Using dplyr:filter to create new variables in for loop for rMarkdown - for-loop

Question

I have some R code that is meant to run a .rmd file so that I can create a unique report for multiple individuals at the same time.
Simplistically, my issue is that code chunk 1 creates a PDF output that is correct, however, will only create one PDF, and not one for each athlete in my dataset.
Code chunk 2 will create multiple PDF outputs (one for each athlete in the dataset), however, the variables created within the for loop (i.e., Athlete_full_name_i, Athlete_Sport_i) do not work. In the PDF output, these values are presented as "c("values","in","the","list")".
I think the code is close to working well but I would Love some advice to make this run smoother.
Thank you!
code chunk 1:
'''
#libraries
library(tidyverse)
library(rmarkdown)
library(dplyr)
#extra information
Folder_path1 <- "path to folder"
Excel_sheet1 <- "Data"
StartDate1 <- "2021-09-01"
EndDate1 <- Sys.Date()
#create athlete dataframe to run one, or multiple athlete reports at once.
Athlete_full_name <- c("John Smith", "Joe Tree") #as the name should appear in the report
Athlete_file_name <- c("SmithJ", "TreeJ") #Last name, first initial
Athlete_Team <- c("Men's Football", "Men's Darts") #Sport as it should appear in the report
Athlete_df <- data.frame(Athlete_full_name, Athlete_file_name, Athlete_Team)
Names <- unique(Athlete_df$Athlete_file_name)
#For loop - each athlete in Athlete_df gets unique report
for (i in 1:length(Names)) {
#creating new variables for each iteration
#determine athlete full name
Athlete_full_name_i <- Athlete_df %>%
filter(Athlete_file_name == Names[i]) %>%
subset(select = 1)
#determine athlete sport
Athlete_Sport_i <- Athlete_df %>%
filter(Athlete_file_name == Names[i]) %>%
subset(select = 3)
#create Athlete report with unique params and unique filename
rmarkdown::render("R2S_Dinos_JumpV3.Rmd",
params = list(Athlete_csvname = Names[i],
Athlete_fullname = Athlete_full_name_i,
Team = Athlete_Sport_i,
Folder_path = Folder_path1,
Excel_sheet = Excel_sheet1,
StartDate = StartDate1,
EndDate = EndDate1),
output_format = "pdf_document",
output_file=paste0("Athlete Reports/", Names[i], "_Report_", Sys.Date(), ".pdf"))
}
'''
code chunk 2:
'''
'''
#libraries
library(tidyverse)
library(rmarkdown)
library(dplyr)
#extra information
Folder_path1 <- "path to folder"
Excel_sheet1 <- "Data"
StartDate1 <- "2021-09-01"
EndDate1 <- Sys.Date()
#create athlete dataframe to run one, or multiple athlete reports at once.
Athlete_full_name <- c("John Smith", "Joe Tree") #as the name should appear in the report
Athlete_file_name <- c("SmithJ", "TreeJ") #Last name, first initial
Athlete_Team <- c("Men's Football", "Men's Darts") #Sport as it should appear in the report
Athlete_df <- data.frame(Athlete_full_name, Athlete_file_name, Athlete_Team)
#For loop - each athlete in Athlete_df gets unique report
for (Athlete_file_name in Athlete_df$Athlete_file_name) {
#creating new variables for each iteration
#determine athlete full name
Athlete_full_name_i <- Athlete_df %>%
filter(Athlete_file_name == Athlete_file_name) %>%
subset(select = 1)
#determine athlete sport
Athlete_Sport_i <- Athlete_df %>%
filter(Athlete_file_name == Athlete_file_name) %>%
subset(select = 3)
#create Athlete report with unique params and unique filename
rmarkdown::render("R2S_Dinos_JumpV3.Rmd",
params = list(Athlete_csvname = Athlete_file_name,
Athlete_fullname = Athlete_full_name_i,
Team = Athlete_Sport_i,
Folder_path = Folder_path1,
Excel_sheet = Excel_sheet1,
StartDate = StartDate1,
EndDate = EndDate1),
output_format = "pdf_document",
output_file=paste0("Athlete Reports/", Athlete_file_name, "_Report_", Sys.Date(), ".pdf"))
}
'''

Answer 1

When I run Code chunk 1 with a test Rmd output file it works as expected (two pdf files):
test_out.Rmd file:
---
title: "test_out"
params:
name: Bob
personid: 1
---
`r params$name` is person number `r params$personid`
Shortened slightly for clarity:
library(tidyverse)
library(rmarkdown)
Athlete_full_name <- c("John Smith", "Joe Tree")
Athlete_file_name <- c("SmithJ", "TreeJ")
Athlete_Team <- c("Men's Football", "Men's Darts")
Athlete_df <- data.frame(Athlete_full_name, Athlete_file_name, Athlete_Team)
Names <- unique(Athlete_df$Athlete_file_name)
for (i in 1:length(Names)) {
Athlete_full_name_i <- Athlete_df %>%
filter(Athlete_file_name == Names[i]) %>%
subset(select = 1)
Athlete_Sport_i <- Athlete_df %>%
filter(Athlete_file_name == Names[i]) %>%
subset(select = 3)
rmarkdown::render(
"test_out.Rmd",
params = list(Athlete_fullname = Athlete_full_name_i,
Team = Athlete_Sport_i),
output_format = "pdf_document",
output_file = paste0("test_out/", Names[i], "_Report_", Sys.Date(), ".pdf")
)
}
You could make this tidier and easier to debug with an anonymous function inside group_walk - this is the way I'd recommend doing it:
Athlete_df |>
rowwise() |>
group_walk(function(data, key) {
rmarkdown::render(
"test_out.Rmd",
params = list(
Athlete_fullname = data$Athlete_full_name,
Team = data$Athlete_Team
),
output_format = "pdf_document",
output_file = paste0("test_out/", data$Athlete_file_name, "_Report", ".pdf")
)
})
(same result)
In your code chunk 2 the problem comes when you filter with Athlete_file_name == Athlete_file_name. This tests whether these variables are equal within the dataframe, i.e. keep every row where the Athlete_file_name column equals the Athlete_file_name column, which means every row every time! Change the name of the iterating variable to e.g. in_name:
for (in_name in Athlete_df$Athlete_file_name) {
...
filter(Athlete_file_name == in_name) %>% # twice
...
output_file = paste0("test_out/", in_name,
"_Report_", Sys.Date(), ".pdf"
...
}

Answer 2

Thanks for the feedback everyone, there was an error in the for loop. The solution is as follows:
'''
#libraries
library(tidyverse)
library(rmarkdown)
library(dplyr)
#extra information
Folder_path1 <- "path to folder"
Excel_sheet1 <- "Data"
StartDate1 <- "2021-09-01"
EndDate1 <- Sys.Date()
#create athlete dataframe to run one, or multiple athlete reports at once.
Athlete_full_name <- c("John Smith", "Joe Tree") #as the name should appear in the report
Athlete_file_name <- c("SmithJ", "TreeJ") #Last name, first initial
Athlete_Team <- c("Men's Football", "Men's Darts") #Sport as it should appear in the report
Athlete_df <- data.frame(Athlete_full_name, Athlete_file_name, Athlete_Team)
Names <- unique(Athlete_df$Athlete_file_name)
#For loop - each athlete in Athlete_df gets unique report
for (i in Names) {
#creating new variables for each iteration
#determine athlete full name
Athlete_full_name_i <- Athlete_df %>%
filter(Athlete_file_name == i) %>%
subset(select = 1)
#determine athlete sport
Athlete_Sport_i <- Athlete_df %>%
filter(Athlete_file_name == i) %>%
subset(select = 3)
#create Athlete report with unique params and unique filename
rmarkdown::render("R2S_Dinos_JumpV3.Rmd",
params = list(Athlete_csvname = i,
Athlete_fullname = Athlete_full_name_i,
Team = Athlete_Sport_i,
Folder_path = Folder_path1,
Excel_sheet = Excel_sheet1,
StartDate = StartDate1,
EndDate = EndDate1),
output_format = "pdf_document",
output_file=paste0("Athlete Reports/", i, "_Report_", Sys.Date(), ".pdf"))
}