I would like to make a table in R markdown that prints a crosstabulation of two variables and includes the variable name above it and on the left side. Also, I need to print this to a PDF so I require code that is compatible with kable("latex").
Reproducible example:
set.seed(143)
x <- sample(x = c("yes", "no"), size = 20, replace = TRUE)
y <- sample(x = c("yes", "no"), size = 20, replace = TRUE)
table(x,y) %>%
kable("latex") %>%
pack_rows("X", 1, 2) %>%
add_header_above(c(" ", "Y" = 2))
Which gives the following output:
However I would like it to look like this (created in Word for example):
Related
I am a basic-level learner of R. I am having a problem knitting out tables with a code my professor designed for the students. The code for table designs is set as below. I put this in my R markdown as below.
```{r, results="hide", message=FALSE, warning = FALSE, error = FALSE}
## my style latex summary of regression
jhp_report <- function(...){
output <- capture.output(stargazer(..., omit.stat=c("f", "ser")))
# The first three lines are the ones we want to remove...
output <- output[4:length(output)]
# cat out the results - this is essentially just what stargazer does too
cat(paste(output, collapse = "\n"), "\n")
}
```
After this, I tried printing this out with knitr.
```{r, message=FALSE, warning = FALSE, error = FALSE}
set.seed(1973)
N <- 100
x <- runif(N, 6, 20)
D <- rbinom(N, 1, .5)
t <- 1 + 0.5*x - .4*D + rnorm(N)
df.lm <- data.frame(y = y, x =x, D =D)
df.lm$D <- factor(df.lm$D, labels = c('Male', 'Female'))
##REGRESSION
reg.parallel <- lm(y ~ x + D, data = df.lm)
jhp_report(reg.parallel, title = "Result", label = "tab:D", dep.var.labels = "$y$")
```
As a result, instead of a table, it keeps on showing only the pure codes. I would like to know how I have to set up R markdown for it to print out the table instead of the codes. This is how the result looks like when I knit it.
I expected that there must be some setup options to print the table out. But I couldn't find the right one. Also, my assignment for class requires students to use this code. I did find other options like knitr::kable but I would like to use the given code for this assignment.
Thank you in advance!
I am trying to create a .rmd file that takes all of the pictures for a field day and the notes that was taken and create a report. I am able to get the pictures to plot but the no matter what I try the table with the notes does not want to print. Below is the loop I am utilizing:
for(i in 1:nrow(subset_Inventory_data)) {
singlept <- subset_Inventory_data[i,]
picture <- pictureLookup[singlept$GlobalID == pictureLookup$REL_GLOBAL,]
#PRINT PICTURE
plot(image_read(paste(baseURL,picture$UID,sep = "")) %>%
# image_resize("400x400") %>%
image_rotate(degrees = 90)
)
#creating table underneath picture
Categories <- c("Latitude", "Longitude", "Road Width", "Conditon", "Lock Present","Additional Notes")
sum_table <- data.frame(Category = character(),
Information = character(),
stringsAsFactors = FALSE)
sum_table <- rbind(sum_table,Categories,
stringsAsFactors = FALSE)
colnames(sum_table) <- Categories
sum_table$Latitude <- sprintf("%f",singlept$LAT)
sum_table$Longitude <-sprintf("%f",singlept$LONG)
sum_table$`Road Width` <- paste(singlept$Gate_Width,"feet")
sum_table$Conditon <- singlept$Condition
sum_table$`Lock Present` <- singlept$GlobalID
sum_table$`Additional Notes` <- singlept$General_Notes
#TRIED FLEXTABLE
ft <- flextable(sum_table)
ft <- fontsize(ft, size = 12)
ft <- autofit(ft)
print(ft)
#TRIED KABLE
print(kable(sum_table,"latex"))
}
I'm using leaflet and shiny. I would like to color my markers based on a column that can be changed via input. It's almost the same as Modifying Existing Maps with leafletProxy. In this example, the user can change the color palette. In my example, I would like to change the column that the palette is applied on.
I'm trying to use something like:
fillColor = ~pal(!!sym(input$col_to_apply)) # input$col_to_apply is a column name (string) I want to use
However, this doesn't work. I'm also not sure if I have to use reactive() in this case.
Sure. My suggestion would be to do it before the palette is created. Palettes are tricky enough as it is. See the below minimal example:
library(leaflet)
library(maps)
library(shiny)
ui <- fluidPage(
leafletOutput("map_1"),
selectInput(inputId = "input_species", label = "Species Selection", choices = c("Species_1", "Species_2", "Species_3"))
)
server <- function(input, output, session) {
#Load a map of the US from the 'map' package (runs once when apps starts)
shp_map = map("state", fill = TRUE, plot = FALSE)
#Make up a dataframe with some data for three species for each state (runs once when apps starts)
df_data <- data.frame(state = unique(shp_map$names), Species_1 = sample(100:199, 63), Species_2 = sample(200:299, 63), Species_3 = sample(300:399, 63))
#Create map
output$map_1 <- renderLeaflet({
df_map <- df_data
#Create a column called species selected based on which is selected in the dropdown box
df_map$Species_Selected <- df_map[, paste(input$input_species)]
#Create a palette function
palette <- colorNumeric(palette = "Blues", domain = df_map$Species_Selected)
#Use the palette function created above to add the appropriate RGB value to our dataframe
df_map$color <- palette(df_map$Species_Selected)
#Create map
map_1 <- leaflet(data = shp_map) %>%
addPolygons(fillColor = df_map$color, fillOpacity = 1, weight = 1, color = "#000000", popup = paste(sep = "", "<b>", paste(shp_map$names), " ", "</b><br>", df_map$Species_Selected))
map_1
})
}
shinyApp(ui, server)
Please I need assistant concerning a shiny code. I want to manipulate a data frame input by separating them into column vector for computation but I keep getting this error
Warning in <reactive>(...): NAs introduced by coercion
the code is as follows
library(shiny)
ui <- fluidPage(
# dataset
data <- data.frame(e1 = c(3, 7, 2, 14, 66),
e2 = c(2, 16, 15, 66, 30),
n1 = c(18, 25, 45, 62, 81),
n2= c(20, 30, 79, 64, 89))
# Application title
titlePanel("Demo"),
# Sidebar with a slider input for number of bins
sidebarLayout(
sidebarPanel(
# Input: Upload file
fileInput(inputId = 'file', label = 'upload the file')
),
# Display Output
mainPanel(
uiOutput("final")
)
)
)
# Define server logic required to draw a histogram
server <- function(input, output) {
# separating the dataframe into 4 column vectors
e1 <- reactive(as.numeric(input$file[,1]))
e2 <- reactive(as.numeric(input$file[,2]))
n1 <- reactive(as.numeric(input$file[,3]))
n2 <- reactive(as.numeric(input$file[,4]))
# File Upload function
data <- reactive({
file1 <- input$file
if(is.null(file1)){return()}
read.table(file = file1$datapath, sep = ',', header = TRUE)
})
output$result <- renderUI({
y <- (e1()/n1()) - (e2()/n2())
lg_y <- log(y)
v2 <- ((n1() - e1())/e1() * n1()) + ((n2() - e2())/e2() * n2())
w <- 1/v2
w1 <- sum(w)
w2 <- sum(w^2)
c <- w1 - (w2/w1)
s2 <- w * lg_y
ybar <- sum(s2)/sum(w)
Q <- sum(w*((lg_y - ybar)^{2}))# Cochrane homogeneity test statistic
Q.pval <- reactive(pchisq(Q, k() - 1,lower.tail = FALSE))
Isqd <- max(100*((Q-(k()-1))/Q),0)
})
}
# Run the application
shinyApp(ui = ui, server = server)
I have searched almost every question on this forum and haven't seen where the question was answered. please I look forward to your help
Still can't run the code above because you don't define function k(). Also FYI, your renderUI is set for "result" but your uiOutput is set for "final".
You get the warning Warning in <reactive>(...): NAs introduced by coercion because your true data set probably includes a non-numeric in it. I did not get any issues with the data set you provided above.
There are a couple ways forward:
1) Write a function to remove all non-numerics before you process the data. See here for a few examples.
2) Just keep the warning, it is a warning after all so it won't stop your code from running. Currently it turns your non-numerics into NA
3) Use suppressWarnings() but that is usually not recommended.
I do have a suggestion to clean up your code though:
# File Upload function
data <- reactive({
file1 <- input$file
if(is.null(file1)){return()}
read.table(file = file1$datapath, sep = ',', header = TRUE, stringsAsFactors = FALSE)
})
# separating the dataframe into 4 column vectors
e1 <- reactive(as.numeric(data()[,1]))
e2 <- reactive(as.numeric(data()[,2]))
n1 <- reactive(as.numeric(data()[,3]))
n2 <- reactive(as.numeric(data()[,4]))
I have 5 files which contain metabolites (details of different bacteria models). I'm writing a function to append a specified number of files. File names look like the following.
[1] "01_iAPECO1_1312_metabolites.csv" "02_iB21_1397_metabolites.csv"
[3] "03_iBWG_1329_metabolites.csv" "04_ic_1306_metabolites.csv"
[5] "05_iE2348C_1286_metabolites.csv"
Below is my function.
strat = 3 # defines the starting position of the range
end = 5 # defines the ending position of the range
type = "metabolites" # two types of files - for metabolites and reactions
files <- NULL
if (type == "metabolites"){
files <- list.files(pattern = "*metabolites\\.csv$")
}else if(type == "reactions"){
files <- list.files(pattern = "*reactions\\.csv$")
}
#reading each file within the range and append them to create one file
for (i in start:end){
temp_df <- data.frame(ModelName = character(), Object = character(),stringsAsFactors = F)
#reading the current file
temp = rbind(one,temp_df)
}
#writing the appended file
write.csv(temp,"appended.csv",row.names = F,quote = F)
temp_df <- NULL
For example, if I specify the start=3 and end = 5, the code is supposed to read files 03, 04 and 05 and append them. Note: the two integers at the beginning of the file names are used to get the file referenced by the range. I'm unable to select the required file within the for loop using a regular expression. When I specify the number it picks up but I'm looking for a generalized version with i in it.
currentFile = grep("01.+",files)
Any help is appreciated.
For the test data shown below this returns a vector containing the file names of the files that start with 02, 03, 04 and 05 and end with "reactions.csv"
# create some test files
for(i in 1:5) cat(file = sprintf("%02djunkreactions[.]csv", i))
# test input
start <- 2
end <- 5
type <- "reactions"
list.files(pattern = paste(sprintf("^%02d.*%s[.]csv$", start:end, type), collapse = "|"))
giving:
[1] "02junkreactions.csv" "03junkreactions.csv" "04junkreactions.csv"
[4] "05junkreactions.csv"
Note: If start and end are both always one digit then a simplification is possible:
list.files(pattern = sprintf("^0[%d-%d].*%s.csv$", start, end, type))
You can do this with a cross-join.
library(dplyr)
library(stringi)
start = 3
end = 5
type = "metabolites"
all_files = data_frame(file = list.files() )
desired_files = data_frame(
number = start:end,
regex = sprintf("^%02.f.*%s", number, file_type) )
all_files %>%
merge(desired_files) %>%
filter(stri_detect_regex(file, regex)) %>%
group_by(number) %>%
do(read.csv(.$file) ) %>%
write.csv("appended.csv", row.names = F, quote = F)
Are you looking for something like this?
files <- c("01_iAPECO1_1312_metabolites.csv", "02_iB21_1397_metabolites.csv","03_iBWG_1329_metabolites.csv", "04_ic_1306_metabolites.csv","05_iE2348C_1286_metabolites.csv")
for(i in 2:4) print(grep(sprintf("^(%02d){1}_",i),files,value=T))