08-sacc_tDCS_supplement.Rmd

```{r setup, include=FALSE}
#Setup
library(kableExtra) # complex tables
library(tidyverse) # importing, transforming, and visualizing data frames

knitr::opts_chunk$set(results = 'hide', echo = FALSE, message = FALSE, warning = FALSE)

# create variable to resize figures/text depending on output
if (knitr::is_latex_output()) {
  tbl_font_size <- 8
  line_break <- function(...) {kableExtra::linebreak(...)}
} else {
  tbl_font_size <- 12
  # use html version of linebreak function
  line_break <- function(x, ...) {
    if (is.numeric(x) | is.logical(x)) return(x)
    ifelse(stringr::str_detect(x, "\n"), stringr::str_replace_all(x, "\n", "<br />"), x)
  }
}

```

# (APPENDIX) Appendix {-}
\cleardoublepage
\phantomsection
\addcontentsline{toc}{part}{Appendices}
\appendixpage*
\setlength\beforechapskip{-\baselineskip}

`r if (knitr::is_html_output()) '
# Supplement to Chapter 3 {#sacc-tDCS-supplement}
' else '
# Supplement to Chapter \\@ref(sacc-tDCS) {#sacc-tDCS-supplement}
'`

## tDCS adverse effects

```{r read data}
tDCS_AE <- read_csv2("sacc_tDCS_files/tdcs_sensations.csv", col_names = TRUE, progress = FALSE, col_types = cols(
  session = readr::col_factor(c("first", "second")), 
  stimulation = readr::col_factor(c("anodal", "cathodal")))) %>%
  filter(rowSums(is.na(.)) != ncol(.) - 3) # discard rows with all NAs (except 3 factor columns)
```

```{r}
# Make long form data frame of sensation intensity
intensity <- tDCS_AE %>%
  select(everything(), -contains("conf"), -felt.more) %>% # drop other columns
  gather(sensation, intensity, itching:nausea) # make long form 

# Make long form data frame of sensation confidence
confidence <- tDCS_AE %>%
  select(contains("conf"), subject, session, stimulation) %>% 
  gather(sensation, confidence, conf.itching:conf.nausea) %>%
  # get rid of "conf." prefix so it matches the sensation intensity table
  mutate(sensation = str_replace(sensation, "conf.", "")) 

int_conf <- full_join(intensity,confidence)  %>%
  # gather confidence/intensity to make one plot for each
  gather(measure, rating, intensity, confidence) %>% 
  mutate(measure = factor(measure, levels = c("intensity", "confidence")))
```

\begingroup
\renewcommand{\arraystretch}{1.25}
\setlength{\LTleft}{-20cm plus -1fill}
\setlength{\LTright}{\LTleft}

```{r tab-sacc-tDCS-AE, results='asis'}
if (knitr::is_latex_output() | knitr::is_html_output()) {
tbl_int_anodal <- intensity %>%
  filter(stimulation == "anodal") %>%
  count(sensation, intensity) %>%
  spread(intensity, n) %>%
  replace(is.na(.), 0) %>%
  mutate_if(is.double, as.integer)

tbl_int_cathodal <- intensity %>%
  filter(stimulation == "cathodal") %>%
  count(sensation, intensity) %>%
  spread(intensity, n) %>%
  replace(is.na(.), 0) %>%
  mutate_if(is.double, as.integer)

tbl_conf_anodal <- confidence %>%
  filter(stimulation == "anodal") %>%
  count(sensation, confidence) %>%
  spread(confidence, n) %>%
  replace(is.na(.), 0) %>%
  mutate_if(is.double, as.integer)

tbl_conf_cathodal <- confidence %>%
  filter(stimulation == "cathodal") %>%
  count(sensation, confidence) %>%
  spread(confidence, n) %>%
  replace(is.na(.), 0) %>%
  mutate_if(is.double, as.integer)

ae_colnames <- c(" ",
                 "none", "a\nlittle", "mode-\nrate", "strong", "very\nstrong",
                 "n/a", "un-\nlikely", "possi-\nbly", "likely", "very\nlikely")
                 
bind_rows(full_join(tbl_int_anodal, tbl_conf_anodal, by  = "sensation"),
          full_join(tbl_int_cathodal, tbl_conf_cathodal, by  = "sensation")) %>%
  kable(col.names = line_break(ae_colnames, align = "c"), 
        booktabs = TRUE,
        longtable = TRUE,
        escape = FALSE,
        caption = "Number of reports of tDCS adverse effects") %>%
  kable_styling(bootstrap_options = "striped",
                font_size = tbl_font_size) %>%
  add_header_above(setNames(c(1,5,5), c(" ",
              paste0("Intensity rating", footnote_marker_alphabet(1, double_escape = TRUE)),
              paste0("Confidence rating", footnote_marker_alphabet(2, double_escape = TRUE)))),
              escape = FALSE) %>%
  pack_rows(index = c("anodal session" = 8, "cathodal session" = 8)) %>%
  footnote(alphabet = c(
    '"To which degree were the following sensations present during stimulation?"', 
    '"To which degree do you believe this was caused by the stimulation?"'))
}
```

\endgroup

\newpage
\pagestyle{empty}
\changetext{}{}{-25mm}{}{}
\blandscape

```{r fig-sacc-tDCS-AE, fig.cap='(ref:caption-fig-sacc-tDCS-AE)', results='show'}
knitr::include_graphics("sacc_tDCS_files/figures/figure_S1_AE.png", auto_pdf = TRUE)
```

(ref:caption-fig-sacc-tDCS-AE) __tDCS adverse effects in Chapter \@ref(sacc-tDCS)__. Number of reports out of 62 sessions (either anodal or cathodal tDCS). Top row shows intensity ratings [_little, moderate, strong, very strong_]; bottom row shows participant's confidence that event was related to tDCS [_unlikely, possibly, likely, very likely_]. Adverse effects are sorted in descending order of number of reports (for very rare events (five reports or fewer for a given polarity), some text counts have been removed to prevent overlap).

\newpage
\elandscape
\changetext{}{}{+25mm}{}{}
\pagestyle{\defstyle}

## MNI coordinates

```{r tab-sacc-tDCS-MNI, results='asis'}
read_csv("sacc_tDCS_files/FEF_coords_MNI_excl.csv") %>%
  kable(col.names = c('participant','X','Y','Z','participant','X','Y','Z'),
    align = c('crrrcrrr'),
    linesep = "",
    booktabs = TRUE,
    caption = "Individual MNI coordinates of the right frontal eye field.") %>%
  kable_styling(bootstrap_options = "striped",
                latex_options = "hold_position",
                font_size = tbl_font_size) %>%
  column_spec(5, border_left = TRUE)
```