`, etc.) that has more than one element. Defaults to 1 (for ``).
76 | getTopLevel: function($scope) {
77 | for (var i = 1; i <= 6; i++) {
78 | var $headings = this.findOrFilter($scope, 'h' + i);
79 | if ($headings.length > 1) {
80 | return i;
81 | }
82 | }
83 |
84 | return 1;
85 | },
86 |
87 | // returns the elements for the top level, and the next below it
88 | getHeadings: function($scope, topLevel) {
89 | var topSelector = 'h' + topLevel;
90 |
91 | var secondaryLevel = topLevel + 1;
92 | var secondarySelector = 'h' + secondaryLevel;
93 |
94 | return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
95 | },
96 |
97 | getNavLevel: function(el) {
98 | return parseInt(el.tagName.charAt(1), 10);
99 | },
100 |
101 | populateNav: function($topContext, topLevel, $headings) {
102 | var $context = $topContext;
103 | var $prevNav;
104 |
105 | var helpers = this;
106 | $headings.each(function(i, el) {
107 | var $newNav = helpers.generateNavItem(el);
108 | var navLevel = helpers.getNavLevel(el);
109 |
110 | // determine the proper $context
111 | if (navLevel === topLevel) {
112 | // use top level
113 | $context = $topContext;
114 | } else if ($prevNav && $context === $topContext) {
115 | // create a new level of the tree and switch to it
116 | $context = helpers.createChildNavList($prevNav);
117 | } // else use the current $context
118 |
119 | $context.append($newNav);
120 |
121 | $prevNav = $newNav;
122 | });
123 | },
124 |
125 | parseOps: function(arg) {
126 | var opts;
127 | if (arg.jquery) {
128 | opts = {
129 | $nav: arg
130 | };
131 | } else {
132 | opts = arg;
133 | }
134 | opts.$scope = opts.$scope || $(document.body);
135 | return opts;
136 | }
137 | },
138 |
139 | // accepts a jQuery object, or an options object
140 | init: function(opts) {
141 | opts = this.helpers.parseOps(opts);
142 |
143 | // ensure that the data attribute is in place for styling
144 | opts.$nav.attr('data-toggle', 'toc');
145 |
146 | var $topContext = this.helpers.createChildNavList(opts.$nav);
147 | var topLevel = this.helpers.getTopLevel(opts.$scope);
148 | var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
149 | this.helpers.populateNav($topContext, topLevel, $headings);
150 | }
151 | };
152 |
153 | $(function() {
154 | $('nav[data-toggle="toc"]').each(function(i, el) {
155 | var $nav = $(el);
156 | Toc.init($nav);
157 | });
158 | });
159 | })();
160 |
--------------------------------------------------------------------------------
/notes.R:
--------------------------------------------------------------------------------
1 |
2 | # https://pkgdown.r-lib.org/reference/build_site.html
3 |
4 | # Wish list
5 |
6 | # Links to figures and tables in text
7 | # https://holtzy.github.io/Pimp-my-rmd/#internal_link
8 |
9 | ########### Document Package ############
10 | .rs.restartR()
11 |
12 | # options(rmarkdown.html_vignette.check_title = FALSE)
13 | Sys.setenv('PATH' = paste0('C:/Program Files/qpdf-10.0.1/bin;', Sys.getenv('PATH')))
14 | library(here)
15 | library(devtools)
16 | library(roxygen2)
17 | # rmarkdown::render(paste0(dir_code, "/README.Rmd"),
18 | # output_dir = here::here(),
19 | # output_file = paste0("README.md"))
20 | devtools::document()
21 | setwd("..")
22 | install("NMFSReports")
23 | 3
24 | setwd(here::here())
25 | # devtools::check()
26 |
27 | ## Create Documentation GitHub-Pages -------------------------------------------
28 |
29 | .rs.restartR()
30 | # devtools::install_github("rstudio/fontawesome", force = T)
31 | # library(fontawesome)
32 | library(here)
33 | library(usethis)
34 | library(pkgdown)
35 | # options(rmarkdown.html_vignette.check_title = FALSE)
36 |
37 | # git rm -r --cached .
38 | options(rmarkdown.html_vignette.check_title = FALSE)
39 | # pkgdown::build_favicons()
40 | devtools::build_vignettes()
41 | usethis::use_pkgdown(config_file = "./pkgdown/_pkgdown.yml")
42 |
43 | .rs.restartR()
44 |
45 | pkgdown::build_site(pkg = here::here())
46 | # usethis::use_github_action("pkgdown")
47 |
48 | # usethis::use_github_pages(branch = "main", path = "/docs", cname = NA)
49 |
50 | # template:
51 | # params:
52 | # bootswatch: sandstone
53 |
54 | ########### Submit to CRAN ############
55 |
56 | # devtools::check() # add the console output to cran-commentes.md
57 | # devtools::check_rhub() # check that your email is 'validated.' You'll need a token emailed to you
58 | # devtools::check_win_devel()
59 | # devtools::release()
60 |
61 | ##########build a vignette#########
62 |
63 | # usethis::use_vignette("A_buildReport-test")
64 | # usethis::use_vignette("ScriptLayout")
65 | # usethis::use_vignette("ExampleRunFile")
66 | # usethis::use_vignette("InitialSetUp")
67 |
68 | #########NOTES#########
69 |
70 | # bootstrap shiny design
71 | # https://gallery.shinyapps.io/117-shinythemes/
72 |
73 | # Guide for checking CMD CHECK()
74 | # https://r-pkgs.org/r-cmd-check.html
75 |
76 | # loading qpdf:
77 | # https://stackoverflow.com/questions/41570633/how-to-build-qpdf-on-windows
78 | # https://stackoverflow.com/questions/15035150/r-cmd-check-as-cran-warning
79 | # https://sourceforge.net/projects/qpdf/files/qpdf/10.0.1/
80 | # Sys.setenv('PATH' = paste0('C:/Program Files/qpdf-10.0.1/bin;', Sys.getenv('PATH')))
81 | # Sys.which(Sys.getenv("R_QPDF", "qpdf"))
82 |
83 | # Compress Files
84 | # https://stackoverflow.com/questions/10233593/how-to-effectively-deal-with-uncompressed-saves-during-package-check
85 | # save(land, file="./data/sysdata.rda", compress='xz')
86 |
87 | # Add a favicon
88 | # https://github.com/r-lib/pkgdown/issues/379
89 |
90 | # Licence
91 | # https://stackoverflow.com/questions/56102225/r-devtoolscheck-license-is-not-mentioned-and-other-issues-in-description-file
92 |
93 | # Dealing with "no visible binding for global variable '*'"
94 | # https://stackoverflow.com/questions/9439256/how-can-i-handle-r-cmd-check-no-visible-binding-for-global-variable-notes-when
95 |
96 | # clean up gitignore
97 | # https://stackoverflow.com/questions/48955103/non-standard-file-directory-found-at-top-level-readme-rmd-persists-even-after
98 |
99 | # Make code citable
100 | # https://guides.github.com/activities/citable-code/
101 |
102 | # General Reference
103 | # https://github.com/timjmiller/wham/blob/master/DESCRIPTION
104 | # date: "`r format(Sys.Date(), format='%B %d %Y') `"
105 |
106 | #https://github.com/r-lib/pkgdown/issues/379
107 |
108 |
109 |
110 | ######## OLD STUFF #############
111 |
112 | #'Replace the first value, if missing, with the next nearest value.
113 | #'
114 | #' If the first value of the timeseries of this column (c) is 0/NaN/NA. Change the first value (and subsequent 0/NaN/NA values) to the first available non-0/NaN/NA value. Then, used in before with 'ReplaceMid'.
115 | #' @param colnames Names of columns to apply this action to.
116 | #' @param temp Name of dataset to apply this action to.
117 | #' @keywords Replace, First
118 | #' @export
119 | #' @examples
120 | #' ReplaceFirst()
121 | ReplaceFirst <- function(colnames, temp) {
122 | for (c0 in 1:length(colnames)) {
123 | if (temp[1, colnames[c0]] %in% c(0, NA, NaN, NULL)) {
124 | findfirstvalue <-
125 | temp[which(!(temp[, colnames[c0]] %in% c(0, NA, NaN, NULL))),
126 | colnames[c0]][1]
127 | temp[1, colnames[c0]] <- findfirstvalue
128 | }
129 | }
130 | return(temp)
131 | }
132 |
133 |
134 | #'Replace the first value, if missing, with the next nearest value.
135 | #'
136 | #' If a middle value of the timeseries of this column (c) is 0/NaN/NA. Change the currently 0/NaN/NA value to the previous available non-0/NaN/NA value. Then, used after with 'ReplaceFirst'.
137 | #' @param colnames Names of columns to apply this action to.
138 | #' @param temp Name of dataset to apply this action to.
139 | #' @keywords Replace, Mid, Middle
140 | #' @export
141 | #' @examples
142 | #' ReplaceMid()
143 | ReplaceMid <- function(colnames, temp) {
144 | for (c0 in 1:length(colnames)) {
145 | #If a middle value of the timeseries of this column (c) is 0/NaN/NA
146 | #Change the currently 0/NaN/NA value to the previous available non-0/NaN/NA value
147 | if (sum(temp[, colnames[c0]] %in% c(0, NA, NaN, NULL)) > 0) {
148 | troublenumber <- which(temp[, colnames[c0]] %in% c(0, NA, NaN, NULL))
149 | for (r in 1:length(troublenumber)) {
150 | findlastvalue <- temp[troublenumber[r] - 1, colnames[c0]][1]
151 | temp[troublenumber[r], colnames[c0]] <- findlastvalue
152 | }
153 | }
154 | }
155 | return(temp)
156 | }
157 |
158 |
159 |
--------------------------------------------------------------------------------
/README.Rmd:
--------------------------------------------------------------------------------
1 | ---
2 | output: md_document
3 | ---
4 |
5 |
6 |
7 | ```{r, echo = FALSE, warning=FALSE, message=FALSE}
8 | knitr::opts_chunk$set(
9 | collapse = TRUE,
10 | comment = "#>",
11 | fig.path = "man/figures/",
12 | fig.height = 1
13 | )
14 | require(ggplot2)
15 | ```
16 |
17 | ```{r echo=FALSE, results="hide", message=FALSE, include=FALSE}
18 | library("badger", quietly = TRUE)
19 | ```
20 |
21 | # NMFSReports 
22 |
23 |
24 | ### *Easily write NOAA reports and Tech Memos in R Markdown*
25 |
26 |
27 | ```{r, echo = FALSE, results='asis', message=FALSE}
28 | cat(
29 | badge_devel("EmilyMarkowitz-NOAA/NMFSReports", "blue"),
30 | badge_lifecycle("maturing", "blue"),
31 | badge_last_commit("EmilyMarkowitz-NOAA/NMFSReports")
32 | )
33 | ```
34 |
35 | ## Author
36 |
37 | **Emily Markowitz** (Emily.Markowitz AT noaa.gov)
38 |
39 | Alaska Fisheries Science Center,
40 |
41 | National Marine Fisheries Service,
42 |
43 | National Oceanic and Atmospheric Administration,
44 |
45 | Seattle, WA 98195
46 |
47 | ## Installation
48 |
49 | #### `NMFSReports`
50 |
51 | Learn more about this package at this [pkgdown webpage!](https://emilymarkowitz-noaa.github.io/NMFSReports/)
52 |
53 | The NMFSReports Package has all of the basic architecture you need to create reproducible and repeatable NOAA Tech Memos in R Markdown! This approach is perfect for efficiently rolling out annual (or other regular) reports or reports with formulaic sections (the same chapter structure but for a different area or species). Scripts integrate table, figure, data, and bibliography management and design automation.
54 |
55 |
56 | ```{r, eval=FALSE}
57 | library(devtools)
58 | devtools::install_github("EmilyMarkowitz-NOAA/NMFSReports")
59 | library(NMFSReports)
60 |
61 | # Or, alternatively,
62 | remotes::install_github("EmilyMarkowitz-NOAA/NMFSReports@main")
63 | ```
64 |
65 | #### You may also consider useing this package with `nmfspalette`
66 |
67 | A package for NOAA Fisheries color schemes. More info [here](https://github.com/nmfs-general-modeling-tools/nmfspalette).
68 |
69 | ```{r, eval=FALSE}
70 | library(devtools)
71 | devtools::install_github("nmfs-general-modeling-tools/nmfspalette")
72 | library(nmfspalette)
73 | ```
74 |
75 | ## Notes
76 |
77 | More details about how to use the [https://github.com/RVerse-Tutorials/GoogleDrive1]({googledrive} R pakage) in RMarkdown Documents:
78 |
79 |
80 | ## Conference Presentations
81 |
82 | Markowitz, EH. Reproducible Reports in R Markdown - Perspectives and {NMFSReports}. R Cascadia Conf., June 2021. Remote. ([Slides](https://github.com/EmilyMarkowitz-NOAA/NMFSReports/blob/main/presentations/2021-06-05NMFSReports-RCascadiaConf.pdf), [Recording of Presentation](https://www.youtube.com/watch?v=zNKdQ6jvr-M&list=PLzwtsyfF_Z4pPszfwklTD66AWUuMwS7qw&index=11))
83 |
84 | Markowitz, EH. Reproducible National-level Reports: Using RMarkdown to Recode the Fisheries Economics of the US Report.
85 |
86 | - Women in Statistics and Data Science Conf.; American Statistical Association, September 2020. Remote.
87 | - American Fisheries Society, September 2020. Remote.
88 | - SatRDay Conference, March 2020. Washington, D.C./Remote. ([Recording](https://youtu.be/-mycRwaC60A))
89 |
90 | ## Abstract
91 |
92 | Scientists in government and beyond are often tasked with preparing analysis-driven reports that inform policy and are crucial for documenting the state of their programs at regular intervals (e.g., annually, quarterly, monthly). Although these reports typically follow the same format for each iteration, updating content with new data from previous document line by line can lead to inefficient writing and introduce errors.
93 |
94 | Alternatively, R and R Markdown can be used to systematically modernize report creation. To address this need within our agency I have developed a new R package, `{NMFSReports}`, which uses R and R Markdown to provide an analysis-to-product approach to report writing by centralizing back-end data analyses and efficiently streamlining copy-edit and design sub-processes. The `{NMFSReports}` R package first creates the basic report outline and folder architecture to create reproducible reports, and then provides users with grammar and organization helper functions that assist in report writing. To aid in the final publication process, this workflow can also be used to produce intermediate output files for subject matter experts and collaborators to review and use. `{NMFSReports}` can produce copy-edit ready and accessibility-compliant documents for editors, style guide-formatted and flow-in ready text (including bibliography, footnote, figure, and table management) for authors, tables and figures for graphic designers, and web-ready data files for web tool developers. Though this package is in early stages of development, it is already clear it has the potential to save colleagues across our agency countless hours and improve efficiency and consistency among our teams and offices. Though developed for reports produced by scientists at NOAA Fisheries, the concepts and structures behind `{NMFSReports}` have utility for anyone seeking to streamline reports, graphics, and web tools.
95 |
96 | ## NOAA README
97 |
98 | This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.
99 |
100 | ## NOAA License
101 |
102 | Software code created by U.S. Government employees is not subject to copyright in the United States (17 U.S.C. §105). The United States/Department of Commerce reserve all rights to seek and obtain copyright protection in countries other than the United States for Software authored in its entirety by the Department of Commerce. To this end, the Department of Commerce hereby grants to Recipient a royalty-free, nonexclusive license to use, copy, and create derivative works of the Software outside of the United States.
103 |
104 |
105 | 
106 |
107 | [U.S. Department of Commerce](https://www.commerce.gov/) | [National Oceanographic and Atmospheric Administration](https://www.noaa.gov) | [NOAA Fisheries](https://www.fisheries.noaa.gov/)
108 |
--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
1 |
2 |
3 | # **This repo has now been ARCHIVED AND DEPRECIATED.** Only use this repository for reference.
4 |
5 | # NMFSReports
6 |
7 | ### *Easily write NOAA reports and Tech Memos in R Markdown*
8 |
9 | [](https://github.com/EmilyMarkowitz-NOAA/NMFSReports)
10 | [](https://www.tidyverse.org/lifecycle/#maturing)
11 | [](https://github.com/EmilyMarkowitz-NOAA/NMFSReports/commits/master)
12 |
13 | ## Author
14 |
15 | **Emily Markowitz** (Emily.Markowitz AT noaa.gov)
16 |
17 | Alaska Fisheries Science Center,
18 |
19 | National Marine Fisheries Service,
20 |
21 | National Oceanic and Atmospheric Administration,
22 |
23 | Seattle, WA 98195
24 |
25 | ## Installation
26 |
27 | #### `NMFSReports`
28 |
29 | Learn more about this package at this [pkgdown
30 | webpage!](https://emilymarkowitz-noaa.github.io/NMFSReports/)
31 |
32 | The NMFSReports Package has all of the basic architecture you need to
33 | create reproducible and repeatable NOAA Tech Memos in R Markdown! This
34 | approach is perfect for efficiently rolling out annual (or other
35 | regular) reports or reports with formulaic sections (the same chapter
36 | structure but for a different area or species). Scripts integrate table,
37 | figure, data, and bibliography management and design automation.
38 |
39 | library(devtools)
40 | devtools::install_github("EmilyMarkowitz-NOAA/NMFSReports")
41 | library(NMFSReports)
42 |
43 | # Or, alternatively,
44 | remotes::install_github("EmilyMarkowitz-NOAA/NMFSReports@main")
45 |
46 | #### You may also consider useing this package with `nmfspalette`
47 |
48 | A package for NOAA Fisheries color schemes. More info
49 | [here](https://github.com/nmfs-general-modeling-tools/nmfspalette).
50 |
51 | library(devtools)
52 | devtools::install_github("nmfs-general-modeling-tools/nmfspalette")
53 | library(nmfspalette)
54 |
55 | ## Notes
56 |
57 | More details about how to use the
58 | [https://github.com/RVerse-Tutorials/GoogleDrive1](%7Bgoogledrive%7D%20R%20pakage)
59 | in RMarkdown Documents:
60 |
61 | ## Conference Presentations
62 |
63 | Markowitz, EH. Reproducible Reports in R Markdown - Perspectives and
64 | {NMFSReports}. R Cascadia Conf., June 2021. Remote.
65 | ([Slides](https://github.com/EmilyMarkowitz-NOAA/NMFSReports/blob/main/presentations/2021-06-05NMFSReports-RCascadiaConf.pdf),
66 | [Recording of
67 | Presentation](https://www.youtube.com/watch?v=zNKdQ6jvr-M&list=PLzwtsyfF_Z4pPszfwklTD66AWUuMwS7qw&index=11))
68 |
69 | Markowitz, EH. Reproducible National-level Reports: Using RMarkdown to
70 | Recode the Fisheries Economics of the US Report.
71 |
72 | - Women in Statistics and Data Science Conf.; American Statistical
73 | Association, September 2020. Remote.
74 | - American Fisheries Society, September 2020. Remote.
75 | - SatRDay Conference, March 2020. Washington, D.C./Remote.
76 | ([Recording](https://youtu.be/-mycRwaC60A))
77 |
78 | ## Abstract
79 |
80 | Scientists in government and beyond are often tasked with preparing
81 | analysis-driven reports that inform policy and are crucial for
82 | documenting the state of their programs at regular intervals (e.g.,
83 | annually, quarterly, monthly). Although these reports typically follow
84 | the same format for each iteration, updating content with new data from
85 | previous document line by line can lead to inefficient writing and
86 | introduce errors.
87 |
88 | Alternatively, R and R Markdown can be used to systematically modernize
89 | report creation. To address this need within our agency I have developed
90 | a new R package, `{NMFSReports}`, which uses R and R Markdown to provide
91 | an analysis-to-product approach to report writing by centralizing
92 | back-end data analyses and efficiently streamlining copy-edit and design
93 | sub-processes. The `{NMFSReports}` R package first creates the basic
94 | report outline and folder architecture to create reproducible reports,
95 | and then provides users with grammar and organization helper functions
96 | that assist in report writing. To aid in the final publication process,
97 | this workflow can also be used to produce intermediate output files for
98 | subject matter experts and collaborators to review and use.
99 | `{NMFSReports}` can produce copy-edit ready and accessibility-compliant
100 | documents for editors, style guide-formatted and flow-in ready text
101 | (including bibliography, footnote, figure, and table management) for
102 | authors, tables and figures for graphic designers, and web-ready data
103 | files for web tool developers. Though this package is in early stages of
104 | development, it is already clear it has the potential to save colleagues
105 | across our agency countless hours and improve efficiency and consistency
106 | among our teams and offices. Though developed for reports produced by
107 | scientists at NOAA Fisheries, the concepts and structures behind
108 | `{NMFSReports}` have utility for anyone seeking to streamline reports,
109 | graphics, and web tools.
110 |
111 | ## NOAA README
112 |
113 | This repository is a scientific product and is not official
114 | communication of the National Oceanic and Atmospheric Administration, or
115 | the United States Department of Commerce. All NOAA GitHub project code
116 | is provided on an ‘as is’ basis and the user assumes responsibility for
117 | its use. Any claims against the Department of Commerce or Department of
118 | Commerce bureaus stemming from the use of this GitHub project will be
119 | governed by all applicable Federal law. Any reference to specific
120 | commercial products, processes, or services by service mark, trademark,
121 | manufacturer, or otherwise, does not constitute or imply their
122 | endorsement, recommendation or favoring by the Department of Commerce.
123 | The Department of Commerce seal and logo, or the seal and logo of a DOC
124 | bureau, shall not be used in any manner to imply endorsement of any
125 | commercial product or activity by DOC or the United States Government.
126 |
127 | ## NOAA License
128 |
129 | Software code created by U.S. Government employees is not subject to
130 | copyright in the United States (17 U.S.C. §105). The United
131 | States/Department of Commerce reserve all rights to seek and obtain
132 | copyright protection in countries other than the United States for
133 | Software authored in its entirety by the Department of Commerce. To this
134 | end, the Department of Commerce hereby grants to Recipient a
135 | royalty-free, nonexclusive license to use, copy, and create derivative
136 | works of the Software outside of the United States.
137 |
138 |
139 |
140 | [U.S. Department of Commerce](https://www.commerce.gov/) | [National
141 | Oceanographic and Atmospheric Administration](https://www.noaa.gov) |
142 | [NOAA Fisheries](https://www.fisheries.noaa.gov/)
143 |
--------------------------------------------------------------------------------
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1 |
2 | License • NMFSReports
6 |
7 |
8 |
9 |
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94 |
95 |
96 |
97 |
98 |
99 | License
100 |
101 |
102 | YEAR: 2021
103 | COPYRIGHT HOLDER: Emily Markowitz
104 |
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9 | Record Metadata — CreateMetadata • NMFSReports
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1 |
2 | Changelog • NMFSReports
6 |
7 |
8 |
9 |
93 |
94 |
95 |
96 |
97 |
98 |
99 | Changelog
100 | Source: NEWS.md
101 |
102 |
103 |
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1 |
2 | Articles • NMFSReports
6 |
7 |
8 |
9 |
93 |
94 |
95 |
96 |
97 |
98 |
99 | Articles
100 |
101 |
102 |
103 | NMFS Reports Vignettes
104 | These vignettes provide an introduction to how to rewite reports using the NMFSReports package.
105 |
106 | - Use buildReport() to begin writing your report
107 | -
108 |
- How to use the run.R file to be the skeleton of your report
109 | -
110 |
- Functions and examples to help you write your report
111 | -
112 |
- System and packages used to build NMFSReports
113 | -
114 |
115 |
116 |
117 |
118 |
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22 |
23 |
24 | ### *Easily write NOAA reports and Tech Memos in R Markdown*
25 |
26 |
27 | ```{r, echo = FALSE, results='asis', message=FALSE}
28 | cat(
29 | badge_devel("EmilyMarkowitz-NOAA/NMFSReports", "blue"),
30 | badge_lifecycle("maturing", "blue"),
31 | badge_last_commit("EmilyMarkowitz-NOAA/NMFSReports")
32 | )
33 | ```
34 |
35 | ## Author
36 |
37 | **Emily Markowitz** (Emily.Markowitz AT noaa.gov)
38 |
39 | Alaska Fisheries Science Center,
40 |
41 | National Marine Fisheries Service,
42 |
43 | National Oceanic and Atmospheric Administration,
44 |
45 | Seattle, WA 98195
46 |
47 | ## Installation
48 |
49 | #### `NMFSReports`
50 |
51 | Learn more about this package at this [pkgdown webpage!](https://emilymarkowitz-noaa.github.io/NMFSReports/)
52 |
53 | The NMFSReports Package has all of the basic architecture you need to create reproducible and repeatable NOAA Tech Memos in R Markdown! This approach is perfect for efficiently rolling out annual (or other regular) reports or reports with formulaic sections (the same chapter structure but for a different area or species). Scripts integrate table, figure, data, and bibliography management and design automation.
54 |
55 |
56 | ```{r, eval=FALSE}
57 | library(devtools)
58 | devtools::install_github("EmilyMarkowitz-NOAA/NMFSReports")
59 | library(NMFSReports)
60 |
61 | # Or, alternatively,
62 | remotes::install_github("EmilyMarkowitz-NOAA/NMFSReports@main")
63 | ```
64 |
65 | #### You may also consider useing this package with `nmfspalette`
66 |
67 | A package for NOAA Fisheries color schemes. More info [here](https://github.com/nmfs-general-modeling-tools/nmfspalette).
68 |
69 | ```{r, eval=FALSE}
70 | library(devtools)
71 | devtools::install_github("nmfs-general-modeling-tools/nmfspalette")
72 | library(nmfspalette)
73 | ```
74 |
75 | ## Notes
76 |
77 | More details about how to use the [https://github.com/RVerse-Tutorials/GoogleDrive1]({googledrive} R pakage) in RMarkdown Documents:
78 |
79 |
80 | ## Conference Presentations
81 |
82 | Markowitz, EH. Reproducible Reports in R Markdown - Perspectives and {NMFSReports}. R Cascadia Conf., June 2021. Remote. ([Slides](https://github.com/EmilyMarkowitz-NOAA/NMFSReports/blob/main/presentations/2021-06-05NMFSReports-RCascadiaConf.pdf), [Recording of Presentation](https://www.youtube.com/watch?v=zNKdQ6jvr-M&list=PLzwtsyfF_Z4pPszfwklTD66AWUuMwS7qw&index=11))
83 |
84 | Markowitz, EH. Reproducible National-level Reports: Using RMarkdown to Recode the Fisheries Economics of the US Report.
85 |
86 | - Women in Statistics and Data Science Conf.; American Statistical Association, September 2020. Remote.
87 | - American Fisheries Society, September 2020. Remote.
88 | - SatRDay Conference, March 2020. Washington, D.C./Remote. ([Recording](https://youtu.be/-mycRwaC60A))
89 |
90 | ## Abstract
91 |
92 | Scientists in government and beyond are often tasked with preparing analysis-driven reports that inform policy and are crucial for documenting the state of their programs at regular intervals (e.g., annually, quarterly, monthly). Although these reports typically follow the same format for each iteration, updating content with new data from previous document line by line can lead to inefficient writing and introduce errors.
93 |
94 | Alternatively, R and R Markdown can be used to systematically modernize report creation. To address this need within our agency I have developed a new R package, `{NMFSReports}`, which uses R and R Markdown to provide an analysis-to-product approach to report writing by centralizing back-end data analyses and efficiently streamlining copy-edit and design sub-processes. The `{NMFSReports}` R package first creates the basic report outline and folder architecture to create reproducible reports, and then provides users with grammar and organization helper functions that assist in report writing. To aid in the final publication process, this workflow can also be used to produce intermediate output files for subject matter experts and collaborators to review and use. `{NMFSReports}` can produce copy-edit ready and accessibility-compliant documents for editors, style guide-formatted and flow-in ready text (including bibliography, footnote, figure, and table management) for authors, tables and figures for graphic designers, and web-ready data files for web tool developers. Though this package is in early stages of development, it is already clear it has the potential to save colleagues across our agency countless hours and improve efficiency and consistency among our teams and offices. Though developed for reports produced by scientists at NOAA Fisheries, the concepts and structures behind `{NMFSReports}` have utility for anyone seeking to streamline reports, graphics, and web tools.
95 |
96 | ## NOAA README
97 |
98 | This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.
99 |
100 | ## NOAA License
101 |
102 | Software code created by U.S. Government employees is not subject to copyright in the United States (17 U.S.C. §105). The United States/Department of Commerce reserve all rights to seek and obtain copyright protection in countries other than the United States for Software authored in its entirety by the Department of Commerce. To this end, the Department of Commerce hereby grants to Recipient a royalty-free, nonexclusive license to use, copy, and create derivative works of the Software outside of the United States.
103 |
104 |
105 |
106 |
107 | [U.S. Department of Commerce](https://www.commerce.gov/) | [National Oceanographic and Atmospheric Administration](https://www.noaa.gov) | [NOAA Fisheries](https://www.fisheries.noaa.gov/)
108 |
--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
1 |
2 |
3 | # **This repo has now been ARCHIVED AND DEPRECIATED.** Only use this repository for reference.
4 |
5 | # NMFSReports
6 |
7 | ### *Easily write NOAA reports and Tech Memos in R Markdown*
8 |
9 | [](https://github.com/EmilyMarkowitz-NOAA/NMFSReports)
10 | [](https://www.tidyverse.org/lifecycle/#maturing)
11 | [](https://github.com/EmilyMarkowitz-NOAA/NMFSReports/commits/master)
12 |
13 | ## Author
14 |
15 | **Emily Markowitz** (Emily.Markowitz AT noaa.gov)
16 |
17 | Alaska Fisheries Science Center,
18 |
19 | National Marine Fisheries Service,
20 |
21 | National Oceanic and Atmospheric Administration,
22 |
23 | Seattle, WA 98195
24 |
25 | ## Installation
26 |
27 | #### `NMFSReports`
28 |
29 | Learn more about this package at this [pkgdown
30 | webpage!](https://emilymarkowitz-noaa.github.io/NMFSReports/)
31 |
32 | The NMFSReports Package has all of the basic architecture you need to
33 | create reproducible and repeatable NOAA Tech Memos in R Markdown! This
34 | approach is perfect for efficiently rolling out annual (or other
35 | regular) reports or reports with formulaic sections (the same chapter
36 | structure but for a different area or species). Scripts integrate table,
37 | figure, data, and bibliography management and design automation.
38 |
39 | library(devtools)
40 | devtools::install_github("EmilyMarkowitz-NOAA/NMFSReports")
41 | library(NMFSReports)
42 |
43 | # Or, alternatively,
44 | remotes::install_github("EmilyMarkowitz-NOAA/NMFSReports@main")
45 |
46 | #### You may also consider useing this package with `nmfspalette`
47 |
48 | A package for NOAA Fisheries color schemes. More info
49 | [here](https://github.com/nmfs-general-modeling-tools/nmfspalette).
50 |
51 | library(devtools)
52 | devtools::install_github("nmfs-general-modeling-tools/nmfspalette")
53 | library(nmfspalette)
54 |
55 | ## Notes
56 |
57 | More details about how to use the
58 | [https://github.com/RVerse-Tutorials/GoogleDrive1](%7Bgoogledrive%7D%20R%20pakage)
59 | in RMarkdown Documents:
60 |
61 | ## Conference Presentations
62 |
63 | Markowitz, EH. Reproducible Reports in R Markdown - Perspectives and
64 | {NMFSReports}. R Cascadia Conf., June 2021. Remote.
65 | ([Slides](https://github.com/EmilyMarkowitz-NOAA/NMFSReports/blob/main/presentations/2021-06-05NMFSReports-RCascadiaConf.pdf),
66 | [Recording of
67 | Presentation](https://www.youtube.com/watch?v=zNKdQ6jvr-M&list=PLzwtsyfF_Z4pPszfwklTD66AWUuMwS7qw&index=11))
68 |
69 | Markowitz, EH. Reproducible National-level Reports: Using RMarkdown to
70 | Recode the Fisheries Economics of the US Report.
71 |
72 | - Women in Statistics and Data Science Conf.; American Statistical
73 | Association, September 2020. Remote.
74 | - American Fisheries Society, September 2020. Remote.
75 | - SatRDay Conference, March 2020. Washington, D.C./Remote.
76 | ([Recording](https://youtu.be/-mycRwaC60A))
77 |
78 | ## Abstract
79 |
80 | Scientists in government and beyond are often tasked with preparing
81 | analysis-driven reports that inform policy and are crucial for
82 | documenting the state of their programs at regular intervals (e.g.,
83 | annually, quarterly, monthly). Although these reports typically follow
84 | the same format for each iteration, updating content with new data from
85 | previous document line by line can lead to inefficient writing and
86 | introduce errors.
87 |
88 | Alternatively, R and R Markdown can be used to systematically modernize
89 | report creation. To address this need within our agency I have developed
90 | a new R package, `{NMFSReports}`, which uses R and R Markdown to provide
91 | an analysis-to-product approach to report writing by centralizing
92 | back-end data analyses and efficiently streamlining copy-edit and design
93 | sub-processes. The `{NMFSReports}` R package first creates the basic
94 | report outline and folder architecture to create reproducible reports,
95 | and then provides users with grammar and organization helper functions
96 | that assist in report writing. To aid in the final publication process,
97 | this workflow can also be used to produce intermediate output files for
98 | subject matter experts and collaborators to review and use.
99 | `{NMFSReports}` can produce copy-edit ready and accessibility-compliant
100 | documents for editors, style guide-formatted and flow-in ready text
101 | (including bibliography, footnote, figure, and table management) for
102 | authors, tables and figures for graphic designers, and web-ready data
103 | files for web tool developers. Though this package is in early stages of
104 | development, it is already clear it has the potential to save colleagues
105 | across our agency countless hours and improve efficiency and consistency
106 | among our teams and offices. Though developed for reports produced by
107 | scientists at NOAA Fisheries, the concepts and structures behind
108 | `{NMFSReports}` have utility for anyone seeking to streamline reports,
109 | graphics, and web tools.
110 |
111 | ## NOAA README
112 |
113 | This repository is a scientific product and is not official
114 | communication of the National Oceanic and Atmospheric Administration, or
115 | the United States Department of Commerce. All NOAA GitHub project code
116 | is provided on an ‘as is’ basis and the user assumes responsibility for
117 | its use. Any claims against the Department of Commerce or Department of
118 | Commerce bureaus stemming from the use of this GitHub project will be
119 | governed by all applicable Federal law. Any reference to specific
120 | commercial products, processes, or services by service mark, trademark,
121 | manufacturer, or otherwise, does not constitute or imply their
122 | endorsement, recommendation or favoring by the Department of Commerce.
123 | The Department of Commerce seal and logo, or the seal and logo of a DOC
124 | bureau, shall not be used in any manner to imply endorsement of any
125 | commercial product or activity by DOC or the United States Government.
126 |
127 | ## NOAA License
128 |
129 | Software code created by U.S. Government employees is not subject to
130 | copyright in the United States (17 U.S.C. §105). The United
131 | States/Department of Commerce reserve all rights to seek and obtain
132 | copyright protection in countries other than the United States for
133 | Software authored in its entirety by the Department of Commerce. To this
134 | end, the Department of Commerce hereby grants to Recipient a
135 | royalty-free, nonexclusive license to use, copy, and create derivative
136 | works of the Software outside of the United States.
137 |
138 |
139 |
140 | [U.S. Department of Commerce](https://www.commerce.gov/) | [National
141 | Oceanographic and Atmospheric Administration](https://www.noaa.gov) |
142 | [NOAA Fisheries](https://www.fisheries.noaa.gov/)
143 |
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102 | Articles
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115 | NMFS Reports Vignettes
104 |These vignettes provide an introduction to how to rewite reports using the NMFSReports package.
- Use buildReport() to begin writing your report 107 |
- 108 |
- How to use the run.R file to be the skeleton of your report 109 |
- 110 |
- Functions and examples to help you write your report 111 |
- 112 |
- System and packages used to build NMFSReports 113 |
- 114 |