forked from dbosak01/logr
-
Notifications
You must be signed in to change notification settings - Fork 0
/
logr-example1.Rmd
441 lines (366 loc) · 14.1 KB
/
logr-example1.Rmd
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
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
---
title: "Complete Example"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{example1}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
options(rmarkdown.html_vignette.check_title = FALSE)
```
## Program
The previous examples in the **logr** documentation were intentionally
simplified to focus on the workings of a particular function. It is helpful,
however, to also view **logr** functions in the context of a complete
program. The following example shows a complete program. The example illustrates
how **logr** functions work together, and interact with **tidyverse** and
**sassy** functions to create a comprehensive log.
This example has been chosen
because it incorporates many of the functions that will log automatically.
If you want to maximize the auto-generation features of **logr**, take note of
these functions.
The data for this example has been included in the **logr** package as an
external data file. It may be accessed using the `system.file()` function
as shown below, or downloaded directly from the **logr** GitHub site
[here](https://raw.githubusercontent.com/dbosak01/logr/master/inst/extdata/DM.csv)
```{r eval=FALSE, echo=TRUE}
library(tidyverse)
library(sassy)
options("logr.autolog" = TRUE)
# Get temp location for log and report output
tmp <- tempdir()
# Open the log
lf <- log_open(file.path(tmp, "example1.log"))
# Send code to the log
log_code()
sep("Load the data")
# Get path to sample data
pkg <- system.file("extdata", package = "logr")
# Define data library
libname(sdtm, pkg, "csv")
# Load the library into memory
lib_load(sdtm)
# Prepare Data -------------------------------------------------------------
sep("Prepare the data")
# Define format for age groups
ageg <- value(condition(x > 18 & x <= 29, "18 to 29"),
condition(x >= 30 & x <= 44, "30 to 44"),
condition(x >= 45 & x <= 59, "45 to 59"),
condition(TRUE, "60+"))
# Manipulate data
final <- sdtm.DM %>%
select(USUBJID, BRTHDTC, AGE) %>%
mutate(AGEG = fapply(AGE, ageg)) %>%
arrange(AGEG, AGE) %>%
group_by(AGEG) %>%
datastep(retain = list(SEQ = 0),
calculate = {AGEM <- mean(AGE)},
attrib = list(USUBJID = dsattr(label = "Universal Subject ID"),
BRTHDTC = dsattr(label = "Subject Birth Date",
format = "%m %B %Y"),
AGE = dsattr(label = "Subject Age in Years",
justify = "center"),
AGEG = dsattr(label = "Subject Age Group",
justify = "left"),
AGEB = dsattr(label = "Age Group Boundaries"),
SEQ = dsattr(label = "Subject Age Group Sequence",
justify = "center"),
AGEM = dsattr(label = "Mean Subject Age",
format = "%1.2f"),
AGEMC = dsattr(label = "Subject Age Mean Category",
format = c(B = "Below", A = "Above"),
justify = "right")),
{
# Start and end of Age Groups
if (first. & last.)
AGEB <- "Start - End"
else if (first.)
AGEB <- "Start"
else if (last.)
AGEB <- "End"
else
AGEB <- "-"
# Sequence within Age Groups
if (first.)
SEQ <- 1
else
SEQ <- SEQ + 1
# Above or Below the mean age
if (AGE > AGEM)
AGEMC <- "A"
else
AGEMC <- "B"
}) %>%
ungroup() %>%
put()
# Put dictionary to log
dictionary(final) %>% put()
# Create Report ------------------------------------------------------------
sep("Create report")
# Create table
tbl <- create_table(final)
# Create report
rpt <- create_report(file.path(tmp, "./output/example1.rtf"),
output_type = "RTF", font = "Arial") %>%
titles("Our first SASSY report", bold = TRUE) %>%
add_content(tbl)
# write out the report
res <- write_report(rpt)
# Clean Up -----------------------------------------------------------------
sep("Clean Up")
# Unload libname
lib_unload(sdtm)
# Close the log
log_close()
# View log
writeLines(readLines(lf, encoding = "UTF-8"))
# View Report
# file.show(res$modified_path)
```
## Log
The above program produces the following log:
```
=========================================================================
Log Path: C:/Users/dbosa/AppData/Local/Temp/Rtmp6DW7BF/log/example1.log
Program Path: C:\packages\logr\vignettes\logr-example1.Rmd
Working Directory: C:/packages/logr
User Name: dbosa
R Version: 4.1.2 (2021-11-01)
Machine: SOCRATES x86-64
Operating System: Windows 10 x64 build 19041
Base Packages: stats graphics grDevices utils datasets methods base
Other Packages: tidylog_1.0.2 reporter_1.2.6 libr_1.2.1 fmtr_1.5.3 sassy_1.0.5
forcats_0.5.1 stringr_1.4.0 purrr_0.3.4 readr_2.0.2 tidyr_1.1.4
tibble_3.1.5 ggplot2_3.3.5 tidyverse_1.3.1 logr_1.2.7 dplyr_1.0.7
Log Start Time: 2021-11-16 08:40:18
=========================================================================
> library(tidyverse)
> library(sassy)
>
> options("logr.autolog" = TRUE)
>
> # Open the log
> lf <- log_open()
>
> # Send code to the log
> log_code()
>
> sep("Load the data")
>
> # Get path to sample data
> pkg <- system.file("extdata", package = "logr")
>
> # Define data library
> libname(sdtm, pkg, "csv")
>
> # Load the library into memory
> lib_load(sdtm)
>
>
> # Prepare Data -------------------------------------------------------------
> sep("Prepare the data")
>
> # Define format for age groups
> ageg <- value(condition(x > 18 & x <= 29, "18 to 29"),
> condition(x >= 30 & x <= 44, "30 to 44"),
> condition(x >= 45 & x <= 59, "45 to 59"),
> condition(TRUE, "60+"))
>
>
> # Manipulate data
> final <- sdtm.DM %>%
> select(USUBJID, BRTHDTC, AGE) %>%
> mutate(AGEG = fapply(AGE, ageg)) %>%
> arrange(AGEG, AGE) %>%
> group_by(AGEG) %>%
> datastep(retain = list(SEQ = 0),
> calculate = {AGEM <- mean(AGE)},
> attrib = list(USUBJID = dsattr(label = "Universal Subject ID"),
> BRTHDTC = dsattr(label = "Subject Birth Date",
> format = "%m %B %Y"),
> AGE = dsattr(label = "Subject Age in Years",
> justify = "center"),
> AGEG = dsattr(label = "Subject Age Group",
> justify = "left"),
> AGEB = dsattr(label = "Age Group Boundaries"),
> SEQ = dsattr(label = "Subject Age Group Sequence",
> justify = "center"),
> AGEM = dsattr(label = "Mean Subject Age",
> format = "%1.2f"),
> AGEMC = dsattr(label = "Subject Age Mean Category",
> format = c(B = "Below", A = "Above"),
> justify = "right")),
> {
>
> # Start and end of Age Groups
> if (first. & last.)
> AGEB <- "Start - End"
> else if (first.)
> AGEB <- "Start"
> else if (last.)
> AGEB <- "End"
> else
> AGEB <- "-"
>
> # Sequence within Age Groups
> if (first.)
> SEQ <- 1
> else
> SEQ <- SEQ + 1
>
> # Above or Below the mean age
> if (AGE > AGEM)
> AGEMC <- "A"
> else
> AGEMC <- "B"
>
> }) %>%
> ungroup() %>%
> put()
>
> # Put dictionary to log
> dictionary(final) %>% put()
>
> # Create Report ------------------------------------------------------------
> sep("Create report")
>
>
> # Create table
> tbl <- create_table(final)
>
> # Create report
> rpt <- create_report("./output/example1.rtf",
> output_type = "RTF", font = "Arial") %>%
> titles("Our first SASSY report", bold = TRUE) %>%
> add_content(tbl)
>
> # write out the report
> res <- write_report(rpt)
>
>
> # Clean Up -----------------------------------------------------------------
> sep("Clean Up")
>
> # Unload libname
> lib_unload(sdtm)
>
> # Close the log
> log_close()
>
> # View log
> writeLines(readLines(lf, encoding = "UTF-8"))
>
> # View Report
> # file.show(res$modified_path)
=========================================================================
Load the data
=========================================================================
# library 'sdtm': 8 items
- attributes: csv not loaded
- path: C:/Users/dbosa/Documents/R/win-library/4.1/logr/extdata
- items:
Name Extension Rows Cols Size LastModified
1 AE csv 150 27 88.3 Kb 2021-10-08 15:02:15
2 DA csv 3587 18 528.1 Kb 2021-10-08 15:02:15
3 DM csv 87 24 45.4 Kb 2021-10-08 15:02:15
4 DS csv 174 9 33.9 Kb 2021-10-08 15:02:15
5 EX csv 84 11 26.2 Kb 2021-10-08 15:02:15
6 IE csv 2 14 13.2 Kb 2021-10-08 15:02:15
7 SV csv 685 10 70.2 Kb 2021-10-08 15:02:15
8 VS csv 3358 17 467.3 Kb 2021-10-08 15:02:15
NOTE: Log Print Time: 2021-11-16 08:40:54
NOTE: Elapsed Time in seconds: 35.2692317962646
lib_load: library 'sdtm' loaded
NOTE: Log Print Time: 2021-11-16 08:41:00
NOTE: Elapsed Time in seconds: 5.96066999435425
=========================================================================
Prepare the data
=========================================================================
select: dropped 21 variables (STUDYID, DOMAIN, SUBJID, RFSTDTC, RFENDTC, <U+0085>)
NOTE: Log Print Time: 2021-11-16 08:41:09
NOTE: Elapsed Time in seconds: 9.39324498176575
mutate: new variable 'AGEG' (character) with 4 unique values and 0% NA
NOTE: Log Print Time: 2021-11-16 08:41:09
NOTE: Elapsed Time in seconds: 0.0129940509796143
group_by: one grouping variable (AGEG)
NOTE: Log Print Time: 2021-11-16 08:41:09
NOTE: Elapsed Time in seconds: 0.0119409561157227
datastep: columns increased from 4 to 8
NOTE: Log Print Time: 2021-11-16 08:41:09
NOTE: Elapsed Time in seconds: 0.0947761535644531
ungroup: no grouping variables
NOTE: Log Print Time: 2021-11-16 08:41:09
NOTE: Elapsed Time in seconds: 0.0029609203338623
# A tibble: 87 x 8
USUBJID BRTHDTC AGE AGEG AGEM AGEB SEQ AGEMC
<chr> <date> <dbl> <chr> <dbl> <chr> <dbl> <chr>
1 ABC-04-128 1987-05-24 19 18 to 29 49.4 Start 1 B
2 ABC-07-011 1985-01-18 21 18 to 29 49.4 - 2 B
3 ABC-09-139 1985-11-13 21 18 to 29 49.4 - 3 B
4 ABC-09-018 1984-08-29 22 18 to 29 49.4 - 4 B
5 ABC-04-074 1983-03-28 23 18 to 29 49.4 - 5 B
6 ABC-01-053 1980-04-07 26 18 to 29 49.4 - 6 B
7 ABC-06-070 1980-02-01 26 18 to 29 49.4 End 7 B
8 ABC-02-112 1976-11-01 30 30 to 44 49.4 Start 1 B
9 ABC-01-056 1975-05-02 31 30 to 44 49.4 - 2 B
10 ABC-03-089 1975-10-02 31 30 to 44 49.4 - 3 B
# ... with 77 more rows
NOTE: Data frame has 87 rows and 8 columns.
NOTE: Log Print Time: 2021-11-16 08:41:09
NOTE: Elapsed Time in seconds: 0.0398931503295898
# A tibble: 8 x 10
Name Column Class Label Description Format Width Justify Rows NAs
<chr> <chr> <chr> <chr> <chr> <chr> <int> <chr> <int> <int>
1 final USUBJID character Universa~ <NA> <NA> 10 <NA> 87 0
2 final BRTHDTC Date Subject ~ <NA> "%m %B~ NA <NA> 87 0
3 final AGE numeric Subject ~ <NA> <NA> NA center 87 0
4 final AGEG character Subject ~ <NA> <NA> 8 left 87 0
5 final AGEM numeric Mean Sub~ <NA> "%1.2f" NA <NA> 87 0
6 final AGEB character Age Grou~ <NA> <NA> 5 <NA> 87 0
7 final SEQ numeric Subject ~ <NA> <NA> NA center 87 0
8 final AGEMC character Subject ~ <NA> "Below~ 1 right 87 0
NOTE: Data frame has 8 rows and 10 columns.
NOTE: Log Print Time: 2021-11-16 08:41:11
NOTE: Elapsed Time in seconds: 2.2303478717804
=========================================================================
Create report
=========================================================================
# A report specification: 3 pages
- file_path: 'C:\Users\dbosa\AppData\Local\Temp\Rtmp6DW7BF/./output/example1.rtf'
- output_type: RTF
- units: inches
- orientation: landscape
- margins: top 0.5 bottom 0.5 left 1 right 1
- line size/count: 9/46
- title 1: 'Our first SASSY report'
- content:
# A table specification:
- data: tibble 'final' 87 rows 8 cols
- show_cols: all
- use_attributes: all
NOTE: Log Print Time: 2021-11-16 08:41:16
NOTE: Elapsed Time in seconds: 4.57250308990479
=========================================================================
Clean Up
=========================================================================
lib_sync: synchronized data in library 'sdtm'
NOTE: Log Print Time: 2021-11-16 08:41:17
NOTE: Elapsed Time in seconds: 1.38584780693054
lib_unload: library 'sdtm' unloaded
NOTE: Log Print Time: 2021-11-16 08:41:17
NOTE: Elapsed Time in seconds: 0.00399112701416016
=========================================================================
Log End Time: 2021-11-16 08:41:19
Log Elapsed Time: 0 00:00:01
=========================================================================
```
## Output
Here is the report produced by the sample program above:
<img src="../man/images/example1a.png"/>
<img src="../man/images/example1b.png"/>
<img src="../man/images/example1c.png"/>