-
Notifications
You must be signed in to change notification settings - Fork 0
/
run.R
160 lines (116 loc) · 5.52 KB
/
run.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
#' ---
#' title: 'The best report ever'
#' author: 'Me, Myself, and I'
#' purpose: Run Scripts and R Markdown Files
#' start date: 2022-07-22
#' date modified: 2022-07-22 # CHANGE
#' Notes: # CHANGE
#' ---
# START ------------------------------------------------------------------------
# *** REPORT KNOWNS ------------------------------------------------------------
report_title <- 'The best report ever'
report_authors <- 'Me, Myself, and I'
report_yr <- substr(x = Sys.Date(), start = 1, stop = 4) # SUGGESTION
# *** OUTPUT TYPE --------------------------------------------------------------
#Is this for InDesign?
indesign_flowin <- FALSE
# *** SOURCE SUPPORT SCRIPTS ---------------------------------------------------
source('./code/directories.R')
source('./code/functions.R')
source('./code/dataDL.R')
source('./code/data.R')
# *** RENV: SAVE PACKAGES USED TO CREATE THIS REPORT ---------------------------
# renv::init()
# renv::snapshot()
# *** SIGN INTO GOOGLE DRIVE----------------------------------------------------
# googledrive::drive_deauth()
# googledrive::drive_auth()
# 1
# RUN FIGURES, TABLES, & EQUATIONS FOR REPORT ----------------------------------
if (TRUE) {
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"))
}
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"))
# RUN EACH REPORT SECTION ------------------------------------------------------
# *** RUN EACH REPORT SECTION --------------------------------------------------
# *** 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"))
# *** 1 - Abstract ------------------------
cnt_chapt<-auto_counter(cnt_chapt)
cnt_chapt_content<-"001"
filename0<-paste0(cnt_chapt, "_abstract_")
rmarkdown::render(paste0(dir_code, "/1_abstract.Rmd"),
output_dir = dir_out_chapters,
output_file = paste0(filename0, cnt_chapt_content, ".docx"))
# *** 2 - Introduction ------------------------
cnt_chapt<-auto_counter(cnt_chapt)
cnt_chapt_content<-"001"
filename0<-paste0(cnt_chapt, "_introduction_")
rmarkdown::render(paste0(dir_code, "/2_introduction.Rmd"),
output_dir = dir_out_chapters,
output_file = paste0(filename0, cnt_chapt_content, ".docx"))
# *** 3 - History ------------------------
cnt_chapt<-auto_counter(cnt_chapt)
cnt_chapt_content<-"001"
filename0<-paste0(cnt_chapt, "_history_")
rmarkdown::render(paste0(dir_code, "/3_history.Rmd"),
output_dir = dir_out_chapters,
output_file = paste0(filename0, cnt_chapt_content, ".docx"))
# *** 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"))
# *** 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"))
# *** 6 - Results_discussion ------------------------
cnt_chapt<-auto_counter(cnt_chapt)
cnt_chapt_content<-"001"
filename0<-paste0(cnt_chapt, "_results_discussion_")
rmarkdown::render(paste0(dir_code, "/6_results_discussion.Rmd"),
output_dir = dir_out_chapters,
output_file = paste0(filename0, cnt_chapt_content, ".docx"))
# *** 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"))
# *** 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"))
# MAKE MASTER DOCX -------------------------------------------------------------
#USE GUIDENCE FROM THIS LINK
#https://support.microsoft.com/en-us/help/2665750/how-to-merge-multiple-word-documents-into-one
# SAVE METADATA ----------------------------------------------------------------
con <- file(paste0(dir_out_todaysrun, "metadata.log"))
sink(con, append=TRUE)
sessionInfo()
sink() # Restore output to console
# cat(readLines("notes.log"), sep="\n") # Look at the log