I am trying to subset data within lapply for different columns to produce repeated single arm meta-analysis using metaprop command for many outcomes in 1 step as I have a giant number of outcomes.

Some outcomes have empty cells, so I need to properly subset data within lapply

Here is my data and code:

############################### Data sample  #####################################
data<- read.table(text="
studlab Number.of.patients  Procedure   Mortality   Post.op.stroke  
Lee2015 15  SPT 0   0
Wang2019    44  SPT     1
Nachira2018 12  SPT 1   1
Zhang2020   20  SPT 1   1
Lee2017 48  SPT 0   1
Lv2018  10  SPT 0   0
Weiping2018 28  SPT 0   0
Liu2021 60  SPM 0   
Gan2020 56  SPM     
Ye2021  105 SPM 1   1
Takeda2021  12  SPM     
Yin2020 22  SPM     0
Gan2020 28  SPM     
Egberts2019 4   SPM 1   1
Wang2019    80  SPM     0
Fujiwara2017    60  SPM 0   1
Mori2017    7   SPM 0   0
Parker2011  8   SPM 0   1
Zhu2021 19  SPM 0   1", header=T, sep="\t")

############################ Same data with dput command ####################
dput(data)
structure(list(studlab = c("Lee2015", "Wang2019", "Nachira2018", 
"Zhang2020", "Lee2017", "Lv2018", "Weiping2018", "Liu2021", "Gan2020", 
"Ye2021", "Takeda2021", "Yin2020", "Gan2020", "Egberts2019", 
"Wang2019", "Fujiwara2017", "Mori2017", "Parker2011", "Zhu2021"
), Number.of.patients = c(15L, 44L, 12L, 20L, 48L, 10L, 28L, 
60L, 56L, 105L, 12L, 22L, 28L, 4L, 80L, 60L, 7L, 8L, 19L), Procedure = c("SPT", 
"SPT", "SPT", "SPT", "SPT", "SPT", "SPT", "SPM", "SPM", "SPM", 
"SPM", "SPM", "SPM", "SPM", "SPM", "SPM", "SPM", "SPM", "SPM"
), Mortality = c(0L, NA, 1L, 1L, 0L, 0L, 0L, 0L, NA, 1L, NA, 
NA, NA, 1L, NA, 0L, 0L, 0L, 0L), Post.op.stroke = c(0L, 1L, 1L, 
1L, 1L, 0L, 0L, NA, NA, 1L, NA, 0L, NA, 1L, 0L, 1L, 0L, 1L, 1L
)), class = "data.frame", row.names = c(NA, -19L))

############################### Used code  #####################################
library(tidyr); library(ggplot2); library(meta); library(metafor)
lapply(names(data)[4:5], function(columntoplot){
 ## To subset based on the outcome column ## 
  df <-subset( data, data[[columntoplot ]] >=0 )  ## NOT WORKING PROPERLY
  
 mp<-metaprop(columntoplot,Number.of.patients,  data=df, studlab=studlab,  method = "Inverse",method.tau = "DL");mp
  
 mp2<- update (mp, byvar=Procedure);mp2
 pdf(filename = paste0(graphname, ".pdf"), width = 20, height = 20)
 forest (mp );   forest (mp2 )
  dev.off()
  })
#################################################################################

CodePudding user response：

There are a couple of issues with your code.

1. In metaprop, the event and n arguments must be symbols (not character strings) referring to columns in data.
2. As you correctly identified, the subset command is syntactically incorrect.
3. The filename argument inside pdf is file = , not filename = .
4. I strongly recommend using a linter to ensure consistent code formatting & indentation. Or at the very least, adopt & stick to a style guide to increase the readability of your code.

As to your question, the following seems to work.

# Variables of interest
vars <- names(data)[4:5]

# Reshape `data` from wide to long for the variables of interest
df <- data %>% pivot_longer(all_of(vars))

# Since the loop is not returning anything and only generates plots, 
# use `purrr::walk` to loop through all variables of interest.
vars %>%
    walk(function(var) {
        # Meta-analysis        
        mp <- metaprop(
            event = value, 
            n = Number.of.patients,
            studlab = studlab,
            data = df %>% filter(name == var, !is.na(value)),
            method = "Inverse",
            method.tau = "DL")
        mp2 <- update(mp, byvar = Procedure)
        
        #Plot
        pdf(file = paste0(var, ".pdf"), width = 20, height = 20)
        forest(mp)
        forest(mp2)
        dev.off()
    })