study.sankey

Available at:

• Site: https://fcacollin.github.io/study.sankey
• Source: https://github.com/FCACollin/study.sankey

git clone https://github.com/FCACollin/study.sankey.git

knitr::opts_chunk$set(
  comment = "#>",
  echo = TRUE,
  error = TRUE,
  fig.path = "man/figures/README-",
  comment = "#>",
  out.width = "100%",
  fig.height = 8.3 * .66,
  fig.width = 11.7 * .66,
  dpi = 300
)

1. Controlled execution

As any R Markdown file, the params argument in the YAML front matter offers controlled-execution settings. For instance:

• when the following parameter is used:

params:
  diag: true

• this code chunk is evaluated and included:

```{r, check, eval=params$diag, include=params$diag}
devtools::check(quiet = TRUE)
```

• note: devtools::check() provides diagnostic/quality information about the package but is lengthy, hence the rendering time is substantially increased for diag: true.

devtools::check(quiet = TRUE)

#> ℹ Loading study.sankey

#> Loading required package: grid

#> ── R CMD check results ───────────────────────────────── study.sankey 0.1.0 ────
#> Duration: 2m 14.2s
#> 
#> > checking for unstated dependencies in examples ... OK
#>    WARNING
#>   ‘qpdf’ is needed for checks on size reduction of PDFs
#> 
#> > checking for future file timestamps ... NOTE
#>   unable to verify current time
#> 
#> 0 errors ✓ | 1 warning x | 1 note x

#> Error: R CMD check found WARNINGs

The code chunks in inst/study.R are identified by knitr::read_chunk(); then can then selectively called from the README.Rmd file.

file_nm <- "inst/study.R"
knitr::read_chunk(file_nm)
message("R code chunks read from:\n", file_nm)

#> R code chunks read from:
#> inst/study.R

2. Analysis

devtools::load_all()

#> ℹ Loading study.sankey

library(ggalluvial)

#> Loading required package: ggplot2

library(dplyr)

#> 
#> Attaching package: 'dplyr'

#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag

#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

library(magrittr)

2.1. Dataset preparation

test_dta <- adam_ww(50)
attach(test_dta, warn.conflicts = FALSE)

knitr::kable(head(adsl), caption = "Dummy ADSL dataset")

	USUBJID	TRT	BASELINE	ARMCD
37	SUBJECT 037	ACTIVE TREATMENT DOSE 01	27.8	ARM B
39	SUBJECT 039	ACTIVE TREATMENT DOSE 01	25.0	ARM B
40	SUBJECT 040	ACTIVE TREATMENT DOSE 01	20.7	ARM B
105	SUBJECT 105	ACTIVE TREATMENT DOSE 01	22.8	ARM B
111	SUBJECT 111	ACTIVE TREATMENT DOSE 01	16.9	ARM B
121	SUBJECT 121	ACTIVE TREATMENT DOSE 01	21.2	ARM B

knitr::kable(head(adpasi), caption = "Dummy ADPASI dataset")

USUBJID	AVISIT	AVAL	PARAMCD
SUBJECT 037	WEEK00	27.8	PASITOT
SUBJECT 039	WEEK00	25.0	PASITOT
SUBJECT 040	WEEK00	20.7	PASITOT
SUBJECT 105	WEEK00	22.8	PASITOT
SUBJECT 111	WEEK00	16.9	PASITOT
SUBJECT 121	WEEK00	21.2	PASITOT

ads <- adpasi %>%
  filter(AVISIT %in% c("WEEK00", "WEEK01", "WEEK08", "WEEK52")) %>%
  mutate(
    time = factor(AVISIT),
    rsp = cut(AVAL, breaks = 3, labels = c("Low", "Mid", "High")),
    rsp = add_missing(rsp),
    subj = gsub("^SUBJECT (.*)$", x = USUBJID, replacement = "\\1")
  ) %>%
  select(subj, time, rsp) %>%
  arrange(rsp, time, subj)

knitr::kable(
  x = head(ads),
  # lintr demo: only use double-quotes
  caption = 'Outlook of the analysis dataset data'
)

subj	time	rsp
187	WEEK00	Low
040	WEEK01	Low
111	WEEK01	Low
248	WEEK01	Low
299	WEEK01	Low
307	WEEK01	Low

2.2. Graphics

# lintr demonstration: commented code should be removed
# test <- viridis::viridis(5)

# lintr demonstration: keep using snake_case for variable and functions names
colorScale <- color_scale <-  viridis::viridis(
  nlevels(ads$rsp),
  begin = .2, end = .8, option = "C",
  direction = -1
)
names(color_scale) <- levels(ads$rsp)

gg_sankey <- ads %>%
  ggplot(aes(x = time, stratum = rsp, alluvium = subj, fill = rsp)) +
  geom_stratum(colour = NA) +
  geom_flow(stat = "alluvium", color = "gray85", lwd = .01) +
  ggtitle("Alluvial plot: Response category by visit") +
  scale_fill_manual(values = color_scale) +
  theme_diane()

gg_sankey <- clean_slate(margin = unit(c(1, 1, 1, 1), "cm")) %>%
  add_header(left = "Topic", right = c("Not Yet Confidential", "Draft")) %>%
  add_title(c(
    "Figure 1 - Prototype of Alluvial plot",
    "Analysis set: 50 random subjects"
  )) %>%
  add_figure(gg_sankey, width = unit(5, "in"), height = unit(2, "in")) %>%
  add_footer("Program: prototype study.sankey", "Page 1 of 1") %T>%
  grid.draw()