r,knitr,pandoc,rmarkdown , Reference to a chunk in Rmarkdown (v2)

## Question:

Tag: r,knitr,pandoc,rmarkdown

After a while using knitr with latex I'm trying Rmarkdown, principallly because the possibility of having multiple outputs make easier the sharing with colleagues.

My problem is how to reference to chunk for figures in Rmd?

in Rnw classically you make \ref{fig:chunk_name}

Is reference to chunk directly supported, in Rmarkdown, or just internal links to sections etc. are supported? In a positive case, how refer to a chunk like the following?

{r my_chunk}
attach(mtcars)
plot(wt, mpg)



Edit This is the header, I need something more?

---
title: "Title"
author: "bbrill"
date: "2015/01/15"
output:
pdf_document:
fig_caption : true
---


Ok the problem was in the knitr formatting options, because it lacks of fig.cap ="", which is needed by Latex to build a figure environnement.

Because of my first try with Rmarkdown I thought the problem was that hyperref was not supported (it was evidently not supported in markdown v1), or to other things related to my newbie use of markdown...

I'm sorry, I was crazy for nothing.

The problem was in the lack of fig.cap in the options so, this works:

{r my_chunk, fig.cap = ""}
attach(mtcars)
plot(wt, mpg)



see fig \ref{my_chunk}

# Related:

## ggplot equivalent for matplot

r,ggplot2
Is there an equivalent in ggplot2 to plot this dataset? I use matplot, and read that qplot could be used, but it really does not work. ggplot/matplot data<-rbind(c(6,16,25), c(1,4,7), c(NA, 1,2), c(NA, NA, 1)) as.data.frame(data) matplot(data, log="y",type='b', pch=1) ...

## R — frequencies within a variable for repeating values

r,count,duplicates
I've got a column A, which has several values, some of them repeating. So, example: A = c(5, 9, 6, 5, 5). I need to go through A and count the frequencies of each of the values in A. So, for this example, for the set of 5s in A,...

## Remove quotes to use result as dataset name

r,string
I've got a vector with a long list of dataset names. E.g myvector<-c('ds1','ds2,'ds3') I'd like to use the names ds1..ds3 to write a file, taking the file name from the vector. Like this: write.csv(dataset[i],file=paste(myvector[i],'.csv',sep='') with dataset being d1...ds3, but without quotes. How can I remove the quotes and refer to...

## dplyr multiple inputs from Shiny

r,shiny,dplyr
I have a Shiny app that takes input from radio button and then use that to perform filter to the data frame using dplyr in the server side. It works, but now I want to expand it to take multiple inputs to filter, and I have no idea how to...

## Serial modification of objects in R

r,oop
I have a number of matrices of the same size: m1.m <- matrix(c(1,2,3,4), nrow=2, ncol=2) m2.m <- matrix(c(5,6,7,8), nrow=2, ncol=2) ... I want to set uniform column and row names to all of them. Currently I am doing it like this: new_col_names <- c("Col1","Col2") new_row_names <- c("Row1","Row2") change_names <- function(m,...

## Replace -inf, NaN and NA values with zero in a dataset in R

r,time-series,nan,zoo
I am trying to run some trading strategies in R. I have downloaded some stock prices and calculated returns. The new return dataset has a number of -inf, NaN, and NA values. I am reproducing a row of the dataset (log_ret). Its a zoo dataset. library(zoo) log_ret <- structure( c(0.234,-0.012,-Inf,NaN,0.454,Inf),...

## Sleep Shiny WebApp to let it refresh… Any alternative?

r,shiny,sleep
I have a WebApp that have some renderUI({})... and some of them depend on the input of another. This makes that, briefly, a red error in the webpage appear when I select some options. Because the if() clause of some renderUI({}) depend on the input of a selectizer. The error...

## Fitted values in R forecast missing date / time component

r,time-series,forecasting
I've been doing a variety of models in R with time series data (in XTS format) and I keep running into the same issue where there's no date / time component to the fitted values / forecasts and thus I can't graph them on the same graph as the original...

## copy a list of data.tables

r,data.table
I have the following situation: 1) a list of data tables 2) For testing purposes I deliberately want to (deeply) copy the whole list including the data tables 3) I want to take some element from the copied list and add a new column. Here is the code: library(data.table) x...

## Highlighting specific ranges on a Graph in R

r,graph,highlight
library(season) plot(CVD$yrmon, CVD$cvd, type = 'o',pch = 19,ylab = 'Number of CVD deaths per month',xlab = 'Time') if i wanted to highlight a region of the graph based on x values say from 1994-1998 how do i do this? Any thought would be appreciated Thanks....

## Keep the second occurrence in a column in R

r,conditional,subset,find-occurrences
I have quite a simple dataset: ID Value Time 1 censored 1 1 censored 2 1 uncensored 3 1 uncensored 4 1 censored 5 1 censored 6 2 censored 1 2 uncensored 2 2 uncensored 3 2 uncensored 4 2 censored 5 I want to keep the first uncensored occurrence,...

## R: Using the “names” function on a dataset created within a loop

r,paste,assign,names
I am using a for loop to read in multiple csv files and naming the datasets import1, import2, etc. For example: assign(paste("import",i,sep=""), read.csv(files[i], header=FALSE)) However, I now want to rename the variables in each dataset. I have tried the following: names(as.name(paste("import",i,sep=""))) <- c("xxxx", "yyyy") But get the error "target of...

## Am I using sapply incorrectly?

r,sapply
This code is suppose to take in a word, and compute values for letters of the word, based on the position of the letter in the word. So for a word like "broke" it's suppose to compute the values for the letter "r" and "k" strg <- 'broke' #this part...

## Convert strings of data to “Data” objects in R [duplicate]

r,date,csv
This question already has an answer here: as.Date with dates in format m/d/y in R 2 answers My problem is that the as.Date function does not convert the values in a "date" column of a data frame into Date objects. I have a data.frame nmmaps. Here is a short...

## Twitter: Get followers from multiple users at once

I am working on a project where I need to find the reach of some social events. I want to know how many people who were exposed to comments on a festival called Tinderbox in Denmark. What I do is to get the statusses on Twitter including the word "tinderbox"...

## How to set x-axis with decreasing power values in equal sizes

r,plot,ggplot2,cdf
Currently I am doing some cumulative distribution plot using R and I tried to set x-axis with decreasing power values (such as 10000,1000,100,10,1) in equal sizes but I failed: n<-ceiling(max(test)) qplot(1:n, ecdf(test)(1:n), geom="point",xlab="check-ins", ylab="Pr(X>=x)")+ geom_step() +scale_x_reverse(breaks=c(10000,1000,100,10,1)) +scale_shape_manual(values=c(15,19)) It seems that the output has large interval for 10000, then all the...

## Find multiple consecutive empty lines

r
I'm trying to chop up a text file into the articles it contains. Usually this is done by identifying a pattern each article begins with. Unfortunately the database I downloaded the articles from doesn't have that. The only pattern I can find is that after each article there are 3...

## R: recursive function to give groups of consecutive numbers

r,if-statement,recursion,vector,integer
Given a sorted vector x: x <- c(1,2,4,6,7,10,11,12,15) I am trying to write a small function that will yield a similar sized vector y giving the last consecutive integer in order to group consecutive numbers. In my case it is (defining groups 2, 4, 7, 12 and 15): > y...

## Correlate by levels of a variable in R

r,correlation
I would like to correlate two variables and have the output reported separately for levels of a third variable. My data are similar to this example: var1 <- c(7, 8, 9, 10, 11, 12) var2 <- c(18, 17, 16, 15, 14, 13) categories <- c(1, 2, 3, 1, 2, 3)...

## Converting column from military time to standard time

r,excel
I'm trying to convert a column showing the time of road traffic accidents from military time to standard time. The data looks like this: Col1 Time..24hr. 1 1404 2 322 3 1945 4 1005 5 945 I'd then like to convert to 12hr so for '322' I'd like to make...

## Select / subset spatial data in R

r,dictionary,spatial
I am working on a large data set with spatial data (lat/long). My data set contains some positions that I don´t want in my analysis (it makes the files to heavy to process in ArcMap- many Go of data). This is why I want to subset the relevant data for...

## Fitting a subset model with just one lag, using R package FitAR

r,time-series
I am trying to fit a subset model with only lag 4. In the manual it's written "you must use p=c(0,0,0,4) since p=4 will fit a full AR(4)". I did this. #fit a subset model with just lag 4 Fit=FitAR(p=c(0,0,0,4), lag.max = "default", ARModel = "ARz") However, I get the...

## How to quickly read a large txt data file (5GB) into R(RStudio) (Centrino 2 P8600, 4Gb RAM)

r,large-data
I have a large data set, one of the files is 5GB. Can someone suggest me how to quickly read it into R (RStudio)? Thanks

## Return Column Names when True in R

r
I am using R for a project and I have a data frame in in the following format: A B C 1 1 0 0 2 0 1 1 I want to return a data frame that gives the Column Name when the value is 1. i.e. Impair1 Impair2 1...

## Set a timer in R to execute a program

r,timer
I have a program to execute per 15 seconds, how can I achieve this, the program is as followed: print_test<-function{ cat("hello world") } ...

## How to plot data points at particular location in a map in R

I have a dataset that looks like this: LOCALITY numbers 1 Airoli 72 2 Andheri East 286 3 Andheri west 208 4 Arya Nagar 5 5 Asalfa 7 6 Bandra East 36 7 Bandra West 72 I want to plot bubbles (bigger the number bigger would be the bubble) inside...

## how to read a string as a complex number?

r
I have a string which has a complex format, how can I use complex() to treat it as a complex number? For example: myStr="0.76+0.41j" now I want to do sth like: myStr_complex=complex(myStr) # my question is how should I do this part? Eventually Im(myStr_complex) should print 0.41 ...

## How (in a vectorized manner) to retrieve single value quantities from dataframe cells containing numeric arrays?

r,dataframes,vectorization
I've got a dataframe that includes columns like the one on the right here: lengthArray speed_max 1 4 24, 18, 24, 18 2 10 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 3 4 -999, -999, -999, -999 4 2 -999, -999 5 2 18, 18 6 1...

## Limit the color variation in R using scale_color_grey

r,colors,ggplot2
Before I start, allow me to explain my graph: I have two Genotypes (WTB and whd) and each have two conditions (0 and 7), so I have four lines. Now, I want to make a plot where each variable and its condition is the same color. Anything with whd will...

## how to call Java method which returns any List from R Language? [on hold]

java,r,rjava
How to call java method which returns list from R Language.

## Appending a data frame with for if and else statements or how do put print in dataframe

r,loops,data.frame,append
How do I put what I printed in a dataframe with a for loop and if else statements? Basically, this code: list<-c("10","20","5") for (j in 1:3){ if (list[j] < 8) print("Greater") else print("Less") }) #[1] "Less" #[1] "Less" #[1] "Greater" Or should it be something more like this? f3 <-...

## optimization algorithm for circular data

r,optimization,circular,maximization
Background: I am interested in localizing a sound source from a suite of audio recorders. Each audio array consists of 6 directional microphones spaced evenly every 60 degrees (0, 60, 120, 180, 240, 300 degrees). I am interested in finding the neighboring pair of microphones with the maximum set of...

## R Program Vector, record Column Percent

r,vector,percentage
This is my vector head(sep) I must find percent of all SEP 11 in each row. For instance, in first row, percent of SEP 11 is 100 * ((63 + 124)/ (63 + 124 + 0 + 0)) And would like this stored in newly created 8th column Thanks dput...

r,rbind