I'm having issues with a footnote not appearing under a table in my R Markdown report. Below is the code I'm using to process which does successfully but with no footnote appearing under the table.
```{r ccxtable7, results="asis", echo=FALSE}
comment <- list(pos = list(0), command = NULL)
comment$pos[[1]] <- c(nrow(indPctChgCC))
comment$command <- c(paste("\\hline\n",
"{\\footnotesize Note: * signifies number of
properties used was 35 or less.}\n", sep = ""))
print(xtable(valPctCon(indPctChgCC, indfreqCC, 35), align = "crrrrr",
label = "tab:indCC", add.to.row = comment, hline.after = c(-1,0),
caption = "Industrial Certified-Certified Percentage Change per Value Segment"))
```
indPctChCC is a 3x5 matrix of strings. Could someone help me understand why the footnote is not appearing under the table with this current code?
add.to.row (and also hline.after) are arguments of the print function, not xtable().
This should get you where you want:
print(xtable(tab, align = "crrr",
label = "tab:indCC",
caption = "Industrial Certified-Certified Percentage Change per Value Segment"),
add.to.row = comment,
hline.after = c(-1,0))
Related
I am in the process of creating a table 1 for my work, but when I knit my R Markdown file to PDF, some of the table gets cut off. Can I modify my code to either knit it landscape or not have half the table cut off?
table_1 <- CreateTableOne(
vars = vars,
data = Cambodia,
factorVars = fvars,
test = FALSE,
)
tab1 <- kable(
print(table_1,
showAllLevels = TRUE,
printToggle = FALSE,
noSpaces = TRUE,
catDigits = 1,
contDigits = 1),
caption = paste(
"Baseline Characteristics of xyz."
)
)
print(tab1)
You can use kable_styling from the kableExtra package. The option would be latex_options="scale_down". You can use font sizes as well, please see https://haozhu233.github.io/kableExtra/awesome_table_in_pdf.pdf
I am trying to create text references for tables and figures. However, I do get it to work following the examples in the documentation. There is neither a text reference nor a table caption using either approach. Here is some example script.
# Results
See Table \#ref(tab:ResultsANOVAI) or Table \#ref(tab:ResultsANOVAII) for ANOVA results. They show that ...
(ref:ResultsANOVAI) Results ANOVA I
```{r ANOVAI, warning=FALSE, tab.cap='(ref:ResultsANOVAI)'}
library(afex)
daten <- data.frame(vp = rep(1:30, each = 6),
cond1 = rep(1:3, each = 2),
cond2 = rep(1:2),
rt = rnorm(180, 600, 100))
aov.res <- aov_ez("vp", "rt", daten, within = c("cond1", "cond2"))
apa_anova <- apa_print.afex_aov(aov.res)
apa_table(apa_anova$table)
```
A little bit of text after the table.
(ref:ResultsANOVAI) Results ANOVA II
```{r ANOVAII, warning=FALSE}
apa_anova <- apa_print.afex_aov(aov.res)
apa_table(apa_anova$table,
caption = "(ref:ResultsANOVAII)")
```
Hints are heartly welcome.
Jens
the following code should work:
# Results
See Table \#ref(tab:ANOVAI) or Table \#ref(tab:ANOVAII) for ANOVA results. They show that ...
(ref:ResultsANOVAI) Results ANOVA I
```{r ANOVAI, warning=FALSE}
library(afex)
daten <- data.frame(vp = rep(1:30, each = 6),
cond1 = rep(1:3, each = 2),
cond2 = rep(1:2),
rt = rnorm(180, 600, 100))
aov.res <- aov_ez("vp", "rt", daten, within = c("cond1", "cond2"))
apa_anova <- apa_print.afex_aov(aov.res)
apa_table(apa_anova$table, caption = "(ref:ResultsANOVAI)")
```
A little bit of text after the table.
(ref:ResultsANOVAII) Results ANOVA II
```{r ANOVAII, warning=FALSE}
apa_anova <- apa_print.afex_aov(aov.res)
apa_table(apa_anova$table,
caption = "(ref:ResultsANOVAII)")
```
So why did your code not work?
When you want to add a caption to a table via text references, add something like caption = "(ref:caption-name)" to your call to apa_table() (the chunk option tab.cap does not work)
When you are using cross references (i.e., "see Table 1 and 2"), use \#ref(tab:chunk-name) -- your chunk names are ANOVAI and ANOVAII in your example, so it has to be \#ref(tab:ANOVAI) and \#ref(tab:ANOVAII)
Hope this helps!
For further reading, the relevant parts of the papaja manual are here:
Table captions
Cross references
I want a table to have bullet points in one column and to have a specific table width (in order to be placed on one page when rendered to PDF).
How can I achieve this in rmarkdown using one of the many packages out there?
What I have tried and have so far:
---
output: pdf_document
---
```{r, include = FALSE}
df <- data.frame(col1 = "Some really long text here. I mean some reeeeeaaly loooong text. So long, it should be wrapped. Really.",
col2 = "* bullet point 1\n * bullet point 2", col3 = "Yes, there is still another column.")
```
# Attempt 1: kableExtra
```{r, echo = FALSE, warning = FALSE}
library(kableExtra)
df1 <- df
df1$col2 <- linebreak(df1$col2)
knitr::kable(df1, escape = FALSE) %>% column_spec(1, width = "15em")
```
# Attempt 2: pander
```{r, echo = FALSE}
pander::pander(df, keep.line.breaks = TRUE, style = 'grid', justify = 'left')
```
This renders to:
As you can see both options have caveats. The kableExtra version does have a specific table width that fits on one page but does not show bullet points nicely. Whereas the pander solution renders the bullet points nicely but spans multiple pages, because I don't know how to specifiy the table width in pander.
Is there a solution that can do both?
Related questions are for example here and there.
An alternative solution based on kableExtra (optional: with footnotes)
This approach allows to add a caption, to manually add footnotes within the table, and to fix column widths.
To create the bullet point list:
"thicker" \cdots from LaTex are employed as bullets (alternatives see here)
linebreaks are forced with \n (indentation is therefore not as nice as with the pander approach from #daroczig).
MWE
library(stringi); library(kableExtra); library(dplyr)
string_short <- "Descriptor"
string_long <- substr(stri_rand_lipsum(1), 1, 50)
# add footnotes manually within table
string_bulletlist <- "$\\boldsymbol{\\cdot}$ bullet point 1: foo$^{a}$ \n $\\boldsymbol{\\cdot}$ bullet point 2: bar$^{b}$"
df <- data.frame(col1 = c(string_short, string_short),
col2 = c(string_bulletlist, string_bulletlist),
col3 = c(string_long, string_long)
)
col_names <- c("Descriptor", "Description with list", "Some comment")
# header: bold column names
colnames(df) <- paste0("\\textbf{", col_names,"}")
# add footnote with kableExtra commands
names(df)[1] <- paste0(names(df)[1], footnote_marker_symbol(1))
df %>%
mutate_all(linebreak) %>% # required for linebreaks to work
kable(
"latex",
escape = F,
booktabs=TRUE,
align = "l",
caption = 'kableTable with bullet list and footnote') %>%
# kable_styling(full_width = F) %>% # makes no difference here
footnote(general = "General comment of the table.",
alphabet = c("Footnote A;", "Footnote B;"),
symbol = c("Footnote Symbol 1")) %>%
column_spec(1, width = "5em") %>% # fix width column 1
column_spec(2, width = "10em") %>% # fix width column 2
column_spec(3, width = "15em") # fix width column 3
To [improve line spacing[(https://stackoverflow.com/questions/53794142/increase-line-row-spacing-with-kableextra), one can add the following before & after code chunk in the Rmd:
\renewcommand{\arraystretch}{1.5} <!-- increase line spacing for the table -->
RMD CHUNK HERE
\renewcommand{\arraystretch}{1} <!-- reset row hight/line spacing -->
Comment:
I also tried the pander approach from #daroczig and made the following experiences:
Pro: nice line spacing plus a "real bullet list" (compared to the $\boldsymbol{\cdot}$-workaround in the kableExtra approach).
Con: a large blank space is included after the bullet list
In addition, when using the pander approach in an Rmd file using the huskydown thesis template the footnotes greatly messed up the table alignment.
Use the split.table parameter of pandoc.table (that is being called by pander in the background) or disable the table splitting in general via panderOptions's table.split.table, eg
pander::pander(df, keep.line.breaks = TRUE, style = 'grid', justify = 'left', split.table = Inf)
or
library(pander)
panderOptions('table.style', 'grid')
panderOptions('table.alignment.default', 'left')
panderOptions('table.split.table', Inf)
panderOptions('keep.line.breaks', TRUE)
pander(df)
In the old bookdown (I forgot the version), there is a punctuation, such as :, between table number and the content of table caption. For example, it may be like Table 1:XXXX. However, it seems the punctuation losses in the newest bookdown. The caption now is Table 1 XXXX. But I like the punctuation more than without it. The following is an example.
---
output: bookdown::word_document2
---
```{r results = 'asis', echo = FALSE, eval = T}
data <- data.frame(ColA = c(1, 2, 3), colB = c('abc', 'def', 'ghi'))
kable(data, format = 'pandoc', booktabs = TRUE, longtable = TRUE, caption = 'test table')
```
Save the codes as test1.Rmd. After that attach the package bookdown and run
rmarkdown::render('test1.Rmd', output_format = 'word_document2', quiet = T)
the table caption is Table 1:test table with the old knitr, but now is Table 1 test table.
So my question goes as follows.
Is there a way to add the punctuation between table number and content of table caption with the newest bookdown?
If there is a way, could I change the punctuations, such from : to ., or from . to $. with the newest bookdown?
I am writing a small exercise book with Markdown. I would like to have the final output with the plots on a column and the document text on the other. Similar problems are addressed here and here. Unfortunately, they mainly desire one output per column. I would like to produce the output on a column and the text on the other. Really interesting is Docco, but it apprently shows the code output with the text.
A possible solution would be the RPres markdown horizontal rule: using ***, it creates two easy to use columns. But I do find documentation on its implementation in Markdown documents.
Here an image showing my results so far and an example of my code:
```{r setoption, cache=TRUE, warning=FALSE, message=FALSE, fig.width=12}
knitr::opts_chunk$set(cache=TRUE, warning=FALSE, message=FALSE, fig.width=4, echo = FALSE)
```
```{r, loadlibraries}
library(knitr)
library(lattice)
```
### Exercise 1 - 22/4/'16
Is the data set shown in the following figure symmetric or skewed? How many modes does this data set have?
```{r 1.1}
e1 <- rep(seq(1, 6, 1), c(6, 4, 2, 2, 4, 6))
barchart(table(e1), horizontal = FALSE, xlab = "", ylab = "Frequency")
```
**Solution:**
The data set is symmetric. Furthermore, it has two modes.
### Exercise 2 - 22/4/'16
Describe the shape of the dataset shown in the following figure.
```{r 2.1}
e2 <- rep(seq(1, 9, 1), c(6, 5, 4, 3, 2, 1, 1, 1, 1))
barchart(table(e2), ylab = "Frequency", horizontal = FALSE)
```
**Solution:**
The dataset is right skewed, also said right skewed, with one mode.
As you're asking for columns, my answer will be: table.
Using pipe_tables, figure and text can be alinged next to each other. However, this comes at a price:
The cells of pipe tables cannot contain block elements like paragraphs and lists, and cannot span multiple lines.
If this limitation is acceptable, pipe_tables provide a quite straightforward solution:
```{r img, fig.show = "hide", echo = FALSE}
library(knitr)
hist(rnorm(1000))
```
Figure|Explanation
-------------------------------|-------------------------
`r include_graphics(paste0(opts_chunk$get("fig.path"), "img-1.png"))`|Histogram of 1000 draws from a standard normal density.
Although the column headers cannot be omitted, you can leave them blank if desired.
Note that I initially suppress the plot (fig.show = "hide") and use include_graphics to include it afterwards. Otherwise, there would be a newline after the plot which disrupts the table.
(In knitr 1.12.3, include_graphics doesn't seem to work properly with inline code chunks. However, the current development version 1.12.25 works well.)
Extension
I hacked together an extension that allows to use a single chunk to generate and show the plots and some more features:
```{r setup, echo = FALSE}
library(knitr)
FigureNextToText <- function(number, # number of plot in chunk
text,
alt = "", # alternative text for image
label = opts_current$get("label"), # set explicitly when using inline!
ext = ".png",
headerL = " ", headerR = " ", # empty string confuses pandoc if only right header is set
widthL = 30, widthR = 30,
...) {
path <- fig_chunk(label = label, ext = ext, number = number, ...)
template <- "%s|%s
%s|%s
|%s\r\n\r\n"
output <- sprintf(
template,
headerL, headerR,
paste0(rep("-", widthL), collapse = ""), paste0(rep("-", widthR), collapse = ""),
alt, path, text
)
return(asis_output(output))
}
```
```{r img, fig.show = "hide", echo = FALSE, results = "asis"}
library(knitr)
hist(rnorm(1000))
hist(runif(n = 1000, min = 0, max = 10))
FigureNextToText(1, text = "Histogram of draws from standard normal density.", widthL = 50, widthR = 10)
FigureNextToText(2, text = "Histogram of draws from uniform distribution.", headerR = "Explanation", alt = "Histogram 2.")
```
Some text.
`r FigureNextToText(2, text = "The same plot, this time inline.", label = "img", headerR = "Explanation", alt = "Histogram 2.")`
Some more text.
I know that the setup looks a little bit scary, but once FigureNextToText is defined, it can be called quite simply, e.g.:
FigureNextToText(2, text = "Histogram of draws from uniform distribution.", headerR = "Explanation", alt = "Histogram 2.")
Finding the correct values for widthL and widthR is somewhat cumbersome. This is because their effect depends on the number of characters in the cell, i.e. the filename of the image in the MD file and the alt text, too.