count], style = "Normal") %>%
slip_in_img(src = file, width = 7.5, height = 5.5)
}
}else{
cc_doc = cc_doc %>%
body_add_par(value = cc_figure_1$description, style = "Normal") %>%
slip_in_img(src = cc_figure_1$file, width = 7.5, height = 5.5)
}
cc_doc = cc_doc %>%
body_end_section_landscape() %>%
# Literature Cited
body_add_par(value = "Literature Cited", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = cc_examples$lit_cited, style = "Normal")
return (cc_doc)
}
#' @title Build Mobile Acoustic Report document in .docx file
#'
#' @description Using the outputs from get_projects(),
#' get_ma_project_summary(), get_ma_bulk_wavs(),
#' and get_observed_nights() this function will create
#' a report .docx file to an out_dir.
#'
#' @import mapview
#' @import officer
#' @import magrittr
#' @import maps
#' @import maptools
#' @import sp
#' @import flextable
#' @import leaflet
#' @import rmarkdown
#' @import htmlwidgets
#' @import htmltools
#'
#' @examples
#'
#' \dontrun{
#' See vignette: build_ma_report (Build Mobile Acoustic Report)
#' }
#'
#'
#' @export
build_ma_doc = function(
out_dir,
file_name = 'ma_doc.docx',
project_df,
project_id,
ma_bulk_df,
species_df,
year,
nightly_observed_list,
date = format(Sys.time(), "%B %d, %Y")){
message ('Enter Stationary Report Function')
# Clean the data
ma_bulk_df = ma_bulk_df %>%
clean_time_fields() %>%
add_observed_nights()
# Setup temps directory to store intermediate files
if (dir.exists(paste0(out_dir, '/temps/'))==FALSE){
dir.create(paste0(out_dir, '/temps/'))
}
if (dir.exists(paste0(out_dir, '/temps/range_maps/'))==FALSE){
dir.create(paste0(out_dir, '/temps/range_maps/'))
}
logo_img_ = system.file("templates", "nabat_logo.png",
package = "nabatr")
circle_logo_ = system.file('templates', 'NABat_Circle_color.jpg',
package = 'nabatr')
proj_id = project_id
project_row_df = subset(project_df,
project_df$project_id == proj_id)
ma_title = project_row_df$project_name
ma_organization = project_row_df$organization
ma_description = project_row_df$project_description
message ('build results')
# Build results text
ma_results = get_ma_results(ma_bulk_df, species_df, year)
message ('build examples')
# get example text for mobile acoustic report
ma_examples = get_ma_examples()
message ('build table 1')
# Build table 1
ma_table_1 = build_ma_table_1(ma_bulk_df, project_id,
project_df, species_df, year)
message ('build table 2')
# Build table 2
ma_table_2 = build_ma_table_2(ma_bulk_df, species_df, year)
message ('build table 3')
# Build table 3
ma_table_3 = build_ma_table_3(ma_bulk_df, nightly_observed_list,
species_df, year)
message ('build figure 1 (map)')
# Build figure 1
ma_figure_1 = build_ma_figure_1(ma_bulk_df, project_id,
project_df, year)
# Save out map to import into officer word doc builder later
map_out_ = paste0(out_dir, '/temps/intermediate_map.png')
message ('Saving map out')
mapshot(ma_figure_1$map, file = map_out_)
message ('build figure 2')
# Build figure 2a/2b
ma_figure_2 = build_ma_figure_2(ma_bulk_df, species_df, year)
# Export to a file to be used to upload into the .docx
fig2a_f = paste0(out_dir, "/temps/fig2a.png")
plotly::export(ma_figure_2$figure_a, file = fig2a_f)
# Export to a file to be used to upload into the .docx
fig2b_f = paste0(out_dir, "/temps/fig2b.png")
plotly::export(ma_figure_2$figure_b, file = fig2b_f)
message ('build figure 3')
# Build Figure 3
ma_figure_3 = build_ma_figure_3(ma_bulk_df, species_df, year)
# Export to a file to be used to upload into the .docx
fig3_f = paste0(out_dir, "/temps/fig3.png")
suppressWarnings(plotly::export(ma_figure_3$figure, file = fig3_f))
bold_face = shortcuts$fp_bold(font.size = 16)
date_font = fp_text(color = 'black', font.family = 'Cambria',
font.size = 12)
par_style = fp_par(text.align = "center")
example_font = fp_text(color = "#bfbfbf", font.size = 12,
bold = FALSE, italic = FALSE, underlined = FALSE,
font.family = "Cambria", vertical.align = "baseline",
shading.color = "transparent")
message ('Build mobile acoustic .docx')
ma_doc = read_docx() %>%
body_add_fpar(fpar(ftext('Mobile Acoustic Report', prop = bold_face),
fp_p = par_style ), style = 'centered') %>%
body_add_fpar(fpar(ftext(paste0(year, ' Data'), prop = date_font),
fp_p = par_style ), style = 'centered') %>%
body_add_par(value = "", style = "centered") %>%
body_add_fpar(fpar(ftext(ma_title, prop = bold_face), fp_p = par_style ),
style = 'centered') %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = ma_organization, style = "centered") %>%
body_add_par(value = date, style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_par(value = "", style = "centered") %>%
body_add_img(src = circle_logo_, width = 2.5, height = 2.5,
style= 'centered') %>%
body_add_break() %>%
# Project Description
body_add_par(value = "Project Description", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = ma_description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(ma_examples$ma_ex_description,
prop = example_font)), style = 'Normal') %>%
body_add_break() %>%
# Methods
body_add_par(value = "Methods", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = "Site Selection", style = "heading 2") %>%
body_add_par(value = ma_examples$ma_methods_1, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = "Data Collection", style = "heading 2") %>%
body_add_par(value = ma_examples$ma_methods_2, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = "Call Processing/Species Identification",
style = "heading 2") %>%
body_add_par(value = ma_examples$ma_methods_3, style = "Normal") %>%
body_add_break() %>%
# Results
body_add_par(value = "Results", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = ma_results, style = "Normal") %>%
body_add_break() %>%
# Summary
body_add_par(value = "Summary", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(ma_examples$ma_summary_1, prop = example_font)),
style = 'Normal') %>%
body_add_par(value = "", style = "Normal") %>%
body_add_fpar(fpar(ftext(ma_examples$ma_summary_2, prop = example_font)),
style = 'Normal') %>%
body_add_break() %>%
# Table 1
body_add_par(value = ma_table_1$description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_flextable(ma_table_1$table, align='left') %>%
body_add_break() %>%
# Table 2
body_add_par(value = ma_table_2$description, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_flextable(ma_table_2$table, align='left') %>%
body_add_break() %>%
body_end_section_continuous()
# Add table 3a/b
auto_ids = unique(ma_bulk_df$auto_id[!is.na(ma_bulk_df$auto_id)])
if (length(auto_ids) > 0){
ma_doc = ma_doc %>%
# Table 3a
body_add_par(value = ma_table_3$description_a, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_flextable(ma_table_3$table_a, align='left') %>%
body_add_break()
}
man_ids = unique(ma_bulk_df$manual_id[!is.na(ma_bulk_df$manual_id)])
if (length(man_ids) > 0){
ma_doc = ma_doc %>%
# Table 3b
body_add_par(value = ma_table_3$description_b, style = "Normal") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_flextable(ma_table_3$table_b, align='left') %>%
body_add_break()
}
ma_doc = ma_doc %>%
# Figure 1
body_add_par(value = ma_figure_1$description, style = "Normal") %>%
body_add_img(src = map_out_, width = 8, height = 6, style= 'centered') %>%
# Figure 2a
body_add_par(value = ma_figure_2$description_a, style = "Normal") %>%
slip_in_img(src = fig2a_f, width = 7, height = 5) %>%
body_add_break() %>%
# Figure 2b
body_add_par(value = ma_figure_2$description_b, style = "Normal") %>%
slip_in_img(src = fig2b_f, width = 7, height = 5) %>%
body_add_break() %>%
# Figure 3
body_add_par(value = ma_figure_3$description, style = "Normal") %>%
slip_in_img(src = fig3_f, width = 7, height = 5) %>%
body_end_section_landscape() %>%
# Literature Cited
body_add_par(value = "Literature Cited", style = "heading 1") %>%
body_add_par(value = "", style = "Normal") %>%
body_add_par(value = ma_examples$ma_lit_cited, style = "Normal")
return (ma_doc)
}
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