From 1dae7c2119865f6a7afec4aa7220184a6f0d3d7d Mon Sep 17 00:00:00 2001 From: emilyhmarkowitz Date: Sun, 2 Jan 2022 01:50:40 -0500 Subject: [PATCH 1/9] added 0_figtab.Rmd to run.R script set up, added anchors to figures and tables so they can be linked through the document, and added changes to vignettes --- .Rbuildignore | 1 + .gitignore | 1 + DESCRIPTION | 2 +- R/NMFSReports.R | 23 ++- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/LICENSE.html | 2 +- docs/apple-touch-icon-120x120.png | Bin 11467 -> 11467 bytes docs/apple-touch-icon-152x152.png | Bin 15063 -> 15063 bytes docs/apple-touch-icon-180x180.png | Bin 18373 -> 18373 bytes docs/apple-touch-icon-60x60.png | Bin 4461 -> 4461 bytes docs/apple-touch-icon-76x76.png | Bin 6129 -> 6129 bytes docs/apple-touch-icon.png | Bin 18373 -> 18373 bytes docs/articles/A_use-buildReport.html | 4 +- docs/articles/B_run-script-demo.html | 128 ++++++++-------- .../C_functions-to-help-write-report.html | 137 +++++++++--------- docs/articles/E_thispkgwasbuiltusing.html | 4 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/favicon-16x16.png | Bin 1136 -> 1136 bytes docs/favicon-32x32.png | Bin 2215 -> 2215 bytes docs/index.html | 2 +- docs/news/index.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/TitleCase.html | 2 +- docs/reference/add_table_footnotes.html | 2 +- docs/reference/auto_counter.html | 2 +- docs/reference/buildReport.html | 2 +- docs/reference/create_metadata.html | 2 +- docs/reference/crossref.html | 28 ++-- docs/reference/df2js.html | 2 +- docs/reference/format_cells.html | 2 +- docs/reference/googledrive_txt_dl.html | 2 +- docs/reference/index.html | 4 +- .../is_something_in_this_matrix.html | 2 +- docs/reference/mod_number.html | 2 +- docs/reference/numbers0.html | 2 +- docs/reference/numbers2words.html | 2 +- docs/reference/numbers2words_th.html | 2 +- docs/reference/pchange.html | 2 +- docs/reference/save_equations.html | 10 +- docs/reference/save_figures.html | 8 +- docs/reference/save_tables.html | 8 +- docs/reference/stndth.html | 2 +- docs/reference/text_list.html | 2 +- docs/reference/theme_flextable_nmfstm.html | 2 +- docs/reference/tolower2.html | 2 +- docs/reference/xunits.html | 2 +- docs/reference/xunitspct.html | 2 +- inst/rmd/0_figtab.Rmd | 73 ++++++++++ inst/rmd/_child_save_fig.Rmd | 1 + inst/rmd/run.R | 27 ++-- man/crossref.Rd | 4 +- notes.R | 2 +- pkgdown/favicon/apple-touch-icon-120x120.png | Bin 11467 -> 11467 bytes pkgdown/favicon/apple-touch-icon-152x152.png | Bin 15063 -> 15063 bytes pkgdown/favicon/apple-touch-icon-180x180.png | Bin 18373 -> 18373 bytes pkgdown/favicon/apple-touch-icon-60x60.png | Bin 4461 -> 4461 bytes pkgdown/favicon/apple-touch-icon-76x76.png | Bin 6129 -> 6129 bytes pkgdown/favicon/apple-touch-icon.png | Bin 18373 -> 18373 bytes pkgdown/favicon/favicon-16x16.png | Bin 1136 -> 1136 bytes pkgdown/favicon/favicon-32x32.png | Bin 2215 -> 2215 bytes .../2example6_tab_2_ex_table_foot_print.csv | 10 -- .../2example6_tab_2_ex_table_foot_raw.csv | 10 -- ..._noaalogo.rdata => 4_fig_2_noaalogo.rdata} | Bin 524234 -> 524239 bytes vignettes/B_run-script-demo.Rmd | 124 ++++++++-------- .../C_functions-to-help-write-report.Rmd | 2 + 67 files changed, 378 insertions(+), 289 deletions(-) create mode 100644 inst/rmd/0_figtab.Rmd delete mode 100644 vignettes/2example6_tab_2_ex_table_foot_print.csv delete mode 100644 vignettes/2example6_tab_2_ex_table_foot_raw.csv rename vignettes/{example4_fig_2_noaalogo.rdata => 4_fig_2_noaalogo.rdata} (99%) diff --git a/.Rbuildignore b/.Rbuildignore index 03f0d35..0061729 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -15,3 +15,4 @@ ^doc$ ^docs$ +^documentation$ diff --git a/.gitignore b/.gitignore index 8b9a43e..12f08a7 100644 --- a/.gitignore +++ b/.gitignore @@ -15,3 +15,4 @@ vignettes/*.zip /doc/ docs +/documentation/ diff --git a/DESCRIPTION b/DESCRIPTION index 8951c02..135af7b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: NMFSReports Title: Easily write NOAA reports and Tech Memos in R Markdown! -Version: 0.0.1.1 +Version: 0.0.1.2 Authors@R: person(given = "Emily", family = "Markowitz", diff --git a/R/NMFSReports.R b/R/NMFSReports.R index e5d121c..e9d5ddc 100644 --- a/R/NMFSReports.R +++ b/R/NMFSReports.R @@ -64,6 +64,13 @@ buildReport<-function( # Now... Load those folders with stuff you care about ################## RMD scripts + + # Add figtab + file.copy(from = system.file("rmd", "0_figtab.Rmd", package="NMFSReports"), + to = "./code/0_figtab.Rmd", + overwrite = T) + + # add other files a <- list.files(path = system.file("rmd", package="NMFSReports"), pattern = "0_") b <- c("example", sections) if (!(is.null(styles_reference_pptx))) { @@ -221,6 +228,7 @@ buildReport<-function( # INSERT_SECTIONS b <- list.files(path = "./code/", pattern = ".Rmd") # find the files that are already there + b <- b[b != "0_figtab.Rmd"] bb <- strsplit(x = b, split = "_") sections_no <- unlist(lapply(bb, `[[`, 1)) bb <- strsplit(x = b, split = "[0-9]+_") @@ -1322,7 +1330,7 @@ save_figures<-function(figure, # Title header<-trimws(header) - header<-paste0(type, " ",cnt,". ", + header<-paste0(type, " [",cnt,"](){#",nickname,"}. ", ifelse(substr(x = header, start = nchar(header), stop = nchar(header)) %in% @@ -1333,7 +1341,8 @@ save_figures<-function(figure, header, paste0(header, paste(paste0("^[", footnotes, "]"), collapse = " ^,^ "))) - filename00<-paste0(filename0, cnt_chapt_content, "_fig_",cnt, + filename00<-paste0(#filename0, + cnt_chapt_content, "_fig_",cnt, ifelse(filename_desc!="", paste0("_", filename_desc), "")) # Save @@ -1463,7 +1472,7 @@ save_tables<-function(table_raw = NULL, # Title header<-trimws(header) # header<-stringr::str_to_sentence(header) - header<-paste0(type, " ",cnt,". ", + header<-paste0(type, " [",cnt,"](){#",nickname,"}. ", ifelse(substr(x = header, start = nchar(header), stop = nchar(header)) %in% @@ -1474,7 +1483,8 @@ save_tables<-function(table_raw = NULL, header, paste0(header, paste(paste0("^[", footnotes, "]"), collapse = " ^,^ "))) - filename00<-paste0(filename0, cnt_chapt_content, "_tab_",cnt, + filename00<-paste0(#filename0, + cnt_chapt_content, "_tab_",cnt, ifelse(filename_desc!="", paste0("_", filename_desc), "")) # Save if (!is.null(path)){ @@ -1588,7 +1598,7 @@ save_equations<-function(equation, # Title header<-trimws(header) # header<-stringr::str_to_sentence(header) - header<-paste0(type, " ",cnt,". ", + header<-paste0(type, " [",cnt,"](){#",nickname,"}. ", ifelse(substr(x = header, start = nchar(header), stop = nchar(header)) %in% @@ -1613,7 +1623,7 @@ save_equations<-function(equation, return(list_equations ) } -#' Reference a figure, table, or equation (or other list elements!) +#' Reference a figure, table, or equation with an anchored tag #' #' @param list_obj A list object created by list_figures or list_tables. #' @param nickname A unique string that is used to identify the plot or table in list_figures or list_tables, respectively. @@ -1651,6 +1661,7 @@ crossref <- function(list_obj, ref <- list_obj[which(lapply(list_obj, `[[`, "nickname") %in% nickname)][[1]][sublist] if (sublist == "number") { ref<-as.character(ref) + ref<-paste0("[", ref, "](#", nickname, ")") } return(ref) } diff --git a/docs/404.html b/docs/404.html index e9b68cd..483fbea 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index c700a23..0e6abd4 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 27d014c..4b98da5 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -81,7 +81,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/apple-touch-icon-120x120.png b/docs/apple-touch-icon-120x120.png index c64f2f70057f09a95d97d59805781bfb85e1208d..116fc05b2c55c33c901c76990e482c9e68be383f 100644 GIT binary patch delta 101 zcmX>dc{*}J1=ll1CN>?O^{ZYOZ*1z<_BPTrFw`|L3NbLVGBL3-G}1OOure?($PvHI lz`&qd;u=wsl30>zm7AZEnO4bQWMG6{gQMa4^vN+g`2ah#9Yz2E delta 101 zcmX>dc{*}J1=mv^0X|uYpIXlT8=LyIy$y8@jdTsoLJUo;j4Z8;OtcLQtPBh$eqFwt mfq_A_#5JNMC9x#cDmOnRGp&-r$iN7@h6gL;r6?O^{ZYOZ)}=v>20KIV5n60_8@&RK)9m)Uz delta 101 zcmca!dcAZ)1=mv^0X|vDKHcJ*8=GcZdK>B*8tEFEg&3Mx8ChBxnQ9vtSQ!|YH?0w7 lU|>)!ag8WRNi0dV%FR#7OsixtGBCof!R@}t`pFqq`2b4`9o+x` diff --git a/docs/apple-touch-icon-180x180.png b/docs/apple-touch-icon-180x180.png index 5144d6b9289895a6e1bacd9a55685ddf8520cc18..e4c00b8661f6c2f91b1e9b9702046de048e4146d 100644 GIT binary patch delta 103 zcmX@w&v>+-aY6;xGe#yh9o`#jZ!F!|)amAJq-$WPYhV;&U}j}vVr6KoZD3$!U@%Qu oCZB+-aY6;xQyu|6St)T9rR0rGoo?QSx`sx&hGrp#CRRq4Rz_yp1_o9J25ec| n`WP4(R7+eVN>UO_Qmu0HQ!>*k8H@~!uxltc=QEld=AI7#?4cXu diff --git a/docs/apple-touch-icon-60x60.png b/docs/apple-touch-icon-60x60.png index 6fd6a4e3f18e2d1de9b3011820679e086796e268..08c70e7a4b333f4586a0a3e6653d4dd6940af418 100644 GIT binary patch delta 83 zcmaE>^j2v?1=ll1CN>>z!*jJ0HZ~awNEzuG80s1rg&3GwnV47^8fqIDSQ!{Fw(z=5 TJ}V%OL%QJR)?btV3FHF+?jIOR delta 83 zcmaE>^j2v?1=mv^0X|tVxk-5*8=DLTqzrWpjdTsoLJUo;j4Z8;jI<35tPBi3sZN?Z S`K*9A4(a9!Eyc>z!*jJ0Ha2Y)lQPmZFw`|L3NbLVGBL3-G}JaQure@UY~gjA S94Ic1L%QJR)?bsG#Pb0Pdl(D= delta 83 zcmeyU|51NJ1=mv^0X|vr%&BqrHa2Y)lQPsbG}1LR3o$gYGP1NXGS)UQure?R37V-n SIZ#|2hqNlc;?&7a;`sn7AQtZc diff --git a/docs/apple-touch-icon.png b/docs/apple-touch-icon.png index 36638b2b62614a6bb8dff0a7771087c9b6226a31..40d7d12dfc7534dca062773abff0e7c525b33769 100644 GIT binary patch delta 103 zcmX@w&v>+-aY6;xGe#yh9X`h;o$?!-I^DdDbPWu34U9qz%&bgItPD-G4GgRd41)J4 nJ!D{DP%UwdC`m~yNwvz&PsvQHWH2%?!mdH-;jGxnVea_=KTI9x delta 103 zcmX@w&v>+-aY6;xQyu|6S?L62p|2a8I^Dbtbq$Sl4b4IfO{|P8t&GgI4GgRd3>L`l nwPIjkP%UwdC`m~yNwvz&PsvQHWH2%?!mi<>18dvlF!y`_HtQW; diff --git a/docs/articles/A_use-buildReport.html b/docs/articles/A_use-buildReport.html index c28630d..e309d4f 100644 --- a/docs/articles/A_use-buildReport.html +++ b/docs/articles/A_use-buildReport.html @@ -39,7 +39,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 @@ -129,7 +129,7 @@

Use buildReport() to begin writing your report

-

December 16 2021

+

January 02 2022

Source: vignettes/A_use-buildReport.Rmd diff --git a/docs/articles/B_run-script-demo.html b/docs/articles/B_run-script-demo.html index b1e077b..0baa3ec 100644 --- a/docs/articles/B_run-script-demo.html +++ b/docs/articles/B_run-script-demo.html @@ -39,7 +39,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2
@@ -129,7 +129,7 @@

How to use the run.R file to be the skeleton of your report

-

December 16 2021

+

January 02 2022

Source: vignettes/B_run-script-demo.Rmd @@ -156,7 +156,6 @@

December 16 2021

# Run buildReport() function buildReport( sections = sections, - support_scripts = support_scripts, report_authors = authors, report_title = title, styles_reference_pptx = styles_reference_pptx, @@ -170,19 +169,19 @@

December 16 2021

run.R

#' ---
-#' title: Awesome Report!
-#' author: Me, Myself, and I
+#' title: 'Awesome Report!'
+#' author: 'Me, Myself, and I'
 #' purpose: Run Scripts and R Markdown Files
-#' start date: 2021-03-03
-#' date modified: 2021-03-03                                            # CHANGE
+#' start date: 2022-01-02
+#' date modified: 2022-01-02                                          # CHANGE
 #' Notes:                                                               # CHANGE
 #' ---
 
 # START ------------------------------------------------------------------------
 
 # *** REPORT KNOWNS ------------------------------------------------------------
-report_title <- "Awesome Report!"
-report_authors <- "Me, Myself, and I"
+report_title <- 'Awesome Report!'
+report_authors <- 'Me, Myself, and I'
 report_yr <- substr(x = Sys.Date(), start = 1, stop = 4)            # SUGGESTION
 
 # *** OUTPUT TYPE --------------------------------------------------------------
@@ -191,13 +190,15 @@ 

 
 # *** SOURCE SUPPORT SCRIPTS ---------------------------------------------------
 
-source('./code/directories.R' )
+source('./code/directories.R')
 
-source('./code/functions.R' )
+source('./code/functions.R')
+
+source('./code/dataDL.R')
+
+source('./code/data.R')
 
-source('./code/dataDL.R' )
 
-source('./code/data.R' )
 
 # *** RENV: SAVE PACKAGES USED TO CREATE THIS REPORT ---------------------------
 # renv::init()
@@ -209,105 +210,110 @@ 

 # googledrive::drive_auth()
 # 1
 
-# MAKE REPORT ------------------------------------------------------------------
+# RUN FIGURES, TABLES, & EQUATIONS FOR REPORT ----------------------------------
+
+if (FALSE) {
+  cnt_chapt_content<-"000"
+  filename0<-paste0(cnt_chapt, "_")
+  rmarkdown::render(paste0(dir_code, "/0_figtab.Rmd"),
+                    output_dir = dir_out_ref,
+                    output_file = paste0(filename0, cnt_chapt_content, ".docx"))
+
+  save(list_figures, file=paste0(dir_out_figures, "/report_figures.rdata"))
+  save(list_tables, file=paste0(dir_out_tables, "/report_tables.rdata"))
+  save(list_equations, file=paste0(dir_out_tables, "/report_equations.rdata"))
+}
 
-# *** HOUSEKEEPING -------------------------------------------------------------
+load(file = paste0(dir_out_figures, "/report_figures.rdata"))
+load(file = paste0(dir_out_tables, "/report_tables.rdata"))
+load(file = paste0(list_equations, "/report_equations.rdata"))
 
-# Keep chapter content in a proper order
-cnt_chapt <- "000"
-# Automatically name objects with consecutive numbers
-cnt_figures <- 0 #  e.g., Figure 1
-cnt_tables <- 0 # e.g., Table 1
-cnt_equations <- 0 # e.g., Equation 1
-# Save object content
-list_equations <- list()
-list_tables <- list()
-list_figures <- list()
+# RUN EACH REPORT SECTION ------------------------------------------------------
 
 # *** RUN EACH REPORT SECTION --------------------------------------------------
 
-# *** *** 0 - Example ----------------------------
+
+# *** 0 - Example ------------------------
 cnt_chapt<-auto_counter(cnt_chapt)
 cnt_chapt_content<-"001"
 filename0<-paste0(cnt_chapt, "_example_")
 rmarkdown::render(paste0(dir_code, "/0_example.Rmd"),
-                    output_dir = dir_out_chapters,
-                    output_file = paste0(filename0, cnt_chapt_content, ".docx"))
+                  output_dir = dir_out_chapters,
+                  output_file = paste0(filename0, cnt_chapt_content, ".docx"))
+
 
-# *** *** 1 - Frontmatter ----------------------------
+# *** 1 - Frontmatter ------------------------
 cnt_chapt<-auto_counter(cnt_chapt)
 cnt_chapt_content<-"001"
 filename0<-paste0(cnt_chapt, "_frontmatter_")
 rmarkdown::render(paste0(dir_code, "/1_frontmatter.Rmd"),
-                    output_dir = dir_out_chapters,
-                    output_file = paste0(filename0, cnt_chapt_content, ".docx"))
+                  output_dir = dir_out_chapters,
+                  output_file = paste0(filename0, cnt_chapt_content, ".docx"))
 
-# *** *** 2 - Abstract ----------------------------
+
+# *** 2 - Abstract ------------------------
 cnt_chapt<-auto_counter(cnt_chapt)
 cnt_chapt_content<-"001"
 filename0<-paste0(cnt_chapt, "_abstract_")
 rmarkdown::render(paste0(dir_code, "/2_abstract.Rmd"),
-                    output_dir = dir_out_chapters,
-                    output_file = paste0(filename0, cnt_chapt_content, ".docx"))
+                  output_dir = dir_out_chapters,
+                  output_file = paste0(filename0, cnt_chapt_content, ".docx"))
+
 
-# *** *** 3 - Introduction ----------------------------
+# *** 3 - Introduction ------------------------
 cnt_chapt<-auto_counter(cnt_chapt)
 cnt_chapt_content<-"001"
 filename0<-paste0(cnt_chapt, "_introduction_")
 rmarkdown::render(paste0(dir_code, "/3_introduction.Rmd"),
-                    output_dir = dir_out_chapters,
-                    output_file = paste0(filename0, cnt_chapt_content, ".docx"))
+                  output_dir = dir_out_chapters,
+                  output_file = paste0(filename0, cnt_chapt_content, ".docx"))
+
 
-# *** *** 4 - Methods ----------------------------
+# *** 4 - Methods ------------------------
 cnt_chapt<-auto_counter(cnt_chapt)
 cnt_chapt_content<-"001"
 filename0<-paste0(cnt_chapt, "_methods_")
 rmarkdown::render(paste0(dir_code, "/4_methods.Rmd"),
-                    output_dir = dir_out_chapters,
-                    output_file = paste0(filename0, cnt_chapt_content, ".docx"))
+                  output_dir = dir_out_chapters,
+                  output_file = paste0(filename0, cnt_chapt_content, ".docx"))
 
-# *** *** 5 - Results ----------------------------
+
+# *** 5 - Results ------------------------
 cnt_chapt<-auto_counter(cnt_chapt)
 cnt_chapt_content<-"001"
 filename0<-paste0(cnt_chapt, "_results_")
 rmarkdown::render(paste0(dir_code, "/5_results.Rmd"),
-                    output_dir = dir_out_chapters,
-                    output_file = paste0(filename0, cnt_chapt_content, ".docx"))
+                  output_dir = dir_out_chapters,
+                  output_file = paste0(filename0, cnt_chapt_content, ".docx"))
+
 
-# *** *** 6 - Discussion ----------------------------
+# *** 6 - Discussion ------------------------
 cnt_chapt<-auto_counter(cnt_chapt)
 cnt_chapt_content<-"001"
 filename0<-paste0(cnt_chapt, "_discussion_")
 rmarkdown::render(paste0(dir_code, "/6_discussion.Rmd"),
-                    output_dir = dir_out_chapters,
-                    output_file = paste0(filename0, cnt_chapt_content, ".docx"))
+                  output_dir = dir_out_chapters,
+                  output_file = paste0(filename0, cnt_chapt_content, ".docx"))
+
 
-# *** *** 7 - Endmatter ----------------------------
+# *** 7 - Endmatter ------------------------
 cnt_chapt<-auto_counter(cnt_chapt)
 cnt_chapt_content<-"001"
 filename0<-paste0(cnt_chapt, "_endmatter_")
 rmarkdown::render(paste0(dir_code, "/7_endmatter.Rmd"),
-                    output_dir = dir_out_chapters,
-                    output_file = paste0(filename0, cnt_chapt_content, ".docx"))
+                  output_dir = dir_out_chapters,
+                  output_file = paste0(filename0, cnt_chapt_content, ".docx"))
 
-# *** *** 8 - Presentation ----------------------------
+
+# *** 8 - Presentation ------------------------
 cnt_chapt<-auto_counter(cnt_chapt)
 cnt_chapt_content<-"001"
 filename0<-paste0(cnt_chapt, "_presentation_")
 rmarkdown::render(paste0(dir_code, "/8_presentation.Rmd"),
-                      output_dir = dir_out_chapters,
-                      output_file = paste0(filename0, cnt_chapt_content, ".pptx"))
-
-# SAVE OTHER OUTPUTS -----------------------------------------------------------
-
-save(list_figures,
-     file=paste0(dir_out_figures, "/report_figures.rdata"))
+                  output_dir = dir_out_chapters,
+                  output_file = paste0(filename0, cnt_chapt_content, ".pptx"))
 
-save(list_tables,
-     file=paste0(dir_out_tables, "/report_tables.rdata"))
 
-save(list_equations,
-     file=paste0(dir_out_tables, "/report_equations.rdata"))
 
 # MAKE MASTER DOCX -------------------------------------------------------------
 
diff --git a/docs/articles/C_functions-to-help-write-report.html b/docs/articles/C_functions-to-help-write-report.html
index 6fca0cd..aa7129f 100644
--- a/docs/articles/C_functions-to-help-write-report.html
+++ b/docs/articles/C_functions-to-help-write-report.html
@@ -39,7 +39,7 @@
       
       
         NMFSReports
-        0.0.1.1
+        0.0.1.2
@@ -130,7 +130,7 @@

Functions and examples to help you write your report

-

December 16 2021

+

January 02 2022

Source: vignettes/C_functions-to-help-write-report.Rmd @@ -199,7 +199,7 @@

# ```{r, child = system.file("rmd/_child_save_eq.Rmd", package = "NMFSReports")} # ```

-

Equation 1. Pythagorean theorem.3

+

Equation 1. Pythagorean theorem.3

\[c^2 = b^2 + a^2\]

Alternative text: The Pythagoras theorem is a mathematical law that states that the sum of squares of the lengths of the two short sides of the right triangle is equal to the square of the length of the hypotenuse.

[Text blah blah]

@@ -215,10 +215,10 @@

quiet = TRUE ) # `r res `

-

Equation 2. Newton’s Universal Law of Gravitation.

+

Equation 2. Newton’s Universal Law of Gravitation.

\[F = G \frac {m_1 m_2}{d^2}\]

Alternative text: Newton’s Universal Law of Gravitation

-

Remember the pythagorean theorem from before? That was Equation #1 and it had a footnote that said “footnote about how cool the pythagorean theorem is.”

+

Remember the pythagorean theorem from before? That was Equation #1 and it had a footnote that said “footnote about how cool the pythagorean theorem is.”

@@ -247,7 +247,7 @@

Alternative text: This is a scatter plot of random data.

-

Here in plot 1, we see that…

+

Here in plot 1, we see that…

@@ -276,11 +276,12 @@

Alternative text: The NOAA Meatball and text.

-

Here in figure 2, we see the NOAA logo.

+

Here in figure 2, we see the NOAA logo.

Example Table (Basic)

+

Here, we use the function theme_flextable_nmfstm which mimics many of the NMFS report tech memo motifs.

 header <- "Here is a table!"
 footnote<-"A footnote for this table!"
@@ -311,9 +312,9 @@ 

 # ```

-Table 1. Here is a table!

+Table 1. Here is a table!

-
+

Alternative text: This is a 3-column table of random letters (in the first column) and numbers (in the second and third columns).

-

Here in table 1, we see that…

+

Here in table 1, we see that…

@@ -501,7 +502,7 @@

# `r res `

-Table 2. Here is a table!

+Table 2. Here is a table!

@@ -512,64 +513,64 @@

- + - - + - - + - + - - + + - - + + - - + + - - + + - - + + - - + +
A10.48 -1.6
B1.24 ,5 +-0.474 ,5 -1.8-0.78
C6 0.287 +0.67 0.5-1
D8 ,9 -0.32-0.36 -0.26
E0.730.15-1.3-0.26
F0.063-1.2-0.9-0.26
G-1.3-2.50.651.4
H-0.361.10.652.8
I-2.20.111.5-0.66
J0.170.13-0.58-1.5

Alternative text: Here is a table!

-

Here in table 2, we see that…

+

Here in table 2, we see that…

diff --git a/docs/articles/E_thispkgwasbuiltusing.html b/docs/articles/E_thispkgwasbuiltusing.html index 34c4552..07b8a83 100644 --- a/docs/articles/E_thispkgwasbuiltusing.html +++ b/docs/articles/E_thispkgwasbuiltusing.html @@ -39,7 +39,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2
@@ -129,7 +129,7 @@

System and packages used to build NMFSReports

-

December 16 2021

+

January 02 2022

Source: vignettes/E_thispkgwasbuiltusing.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 8a87572..30025cf 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2
diff --git a/docs/authors.html b/docs/authors.html index 8af4c38..ad35bf5 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/favicon-16x16.png b/docs/favicon-16x16.png index 1c90a850b17c133bbe68d87999e65b85e05f7d2f..27e436fa3bd05ae6f39d7dee68a94e9cbe2674db 100644 GIT binary patch delta 85 zcmeys@quGQCll8*MkY2Lf!(XO)NG#2q|7K~q-$WPYhV;&U}j}vVr6KiZD3$!U~oj) V_{8K3%;Gqtx7Kx+OlD-s2LM0r7!d#f delta 85 zcmeys@quGQCll9G9sxdCg^L=$FK(X9q|7K~sB37XYiJf?Xkuk#X=QArZD3$!U|`oj ViFxt`W^o+S{+G1&PiADv2LMA~7sUVo diff --git a/docs/favicon-32x32.png b/docs/favicon-32x32.png index 641a014d161e833095d567d7fdd2abf0d333a1b8..7399bce36e12f31441d9794e53879bf845447843 100644 GIT binary patch delta 101 zcmZ23xLj~T1=ll1CN>?xGizF2ZEVVB_cqcsFw`|L3NbLVGBL3-G}ksTure@63bCkR lU|>)!ag8WRNi0dV%FR#7OsixtGBCofL721Qz+?-Kd;suR91j2h delta 101 zcmZ23xLj~T1=mv^0X|v9W%{SxH#TLndmHK+8tEFEg&3Mx8ChBx8*3XFSQ!}1_%U-k m0|SFRc?MtW?ChKk%19*4KJ4}a! NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/news/index.html b/docs/news/index.html index 331d5b6..9c5b143 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 94d7cb3..9e279dc 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -6,7 +6,7 @@ articles: B_run-script-demo: B_run-script-demo.html C_functions-to-help-write-report: C_functions-to-help-write-report.html E_thispkgwasbuiltusing: E_thispkgwasbuiltusing.html -last_built: 2021-12-16T14:30Z +last_built: 2022-01-02T06:44Z urls: reference: https://emilymarkowitz-noaa.github.io/NMFSReports//reference article: https://emilymarkowitz-noaa.github.io/NMFSReports//articles diff --git a/docs/reference/TitleCase.html b/docs/reference/TitleCase.html index 60287b8..65088b4 100644 --- a/docs/reference/TitleCase.html +++ b/docs/reference/TitleCase.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/add_table_footnotes.html b/docs/reference/add_table_footnotes.html index db83491..df11099 100644 --- a/docs/reference/add_table_footnotes.html +++ b/docs/reference/add_table_footnotes.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/auto_counter.html b/docs/reference/auto_counter.html index c59393a..b323a65 100644 --- a/docs/reference/auto_counter.html +++ b/docs/reference/auto_counter.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/buildReport.html b/docs/reference/buildReport.html index 4c8b6c6..6c37bc9 100644 --- a/docs/reference/buildReport.html +++ b/docs/reference/buildReport.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/create_metadata.html b/docs/reference/create_metadata.html index f62bbec..e99a083 100644 --- a/docs/reference/create_metadata.html +++ b/docs/reference/create_metadata.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/crossref.html b/docs/reference/crossref.html index 0505150..8bece05 100644 --- a/docs/reference/crossref.html +++ b/docs/reference/crossref.html @@ -6,7 +6,7 @@ -Reference a figure, table, or equation (or other list elements!) — crossref • NMFSReports +Reference a figure, table, or equation with an anchored tag — crossref • NMFSReports @@ -48,8 +48,8 @@ - - + + @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 @@ -170,13 +170,13 @@
-

Reference a figure, table, or equation (or other list elements!)

+

Reference a figure, table, or equation with an anchored tag

Source: R/NMFSReports.R
-

Reference a figure, table, or equation (or other list elements!)

+

Reference a figure, table, or equation with an anchored tag

crossref(list_obj, nickname, sublist = "number")
@@ -220,10 +220,10 @@

Examp cnt = "013") list_figures

#> $example_figure #> $example_figure$caption -#> [1] "Figure 012. blah blah blah." +#> [1] "Figure [012](){#example_figure}. blah blah blah." #> #> $example_figure$header -#> [1] "Figure 012. blah blah blah." +#> [1] "Figure [012](){#example_figure}. blah blah blah." #> #> $example_figure$nickname #> [1] "example_figure" @@ -238,15 +238,15 @@

Examp #> [1] "" #> #> $example_figure$filename -#> [1] "x003_fig_012" +#> [1] "003_fig_012" #> #> #> $example_figure_other #> $example_figure_other$caption -#> [1] "Figure 013. blah blah blah." +#> [1] "Figure [013](){#example_figure_other}. blah blah blah." #> #> $example_figure_other$header -#> [1] "Figure 013. blah blah blah." +#> [1] "Figure [013](){#example_figure_other}. blah blah blah." #> #> $example_figure_other$nickname #> [1] "example_figure_other" @@ -261,14 +261,14 @@

Examp #> [1] "" #> #> $example_figure_other$filename -#> [1] "x003_fig_013" +#> [1] "003_fig_013" #> #>

refnum <- NMFSReports::crossref( list_obj = list_figures, nickname = "example_figure", sublist = "number") -refnum
#> [1] "012"
print(paste0("Please refer to figure ", refnum, - " to see this figure, not the other figure."))
#> [1] "Please refer to figure 012 to see this figure, not the other figure."
+refnum
#> [1] "[012](#example_figure)"
print(paste0("Please refer to figure ", refnum, + " to see this figure, not the other figure."))
#> [1] "Please refer to figure [012](#example_figure) to see this figure, not the other figure."
diff --git a/docs/reference/format_cells.html b/docs/reference/format_cells.html index 370822b..b37500d 100644 --- a/docs/reference/format_cells.html +++ b/docs/reference/format_cells.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/googledrive_txt_dl.html b/docs/reference/googledrive_txt_dl.html index f430aef..c9163ba 100644 --- a/docs/reference/googledrive_txt_dl.html +++ b/docs/reference/googledrive_txt_dl.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/index.html b/docs/reference/index.html index 29a0f80..5b8fb66 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 @@ -382,7 +382,7 @@

crossref()

-

Reference a figure, table, or equation (or other list elements!)

+

Reference a figure, table, or equation with an anchored tag

diff --git a/docs/reference/is_something_in_this_matrix.html b/docs/reference/is_something_in_this_matrix.html index f7a9610..f30267b 100644 --- a/docs/reference/is_something_in_this_matrix.html +++ b/docs/reference/is_something_in_this_matrix.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/mod_number.html b/docs/reference/mod_number.html index aa716c3..753910e 100644 --- a/docs/reference/mod_number.html +++ b/docs/reference/mod_number.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/numbers0.html b/docs/reference/numbers0.html index 61aaef3..41ec8ee 100644 --- a/docs/reference/numbers0.html +++ b/docs/reference/numbers0.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/numbers2words.html b/docs/reference/numbers2words.html index 4ed2249..5e76548 100644 --- a/docs/reference/numbers2words.html +++ b/docs/reference/numbers2words.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/numbers2words_th.html b/docs/reference/numbers2words_th.html index 601bdc5..c81eb90 100644 --- a/docs/reference/numbers2words_th.html +++ b/docs/reference/numbers2words_th.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/pchange.html b/docs/reference/pchange.html index e1680bd..186403d 100644 --- a/docs/reference/pchange.html +++ b/docs/reference/pchange.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/save_equations.html b/docs/reference/save_equations.html index 6ba81cc..bb08ea5 100644 --- a/docs/reference/save_equations.html +++ b/docs/reference/save_equations.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 @@ -268,10 +268,10 @@

Examp #> [1] "$$c^2 = b^2 + a^2$$" #> #> $pythagorean$caption -#> [1] "Equation 1. Pythagorean theorem.^[footnote about how cool the pythagorean theorem is.]" +#> [1] "Equation [1](){#pythagorean}. Pythagorean theorem.^[footnote about how cool the pythagorean theorem is.]" #> #> $pythagorean$header -#> [1] "Equation 1. Pythagorean theorem." +#> [1] "Equation [1](){#pythagorean}. Pythagorean theorem." #> #> $pythagorean$nickname #> [1] "pythagorean" @@ -291,10 +291,10 @@

Examp #> [1] "$$F = G \frac{m_1 m_2}{d^2}$$" #> #> $Newton$caption -#> [1] "Equation 2. Newton's Universal Law of Gravitation." +#> [1] "Equation [2](){#Newton}. Newton's Universal Law of Gravitation." #> #> $Newton$header -#> [1] "Equation 2. Newton's Universal Law of Gravitation." +#> [1] "Equation [2](){#Newton}. Newton's Universal Law of Gravitation." #> #> $Newton$nickname #> [1] "Newton" diff --git a/docs/reference/save_figures.html b/docs/reference/save_figures.html index 453115c..3bb79ac 100644 --- a/docs/reference/save_figures.html +++ b/docs/reference/save_figures.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 @@ -294,10 +294,10 @@

Examp footnote = "footnote example") names(list_figures)
#> [1] ""
list_figures
#> [[1]] #> [[1]]$caption -#> [1] "Figure 1. example.^[footnote example]" +#> [1] "Figure [1](){#}. example.^[footnote example]" #> #> [[1]]$header -#> [1] "Figure 1. example." +#> [1] "Figure [1](){#}. example." #> #> [[1]]$nickname #> [1] "" @@ -312,7 +312,7 @@

Examp #> [1] "footnote example" #> #> [[1]]$filename -#> [1] "x001_fig_1" +#> [1] "001_fig_1" #> #>

diff --git a/docs/reference/save_tables.html b/docs/reference/save_tables.html index 2c5ed99..a66e39f 100644 --- a/docs/reference/save_tables.html +++ b/docs/reference/save_tables.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 @@ -304,10 +304,10 @@

Examp #> 10 0.13 -0.11 a #> #> [[1]]$caption -#> [1] "Table 1. Here is a table!^[A footnote for this table!]" +#> [1] "Table [1](){#}. Here is a table!^[A footnote for this table!]" #> #> [[1]]$header -#> [1] "Table 1. Here is a table!" +#> [1] "Table [1](){#}. Here is a table!" #> #> [[1]]$nickname #> [1] "" @@ -322,7 +322,7 @@

Examp #> [1] "A footnote for this table!" #> #> [[1]]$filename -#> [1] "x001_tab_1" +#> [1] "001_tab_1" #> #> diff --git a/docs/reference/stndth.html b/docs/reference/stndth.html index c53e7e4..4bd2d3d 100644 --- a/docs/reference/stndth.html +++ b/docs/reference/stndth.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/text_list.html b/docs/reference/text_list.html index c09fca0..404c41a 100644 --- a/docs/reference/text_list.html +++ b/docs/reference/text_list.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/theme_flextable_nmfstm.html b/docs/reference/theme_flextable_nmfstm.html index c19f420..3abb674 100644 --- a/docs/reference/theme_flextable_nmfstm.html +++ b/docs/reference/theme_flextable_nmfstm.html @@ -88,7 +88,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/tolower2.html b/docs/reference/tolower2.html index 4193f53..5432b36 100644 --- a/docs/reference/tolower2.html +++ b/docs/reference/tolower2.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/xunits.html b/docs/reference/xunits.html index f998250..0376f6a 100644 --- a/docs/reference/xunits.html +++ b/docs/reference/xunits.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/docs/reference/xunitspct.html b/docs/reference/xunitspct.html index 002ed72..3698c43 100644 --- a/docs/reference/xunitspct.html +++ b/docs/reference/xunitspct.html @@ -82,7 +82,7 @@ NMFSReports - 0.0.1.1 + 0.0.1.2 diff --git a/inst/rmd/0_figtab.Rmd b/inst/rmd/0_figtab.Rmd new file mode 100644 index 0000000..799fac4 --- /dev/null +++ b/inst/rmd/0_figtab.Rmd @@ -0,0 +1,73 @@ +--- +output: + word_document: + pandoc_args: ["--metadata-file=header.yaml"] + reference_docx: styles_reference.docx + df_print: kable +csl: "../cite/citestyle.csl" +bibliography: "../cite/bibliography.bib" +--- + + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = FALSE, warning = FALSE, error = FALSE, message = FALSE) +``` + +# Example figures and tables + +## fig_example + +```{r fig_example} +header <- "Example figure. " +nickname <- "fig_example" +width <- 6 +height <- 6 + +figure <- ggplot2::ggplot(mapping = aes(x = x, y = y), + data = data.frame(x = 1, y = 1)) + + ggplot2::geom_point() + +# save figure +res <- knitr::knit_child( + text = knitr::knit_expand( + file = system.file("rmd/_child_save_fig.Rmd", + package = "NMFSReports")), + quiet = TRUE +) + +list_figures[nickname][[1]]$res <- res <- paste0(" +###### + +",res," + +") + +``` + +## tab_example + +```{r tab_stratum_areas} +header <- "Example table. " +nickname <- "tab_example" + +table_raw <- data.frame(x = 1, y = 1) + +table_print <- flextable::flextable(table_raw) +table_print <- NMFSReports::theme_flextable_nmfstm(table_print) + +# save table +res <- knitr::knit_child( + text = knitr::knit_expand( + file = system.file("rmd/_child_save_tab.Rmd", package = "NMFSReports")), + quiet = TRUE +) + +list_tables[nickname][[1]]$res <- res <- paste0(" +###### + +",res," + +") + +``` + diff --git a/inst/rmd/_child_save_fig.Rmd b/inst/rmd/_child_save_fig.Rmd index f3b4293..4fb1e22 100644 --- a/inst/rmd/_child_save_fig.Rmd +++ b/inst/rmd/_child_save_fig.Rmd @@ -95,5 +95,6 @@ remove(list = remove_who) `r if(indesign_flowin %in% FALSE & (list_figures[[length(list_figures)]]$alttext)!="") { paste0("*Alternative text: ", list_figures[[length(list_figures)]]$alttext, "*") } ` +
diff --git a/inst/rmd/run.R b/inst/rmd/run.R index cadd837..0a9459d 100644 --- a/inst/rmd/run.R +++ b/inst/rmd/run.R @@ -32,22 +32,29 @@ indesign_flowin <- FALSE # googledrive::drive_auth() # 1 -# RUN EACH REPORT SECTION ------------------------------------------------------ +# RUN FIGURES, TABLES, & EQUATIONS FOR REPORT ---------------------------------- -# *** RUN EACH REPORT SECTION -------------------------------------------------- +if (FALSE) { + cnt_chapt_content<-"000" + filename0<-paste0(cnt_chapt, "_") + rmarkdown::render(paste0(dir_code, "/0_figtab.Rmd"), + output_dir = dir_out_ref, + output_file = paste0(filename0, cnt_chapt_content, ".docx")) -# INSERT_SECTIONS + save(list_figures, file=paste0(dir_out_figures, "/report_figures.rdata")) + save(list_tables, file=paste0(dir_out_tables, "/report_tables.rdata")) + save(list_equations, file=paste0(dir_out_tables, "/report_equations.rdata")) +} -# SAVE OTHER OUTPUTS ----------------------------------------------------------- +load(file = paste0(dir_out_figures, "/report_figures.rdata")) +load(file = paste0(dir_out_tables, "/report_tables.rdata")) +load(file = paste0(list_equations, "/report_equations.rdata")) -save(list_figures, - file=paste0(dir_out_figures, "/report_figures.rdata")) +# RUN EACH REPORT SECTION ------------------------------------------------------ -save(list_tables, - file=paste0(dir_out_tables, "/report_tables.rdata")) +# *** RUN EACH REPORT SECTION -------------------------------------------------- -save(list_equations, - file=paste0(dir_out_tables, "/report_equations.rdata")) +# INSERT_SECTIONS # MAKE MASTER DOCX ------------------------------------------------------------- diff --git a/man/crossref.Rd b/man/crossref.Rd index b7ad5ce..7c2c259 100644 --- a/man/crossref.Rd +++ b/man/crossref.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/NMFSReports.R \name{crossref} \alias{crossref} -\title{Reference a figure, table, or equation (or other list elements!)} +\title{Reference a figure, table, or equation with an anchored tag} \usage{ crossref(list_obj, nickname, sublist = "number") } @@ -17,7 +17,7 @@ crossref(list_obj, nickname, sublist = "number") The item in the list. } \description{ -Reference a figure, table, or equation (or other list elements!) +Reference a figure, table, or equation with an anchored tag } \examples{ list_figures <- c() diff --git a/notes.R b/notes.R index 230cd84..c7eaf0f 100644 --- a/notes.R +++ b/notes.R @@ -32,7 +32,7 @@ library(pkgdown) # options(rmarkdown.html_vignette.check_title = FALSE) # git rm -r --cached . - +options(rmarkdown.html_vignette.check_title = FALSE) # pkgdown::build_favicons() devtools::build_vignettes() usethis::use_pkgdown(config_file = "./pkgdown/_pkgdown.yml") diff --git a/pkgdown/favicon/apple-touch-icon-120x120.png b/pkgdown/favicon/apple-touch-icon-120x120.png index c64f2f70057f09a95d97d59805781bfb85e1208d..116fc05b2c55c33c901c76990e482c9e68be383f 100644 GIT binary patch delta 101 zcmX>dc{*}J1=ll1CN>?O^{ZYOZ*1z<_BPTrFw`|L3NbLVGBL3-G}1OOure?($PvHI lz`&qd;u=wsl30>zm7AZEnO4bQWMG6{gQMa4^vN+g`2ah#9Yz2E delta 101 zcmX>dc{*}J1=mv^0X|uYpIXlT8=LyIy$y8@jdTsoLJUo;j4Z8;OtcLQtPBh$eqFwt mfq_A_#5JNMC9x#cDmOnRGp&-r$iN7@h6gL;r6?O^{ZYOZ)}=v>20KIV5n60_8@&RK)9m)Uz delta 101 zcmca!dcAZ)1=mv^0X|vDKHcJ*8=GcZdK>B*8tEFEg&3Mx8ChBxnQ9vtSQ!|YH?0w7 lU|>)!ag8WRNi0dV%FR#7OsixtGBCof!R@}t`pFqq`2b4`9o+x` diff --git a/pkgdown/favicon/apple-touch-icon-180x180.png b/pkgdown/favicon/apple-touch-icon-180x180.png index 5144d6b9289895a6e1bacd9a55685ddf8520cc18..e4c00b8661f6c2f91b1e9b9702046de048e4146d 100644 GIT binary patch delta 103 zcmX@w&v>+-aY6;xGe#yh9o`#jZ!F!|)amAJq-$WPYhV;&U}j}vVr6KoZD3$!U@%Qu oCZB+-aY6;xQyu|6St)T9rR0rGoo?QSx`sx&hGrp#CRRq4Rz_yp1_o9J25ec| n`WP4(R7+eVN>UO_Qmu0HQ!>*k8H@~!uxltc=QEld=AI7#?4cXu diff --git a/pkgdown/favicon/apple-touch-icon-60x60.png b/pkgdown/favicon/apple-touch-icon-60x60.png index 6fd6a4e3f18e2d1de9b3011820679e086796e268..08c70e7a4b333f4586a0a3e6653d4dd6940af418 100644 GIT binary patch delta 83 zcmaE>^j2v?1=ll1CN>>z!*jJ0HZ~awNEzuG80s1rg&3GwnV47^8fqIDSQ!{Fw(z=5 TJ}V%OL%QJR)?btV3FHF+?jIOR delta 83 zcmaE>^j2v?1=mv^0X|tVxk-5*8=DLTqzrWpjdTsoLJUo;j4Z8;jI<35tPBi3sZN?Z S`K*9A4(a9!Eyc>z!*jJ0Ha2Y)lQPmZFw`|L3NbLVGBL3-G}JaQure@UY~gjA S94Ic1L%QJR)?bsG#Pb0Pdl(D= delta 83 zcmeyU|51NJ1=mv^0X|vr%&BqrHa2Y)lQPsbG}1LR3o$gYGP1NXGS)UQure?R37V-n SIZ#|2hqNlc;?&7a;`sn7AQtZc diff --git a/pkgdown/favicon/apple-touch-icon.png b/pkgdown/favicon/apple-touch-icon.png index 36638b2b62614a6bb8dff0a7771087c9b6226a31..40d7d12dfc7534dca062773abff0e7c525b33769 100644 GIT binary patch delta 103 zcmX@w&v>+-aY6;xGe#yh9X`h;o$?!-I^DdDbPWu34U9qz%&bgItPD-G4GgRd41)J4 nJ!D{DP%UwdC`m~yNwvz&PsvQHWH2%?!mdH-;jGxnVea_=KTI9x delta 103 zcmX@w&v>+-aY6;xQyu|6S?L62p|2a8I^Dbtbq$Sl4b4IfO{|P8t&GgI4GgRd3>L`l nwPIjkP%UwdC`m~yNwvz&PsvQHWH2%?!mi<>18dvlF!y`_HtQW; diff --git a/pkgdown/favicon/favicon-16x16.png b/pkgdown/favicon/favicon-16x16.png index 1c90a850b17c133bbe68d87999e65b85e05f7d2f..27e436fa3bd05ae6f39d7dee68a94e9cbe2674db 100644 GIT binary patch delta 85 zcmeys@quGQCll8*MkY2Lf!(XO)NG#2q|7K~q-$WPYhV;&U}j}vVr6KiZD3$!U~oj) V_{8K3%;Gqtx7Kx+OlD-s2LM0r7!d#f delta 85 zcmeys@quGQCll9G9sxdCg^L=$FK(X9q|7K~sB37XYiJf?Xkuk#X=QArZD3$!U|`oj ViFxt`W^o+S{+G1&PiADv2LMA~7sUVo diff --git a/pkgdown/favicon/favicon-32x32.png b/pkgdown/favicon/favicon-32x32.png index 641a014d161e833095d567d7fdd2abf0d333a1b8..7399bce36e12f31441d9794e53879bf845447843 100644 GIT binary patch delta 101 zcmZ23xLj~T1=ll1CN>?xGizF2ZEVVB_cqcsFw`|L3NbLVGBL3-G}ksTure@63bCkR lU|>)!ag8WRNi0dV%FR#7OsixtGBCofL721Qz+?-Kd;suR91j2h delta 101 zcmZ23xLj~T1=mv^0X|v9W%{SxH#TLndmHK+8tEFEg&3Mx8ChBx8*3XFSQ!}1_%U-k m0|SFRc?MtW?ChKk%19*4KJ4}a!*2ecw+j~)k^bRWoc=;QeT)3 zyZy9C8{8*8fOs!IFt<_q+CYaFTFS1WH)TiK&*|AlJBOmKts4QZ`ji5hR9 sveYJIgIIt4;_|sD@zD83qgij5b{#xl+mQ2AZfunQ3lT!-an_c+FSHeH!M zAAUQ~deXsqqf%LFEH=dVJuhCUPJiaJPdqXG>1w5UuClZ=U8yfjhaG!bqz A3(g{ zQN3JI%ZLZ&HjtRRZ_bqIY@>dSDmCzGkZR@gXe1-0-ef@)c?N#Zbb9bzoIz Date: Thu, 20 Jan 2022 12:22:47 -0800 Subject: [PATCH 2/9] changed save_table function to keep column names in csv file output --- R/NMFSReports.R | 21 ++- docs/apple-touch-icon-120x120.png | Bin 11467 -> 11467 bytes docs/apple-touch-icon-152x152.png | Bin 15063 -> 15063 bytes docs/apple-touch-icon-180x180.png | Bin 18373 -> 18373 bytes docs/apple-touch-icon-60x60.png | Bin 4461 -> 4461 bytes docs/apple-touch-icon-76x76.png | Bin 6129 -> 6129 bytes docs/apple-touch-icon.png | Bin 18373 -> 18373 bytes docs/articles/A_use-buildReport.html | 2 +- docs/articles/B_run-script-demo.html | 2 +- .../C_functions-to-help-write-report.html | 134 ++++++++++-------- docs/articles/E_thispkgwasbuiltusing.html | 2 +- docs/favicon-16x16.png | Bin 1136 -> 1136 bytes docs/favicon-32x32.png | Bin 2215 -> 2215 bytes docs/pkgdown.yml | 2 +- docs/reference/googledrive_txt_dl.html | 3 +- docs/reference/text_list.html | 11 +- inst/rmd/0_figtab.Rmd | 2 - inst/rmd/_child_save_fig.Rmd | 8 +- inst/rmd/header.yaml | 12 ++ man/text_list.Rd | 8 +- pkgdown/favicon/apple-touch-icon-120x120.png | Bin 11467 -> 11467 bytes pkgdown/favicon/apple-touch-icon-152x152.png | Bin 15063 -> 15063 bytes pkgdown/favicon/apple-touch-icon-180x180.png | Bin 18373 -> 18373 bytes pkgdown/favicon/apple-touch-icon-60x60.png | Bin 4461 -> 4461 bytes pkgdown/favicon/apple-touch-icon-76x76.png | Bin 6129 -> 6129 bytes pkgdown/favicon/apple-touch-icon.png | Bin 18373 -> 18373 bytes pkgdown/favicon/favicon-16x16.png | Bin 1136 -> 1136 bytes pkgdown/favicon/favicon-32x32.png | Bin 2215 -> 2215 bytes 28 files changed, 125 insertions(+), 82 deletions(-) diff --git a/R/NMFSReports.R b/R/NMFSReports.R index e9d5ddc..b76f4bc 100644 --- a/R/NMFSReports.R +++ b/R/NMFSReports.R @@ -527,22 +527,29 @@ tolower2<-function(str0, #' This function alows you to take a string of words and combine them into a sentance list. For example, 'apples', 'oranges', 'pears' would become 'apples, oranges, and pears'. This function uses oxford commas. #' @param x Character strings you want in your string. #' @param oxford T/F: would you like to use an oxford comma? Default = TRUE -#' @param sep string. default = "," but ";" might be what you need! +#' @param sep string. default = ", " but "; " or " " might be what you need! +#' @param sep_last string. default = " and " but " & " or " , " might be what you need! #' @keywords strings #' @export -#' @examples text_list(c(1,2,"hello",4,"world",6)) -text_list<-function(x, oxford = TRUE, sep = ",") { +#' @examples +#' text_list(c(1,2,"hello",4,"world",6)) +#' paste0("here is a list of things: ", +#' text_list(paste0("list", 1:5), sep = " ", sep_last = " ")) +text_list<-function(x = "", + oxford = TRUE, + sep = ", ", + sep_last = " and ") { x<-x[which(x!="")] # x<-x[which(!is.null(x))] x<-x[which(!is.na(x))] # x<-x[order(x)] if (length(x)==2) { - str1<-paste(x, collapse = " and ") + str1<-paste(x, collapse = sep_last) } else if (length(x)>2) { - str1<-paste(x[1:(length(x)-1)], collapse = paste0(sep, " ")) + str1<-paste(x[1:(length(x)-1)], collapse = paste0(sep)) str1<-paste0(str1, ifelse(oxford == TRUE, sep, ""), - " and ", x[length(x)]) + sep_last, x[length(x)]) } else { str1<-x } @@ -1498,7 +1505,7 @@ save_tables<-function(table_raw = NULL, file = paste0(path, filename00, "_raw.", output_type[i]), sep = ",", - row.names=FALSE, col.names = F, append = F) + row.names=FALSE, col.names = TRUE, append = F) } } else { table_raw <- "" diff --git a/docs/apple-touch-icon-120x120.png b/docs/apple-touch-icon-120x120.png index 116fc05b2c55c33c901c76990e482c9e68be383f..0e670c16427e13d5d4fe19d05d32a3f5579fdbe3 100644 GIT binary patch delta 71 zcmX>dc{*}J6^Dq3khbDh%ZiOnQ?x~m3_^?ytPCxzOpLV+46Fdc{*}J6$cZW4$t~kFN`-fP0+-aY7Y`h=`D0;Qh1TH#YUTxfvOR7#Ua@T3DHwX&V?=85n%se}4-D1A}Ub lYeY#(Vo9o1ZhlH;S|x*#fsv7}fuSyjhL%U^9FxP`^8q&69<%@e delta 96 zcmX@w&v>+-aY7Xb6Pph2jkPzHZfxpvb2BgsF)*_-F|jf<);2J(GBB7XEtAi{z@S>< l8c~vxSdwa$o1c=IR>@#wU}U6gV5p0s;knzA%ag<0^8vwE9a#VX diff --git a/docs/apple-touch-icon-60x60.png b/docs/apple-touch-icon-60x60.png index 08c70e7a4b333f4586a0a3e6653d4dd6940af418..40eda6524c19dee0fc6dfa184d84d1ceb9903a61 100644 GIT binary patch delta 71 zcmaE>^j2v?6^Dq3kmmW_5g{9!%mhS@3_^?ytPCxzOboRR46F}O+G6igDK^j2v?6$cZW4!7aC+6fz*%mhRYj6w{|tV~R-3=Opn46F7!IUYu Lx%JoNCh>d#1_BjJ diff --git a/docs/apple-touch-icon.png b/docs/apple-touch-icon.png index 40d7d12dfc7534dca062773abff0e7c525b33769..c53a8b0f0e6ebbbac432a8a7d5627ad2a271f1be 100644 GIT binary patch delta 96 zcmX@w&v>+-aY7Y`h=`EB+Ks=78=Lyv+>8uDj0~&{Ev!t;wG9lc3=D!#TwwqL)e_f; kl9a@fRIA+ll+3hB1|tI_BV7YST?`FMQ*-uA4s*{30K1nQ(EtDd delta 96 zcmX@w&v>+-aY7Xb6Ppg7

Use buildReport() to begin writing your report

-

January 02 2022

+

January 20 2022

Source: vignettes/A_use-buildReport.Rmd diff --git a/docs/articles/B_run-script-demo.html b/docs/articles/B_run-script-demo.html index 0baa3ec..8e55f05 100644 --- a/docs/articles/B_run-script-demo.html +++ b/docs/articles/B_run-script-demo.html @@ -129,7 +129,7 @@

How to use the run.R file to be the skeleton of your report

-

January 02 2022

+

January 20 2022

Source: vignettes/B_run-script-demo.Rmd diff --git a/docs/articles/C_functions-to-help-write-report.html b/docs/articles/C_functions-to-help-write-report.html index aa7129f..65e5ba9 100644 --- a/docs/articles/C_functions-to-help-write-report.html +++ b/docs/articles/C_functions-to-help-write-report.html @@ -130,7 +130,7 @@

Functions and examples to help you write your report

-

January 02 2022

+

January 20 2022

Source: vignettes/C_functions-to-help-write-report.Rmd @@ -245,10 +245,17 @@

# ```

#> NULL

+ +
+

+Figure 1. Here is a figure! +

+

Alternative text: This is a scatter plot of random data.

Here in plot 1, we see that…

+

Example Figure (Reference Image)

@@ -274,10 +281,17 @@

# `r res `

#> NULL

+ +
+

+Figure . Here is a figure! +

+

Alternative text: The NOAA Meatball and text.

Here in figure 2, we see the NOAA logo.

+

Example Table (Basic)

@@ -314,7 +328,7 @@

Table 1. Here is a table!

-
+