Here is an example of what I'm trying to do. I would like to call in the text a result from a table itself coming from a random computation.
---
title: "RĂ©gression logistique"
subtitle: "Analyse quantitative II"
author:
- name: ""
- affiliation:
date: "TP 4"
output:
html_document:
toc: yes
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r message=FALSE}
bystander <- data.frame(reaction = c(rep(0, 30), rep(1, 30)),
age.victime = c(rep(5, 5),rep(85, 5),rep(7, 5),rep(35, 5),rep(45, 5),rep(50, 5)),
sexe.victime = c(rep(0, 20), rep(1, 10), rep(0, 10), rep(1, 20)),
nbrpers = c(11:40, 0:29),
statutse = c(rep(4, 30), rep(18, 30)))
#install.packages("caret")
library(caret)
# install.packages("lmtest")
library(lmtest)
#install.packages("pscl")
library(pscl)
#install.packages("e1071")
library(e1071)
```
```{r}
Train <- createDataPartition(bystander$reaction, p=0.8, list=FALSE)
training <- bystander[ Train, ]
testing <- bystander[ -Train, ]
training$reaction <- as.factor (training$reaction)
model_fit <- train(reaction ~ age.victime + sexe.victime + nbrepers + statutse, data=training, method="glm")
testing$reaction <- as.factor (testing$reaction)
pred <- predict(model_fit, newdata=testing)
confusionMatrix(data=pred, testing$reaction)
```
We obtain a an accuracy of `r confusionMatrix(data=pred, testing$reaction)`.
I just want the Accuracy from the overall in the confusionMatrix. Is there a way to call only this result because my trial is not working there (pretty logical, it's a list), like in latex when you can reference your results and call it later.
Thank's in advance!
To achieve your desired result assign the result of calling caret::confusionMatrix to variable. Afterwards you could access the Accuracy in an inline chunk like so:
---
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
library(caret)
```
```{r}
conf_mat <- caret::confusionMatrix(iris$Species, sample(iris$Species))
```
We obtain an accuracy of `r conf_mat$overall[["Accuracy"]]`.
After days trying to find a solution, I give up and ask for help.
I decided to use R Markdown very recently. While I can render plots as I want, I cannot succeed in rendering my tables in a pdf doc properly.
Here the corresponding [EDITED]code:
---
title: "My_title"
output:
pdf_document: default
html_document:
df_print: paged
params:
date: "!r Sys.Date()"
---
```{r library, echo=F, message=F, warning=F, paged.print=FALSE}
suppressMessages(library("knitr"))
suppressMessages(library(reshape2))
suppressMessages(library(splines))
suppressMessages(library(kableExtra))
suppressMessages(library(gplots))
```
```{r, setup, echo = F}
opts_knit$set(root.dir = "my_path")
knitr::opts_chunk$set(echo = F)
```
```{r}
dt <- expand.grid(Region=c("a","b","c"), Country=c("d","e","f"), Cancer= c("All", "CRC", "Breast"),
age.1.1=1:2,
age.1.2=1:2,
age.1.3=1:2)
```
```{r Table_1, INCLUDE = TRUE}
cancer.lab <- c("All", "CRC", "Breast")
for (i in 1:3){
b <- dt[dt$Cancer==cancer.lab[i],]
b <- b[,-3]
t <- kable(b, format = ,caption = "Fig", row.names = F) %>%
kable_paper() %>%
kable_styling(font_size = 9) %>%
add_header_above(c(" " = 2, "1998" = 3))
print(t)
}
```
Again I am new and I surely miss something.
I use Mac if it may explain something.
Thank you for your help.
Sophie.
I think this is the same issue as dealt with here: https://stackoverflow.com/a/53632154/2554330. The problem is that you need to use knit_print to print the tables, but you can't do that in a loop.
So if you change the last code chunk to this, it should work:
```{r Table_1, INCLUDE = TRUE}
results <- c()
cancer.lab <- c("All", "CRC", "Breast")
for (i in 1:3){
b <- dt[dt$Cancer==cancer.lab[i],]
b <- b[,-3]
t <- kable(b, format = ,caption = "Fig", row.names = F) %>%
kable_paper() %>%
kable_styling(font_size = 9) %>%
add_header_above(c(" " = 2, "1998" = 3))
results <- c(results, knit_print(t))
}
asis_output(results)
```
I managed to create a html document that creates dynamic tabsets based on a list of items. Adding one plot works fine on one tabset. How can I add now multiple plots on one tabset?
Hereby the code I started from but it only shows 1 plot per tabset when you knit the document to html output. obviously there is still something missing.
---
title: "R Notebook"
output:
html_document:
df_print: paged
editor_options:
chunk_output_type: inline
---
### header 1
```{r}
library(ggplot2)
df <- mtcars
pl_list <- list()
pl1 <- qplot(cyl, disp, data = df[1:12,])
pl2 <- qplot(mpg, cyl, data = df[13:20,])
pl3 <- qplot(mpg, cyl, data = df[21:30,])
pl4 <- qplot(mpg, cyl, data = df[1:12,])
pl_list[[1]] <- list(pl1, pl3, "one")
pl_list[[2]] <- list(pl2, pl4, "two")
```
### header {.tabset}
```{r, results = 'asis', echo = FALSE}
for (i in seq_along(pl_list)){
tmp <- pl_list[[i]]
cat("####", tmp[[3]], " \n")
print(tmp[1])
cat(" \n\n")
}
```
There are a couple of improvements you can do.
Create cat header function with arguments for text and level.
With it you don't need to call cat multiple times and it creates wanted number of # automatically.
catHeader <- function(text = "", level = 3) {
cat(paste0("\n\n",
paste(rep("#", level), collapse = ""),
" ", text, "\n"))
}
print plots using lapply.
Full code looks like this:
---
title: "R Notebook"
output:
html_document:
df_print: paged
editor_options:
chunk_output_type: inline
---
```{r, functions}
catHeader <- function(text = "", level = 3) {
cat(paste0("\n\n",
paste(rep("#", level), collapse = ""),
" ", text, "\n"))
}
```
### header 1
```{r}
library(ggplot2)
df <- mtcars
pl_list <- list()
pl1 <- qplot(cyl, disp, data = df[1:12,])
pl2 <- qplot(mpg, cyl, data = df[13:20,])
pl3 <- qplot(mpg, cyl, data = df[21:30,])
pl4 <- qplot(mpg, cyl, data = df[1:12,])
pl_list[[1]] <- list(pl1, pl3, "one")
pl_list[[2]] <- list(pl2, pl4, "two")
```
## header {.tabset}
```{r, results = "asis", echo = FALSE}
for(i in seq_along(pl_list)){
tmp <- pl_list[[i]]
# As you want to use tabset level here has to be lower than
# parent level (ie, parent is 2, so here you have to use 3)
catHeader(tmp[[3]], 3)
lapply(tmp[1:2], print)
}
```
I am trying to create a table in RMarkdown that looks similar to the following example:
---
title: "Example"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```
```{r cars, echo=FALSE, message=FALSE, warning=FALSE, results='asis'}
library(Hmisc)
latex(mtcars, file = "", cgroup = c("mpg", "cyl"), n.cgroup = c(1,10))
```
I would like to group columns 2 through 10. Any ideas on how I can accomplish this with the Hmisc package or any other R package?
I think just using a blank header name for the first column gives you what you want:
latex(mtcars, file = "", cgroup = c("", "cyl"), n.cgroup = c(1,10))
Result:
Using my package:
library(huxtable)
hux_cars <- as_hux(mtcars, add_colnames = TRUE)
hux_cars <- insert_row(hux_cars, c('mtcars', 'cyl', rep('', 9)))
colspan(hux_cars)[1, 2] <- 10
align(hux_cars)[1, 2] <- 'centre'
bold(hux_cars)[1, ] <- TRUE
position(hux_cars) <- 'left'
quick_pdf(hux_cars)
Which produces:
{r setup, include=FALSE, message=FALSE, results="hide"}
knitr::opts_chunk$set(echo = TRUE)
library(knitr)
library(kfigr)
library(dplyr)
library(png)
library(grid)
library(pander)
library(ggplot2)
Question
Loops in rmarkdown: in-text figure reference? figure captions?
Goal
Use a for loop to create sections with text, in-text results, and multiple figure references with associated figure captions in the figure list. The figure references/numbering should be seemless with figures numbered before and after these new sections.
Note: The figures referenced in the for loop are generated earlier in the text, saved as pngs, and then re-loaded. This might seem clunky for the purpose of this example, but the actual figs are maps and are slow to generate (I plan to comment out the loop that generates the figures once I have them how I want).
{r echo = FALSE, warnings=FALSE, message=FALSE, results="hide"}
Data: Each year we have a different number of strata, hence the need for a loop.
df <- rbind(
data.frame(strata = rep("A", 10), x = rnorm(10, mean= 10), y = rnorm(10, mean = 15),z = rnorm(10, mean = 20)),
data.frame(strata = rep("B", 10), x = rnorm(10, mean= 5), y = rnorm(10, mean = 10), z = rnorm(10, mean = 15)),
data.frame(strata = rep("C", 10), x = rnorm(10, mean= 15), y = rnorm(10, mean = 20), z = rnorm(10, mean = 10)))
first_plot: the figure that should appear in the list before for loop creates the sections by strata
first_plot <- ggplot(df, aes(x, fill=strata)) + geom_histogram()
last_plot: the figure that should appear in the list after the for loop creates the sections by strata
last_plot <- ggplot(df, aes(x = strata, y = z)) + geom_boxplot()
Figure generation (this is the part that will be commented out later in my version once I have the maps how I want)
strat <- unique(df$strata)
for (i in seq_along(strat)) {
sub <- df %>% filter(strata %in% strat[i])
fig1 <- ggplot(sub, aes(x = x, y = y)) + geom_point()
ggsave(fig1, file=paste0("fig1_", strat[i], ".png"))
fig2 <- ggplot(sub, aes(x = x, y = z)) + geom_point()
ggsave(fig2, file=paste0("fig2_", strat[i], ".png"))
}
Load the png's
df_figs <- list.files(pattern = "\\.png$")
for (i in df_figs){
name <- gsub("-",".",i)
name <- gsub(".png","",name)
i <- paste(".\\",i,sep="")
assign(name,readPNG(i))
}
Introduction section
Some introductory text in the report and a figure r figr('first_plot',TRUE, type='Figure').
```{r echo = FALSE, warnings=FALSE, message=FALSE, results = "asis"}
# Summary of results and image file names that will be references in text
results <- df %>%
group_by(strata) %>%
dplyr::summarise_each(funs(mean)) %>%
mutate(fig1 = paste0("fig1_", strata),
fig2 = paste0("fig2_", strata))
#Text template (each strata will have its own section)
template <- "# The %s stratum
The mean of *x* in %s stratum was %1.1f. Relationships between *x* and *y* and *x* and *z* can be found in `r figr('%s', TRUE, type='Figure')` and `r figr('%s', TRUE, type='Figure')`.
"
#Create markdown sections in for loop
for(i in seq(nrow(results))) {
current <- results[i, ]
cat(sprintf(template,
current$strata, current$strata,
current$x,
current$fig1, current$fig2))
}
#Also doesn't work:
template <- "# The %s stratum
The mean in %s stratum was %1.0f. Results can be found in "
template2 <- " and "
template3 <- ".
"
`figr('%s', TRUE, type='Figure')` and `figr('%s', TRUE, type='Figure')`."
#For loop
for(i in seq(nrow(results))) {
current <- results[i, ]
cat(sprintf(template,
current$strata, current$strata,
current$mean,
current$fig_1, current$fig_2))
print(paste0("`r figr(",paste0("'", current$fig1,"'"), TRUE, type='Figure'))
cat(sprintf(template2))
print(paste0("`r figr(",paste0("'", current$fig2,"'"), "TRUE, type='Figure'),`"))
cat(sprintf(template3))
}
```
Conclusion section
Some discussion text in the report and figure r figr('last_plot',TRUE, type='Figure').
Figures
*NOTE:* I don't know how to automate the looped portion of the list of figures here, so I've done it by hand.
```{r 'first_plot', echo=FALSE, warning=FALSE, fig.width=6.5, fig.height=6, fig.cap="The caption for the first figure."}
suppressMessages(print(first_plot))
```
```{r 'fig1_A', echo=FALSE, warning=FALSE, fig.width=6.5, fig.height=6, fig.cap="Caption text for fig1_A."}
grid.raster(fig1_A)
```
```{r 'fig2_A', echo=FALSE, warning=FALSE, fig.width=6.5, fig.height=6, fig.cap="Caption text for fig2_A."}
grid.raster(fig2_A)
```
```{r 'fig1_B', echo=FALSE, warning=FALSE, fig.width=6.5, fig.height=6, fig.cap="Caption text for fig1_B."}
grid.raster(fig1_B)
```
```{r 'fig2_B', echo=FALSE, warning=FALSE, fig.width=6.5, fig.height=6, fig.cap="Caption text for fig2_B."}
grid.raster(fig2_B)
```
```{r 'fig1_C', echo=FALSE, warning=FALSE, fig.width=6.5, fig.height=6, fig.cap="Caption text for fig1_C."}
grid.raster(fig1_C)
```
```{r 'fig2_C', echo=FALSE, warning=FALSE, fig.width=6.5, fig.height=6, fig.cap="Caption text for fig2_C."}
grid.raster(fig2_C)
```
```{r 'last_plot', echo=FALSE, warning=FALSE, fig.width=6.5, fig.height=6, fig.cap="The caption for the last figure."}
suppressMessages(print(last_plot))
```
SOLUTIONS
Use knit_expand()
Use captioner instead of kfigr
This numbers your figures (or tables) in text and at the end of your report.
This script shows you how to create markdown paragraphs in for loops that have in-text references to figures.
It also shows you how to create custom figure captions in for loops while retaining the number order.
If you show how to do #4 and #5 using brew I will give you all the SO points.
Libraries
library(knitr)
library(dplyr)
library(png)
library(grid)
library(pander)
library(ggplot2)
library(devtools)
library(captioner)
Create a fig_nums() function using the captioner package
(https://github.com/adletaw/captioner/blob/master/vignettes/using_captioner.Rmd)
fig_nums <- captioner(prefix = "Figure")
Data
Each year we have a different number of strata, hence the need for a loop.
df <- rbind(
data.frame(strata = rep("A", 10), x = rnorm(10, mean= 10), y = rnorm(10, mean = 15), z = rnorm(10, mean = 20)),
data.frame(strata = rep("B", 10), x = rnorm(10, mean= 5), y = rnorm(10, mean = 10), z = rnorm(10, mean = 15)),
data.frame(strata = rep("C", 10), x = rnorm(10, mean= 15), y = rnorm(10, mean = 20), z = rnorm(10, mean = 10)))
first_plot: the figure that should appear in the list before for loop creates the sections by strata
first_plot <- ggplot(df, aes(x, fill=strata)) + geom_histogram()
fig_nums("first_plot", display = FALSE)
last_plot: the figure that should appear in the list after the for loop creates the sections by strata
last_plot <- ggplot(df, aes(x = strata, y = z)) + geom_boxplot()
Figure generation
Comment this section out once you have figs how you want. This step will not feel convoluted, unnatural, suboptimal, unnecessary, or like a very bad idea if you do a lot of mapping in R.
strat <- unique(df$strata)
for (i in seq_along(strat)) {
sub <- df %>% filter(strata %in% strat[i])
fig1 <- ggplot(sub, aes(x = x, y = y)) + geom_point()
ggsave(fig1, file=paste0("fig1_", strat[i], ".png"))
fig2 <- ggplot(sub, aes(x = x, y = z)) + geom_point()
ggsave(fig2, file=paste0("fig2_", strat[i], ".png"))
}
Load the png's
df_figs <- list.files(pattern = "\\.png$")
for (i in df_figs){
name <- gsub("-",".",i)
name <- gsub(".png","",name)
i <- paste(".\\",i,sep="")
assign(name,readPNG(i))
}
Introduction
Some introductory text in the report and a figure r fig_nums("first_plot", display="cite").
Results and image file names that will be referenced in text:
```{r echo = FALSE, warnings=FALSE, message=FALSE, results = "asis"}
results <- df %>%
group_by(strata) %>%
dplyr::summarise_each(funs(mean)) %>%
mutate(fig1 = paste0("fig1_", strata),
fig2 = paste0("fig2_", strata))
```
```{r run-numeric-md, warning=FALSE, include=FALSE}
#The text for the markdown sections in for loop... the knit_expand() is the work-horse here.
out = NULL
for (i in as.character(unique(results$strata))) {
out = c(out, knit_expand(text=c('#### The *{{i}}* strata',
'\n',
'The mean of *x* is ',
'{{paste(sprintf("%1.1f", results$x[results$strata==i]))}}', '({{fig_nums(results$fig1[results$strata==i],display="cite")}}).',
'\n'
)))
}
```
Creates section for each strata
`r paste(knit(text = out), collapse = '\n')`
Conclusion
Some discussion text in the report and figure r fig_nums("last_plot",display="cite").
List of Figures
`r fig_nums("first_plot",caption="Here is the caption for the first figure.")`
```{r 'first_plot', echo=FALSE, warning=FALSE, fig.width=6.5, fig.height=6}
suppressMessages(print(first_plot))
```
```{r figcaps, include=FALSE}
caps = NULL
for (i in as.character(unique(results$strata))) {
caps = c(caps, knit_expand(
text=c({{fig_nums(results$fig1[results$strata==i], caption="Caption text for strata *{{i}}* goes here.")}},
'``` {r {{results$fig1[results$strata==i]}}, echo=FALSE, warning=FALSE, fig.width=6.5, fig.height=6}',
{{paste0('grid.raster(',results$fig1[results$strata==i],')')}},
'```',
'\n')))
}
#DON'T FORGET TO UNLIST!
src <- unlist(caps)
```
`r paste(knit(text = src),sep='\n')`
`r fig_nums("last_plot", caption="The caption for the last figure.")`
```{r 'last_plot', echo=FALSE, warning=FALSE, fig.width=6.5, fig.height=6}
suppressMessages(print(last_plot))
```