Replace missing values with NA (doesn't work well with POSIXlt format)

[Sha1010]

Hi R friends,

I'm a beginner and I really can't find the way to convert all missing values to NA (I'm running it on Kaggle)

I tried the following function :
library(dplyr)
merged_tripdata %>% mutate_all(na_if,"")

But it returns the following error:
Error in mutate():
! Problem while computing started_at = (function (x, y) ....
Caused by error in as.POSIXlt.character():
! character string is not in a standard unambiguous format
Traceback:

I tried it on a specific column
I have selected a specific column , but even there something goes wrong:
merged_tripdata$start_station_name[merged_tripdata$start_station_name == ""] <- NA

But then R even doesn't run the function.

How can I fix this?

Thank you!
Sharon

[dvetsch75]

I would not use scoped variants of dplyr functions since they've been superseded by across. I would probably do what you are trying to do this way:

library(dplyr)

merged_tripdata %>% 
    mutate(
        across(
            .cols = everything(),
            .fns = function(col) {
                na_if(col, "")
            }
        )
    )

If that doesn't work for you, can you please post a sample of your data?

[Sha1010]

Thank you very much!
I will check it in a few minutes and tell you
Thanks again
Sharon

[Sha1010]

I have run it now, but got the following error (forgive me, it's long)

Error in mutate():
! Problem while computing ..1 = across(...).
Caused by error in across():
! Problem while computing column started_at.
Caused by error in as.POSIXlt.character():
! character string is not in a standard unambiguous format
Traceback:

1. merged_tripdata %>% mutate(across(.cols = everything(), .fns = function(col) {
   . na_if(col, "")
   . }))
2. mutate(., across(.cols = everything(), .fns = function(col) {
   . na_if(col, "")
   . }))
3. mutate.data.frame(., across(.cols = everything(), .fns = function(col) {
   . na_if(col, "")
   . }))
4. mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
5. withCallingHandlers({
   . for (i in seq_along(dots)) {
   . context_poke("column", old_current_column)
   . quosures <- expand_across(dots[[i]])
   . quosures_results <- vector(mode = "list", length = length(quosures))
   . for (k in seq_along(quosures)) {
   . quo <- quosures[[k]]
   . quo_data <- attr(quo, "dplyr:::data")
   . if (!is.null(quo_data$column)) {
   . context_poke("column", quo_data$column)
   . }
   . chunks <- NULL
   . result <- NULL
   . if (quo_is_symbol(quo)) {
   . name <- as_string(quo_get_expr(quo))
   . if (name %in% names(new_columns)) {
   . result <- new_columns[[name]]
   . chunks <- mask$resolve(name)
   . }
   . else if (name %in% names(.data)) {
   . result <- .data[[name]]
   . chunks <- mask$resolve(name)
   . }
   . if (inherits(.data, "rowwise_df") && vec_is_list(result)) {
   . sizes <- list_sizes(result)
   . wrong <- which(sizes != 1)
   . if (length(wrong)) {
   . group <- wrong[1L]
   . mask$set_current_group(group)
   . abort(class = c("dplyr:::mutate_incompatible_size",
   . "dplyr:::internal_error"), dplyr_error_data = list(result_size = sizes[group],
   . expected_size = 1))
   . }
   . }
   . }
   . else if (!quo_is_symbolic(quo) && !is.null(quo_get_expr(quo))) {
   . result <- quo_get_expr(quo)
   . result <- withCallingHandlers(vec_recycle(result,
   . vec_size(.data)), error = function(cnd) {
   . abort(class = c("dplyr:::mutate_constant_recycle_error",
   . "dplyr:::internal_error"), constant_size = vec_size(result),
   . data_size = vec_size(.data))
   . })
   . chunks <- vec_chop(result, rows)
   . }
   . if (is.null(chunks)) {
   . if (is.null(quo_data$column)) {
   . chunks <- mask$eval_all_mutate(quo)
   . }
   . else {
   . chunks <- withCallingHandlers(mask$eval_all_mutate(quo),
   . error = function(cnd) {
   . msg <- glue("Problem while computing column {quo_data$name_auto}.")
   . abort(msg, call = call("across"), parent = cnd)
   . })
   . }
   . }
   . if (is.null(chunks)) {
   . next
   . }
   . if (is.null(result)) {
   . if (length(rows) == 1) {
   . result <- chunks[[1]]
   . }
   . else {
   . chunks <- dplyr_vec_cast_common(chunks, quo_data$name_auto)
   . result <- vec_unchop(chunks, rows)
   . }
   . }
   . quosures_results[[k]] <- list(result = result, chunks = chunks)
   . }
   . for (k in seq_along(quosures)) {
   . quo <- quosures[[k]]
   . quo_data <- attr(quo, "dplyr:::data")
   . quo_result <- quosures_results[[k]]
   . if (is.null(quo_result)) {
   . if (quo_data$is_named) {
   . name <- quo_data$name_given
   . new_columns[[name]] <- zap()
   . mask$remove(name)
   . }
   . next
   . }
   . result <- quo_result$result
   . chunks <- quo_result$chunks
   . if (!quo_data$is_named && is.data.frame(result)) {
   . types <- vec_ptype(result)
   . types_names <- names(types)
   . chunks_extracted <- .Call(dplyr_extract_chunks,
   . chunks, types)
   . for (j in seq_along(types)) {
   . mask$add_one(types_names[j], chunks_extracted[[j]],
   . result = result[[j]])
   . }
   . new_columns[types_names] <- result
   . }
   . else {
   . name <- quo_data$name_auto
   . mask$add_one(name = name, chunks = chunks, result = result)
   . new_columns[[name]] <- result
   . }
   . }
   . }
   . }, error = function(e) {
   . local_error_context(dots = dots, .index = i, mask = mask)
   . bullets <- c(cnd_bullet_header("computing"), mutate_bullets(e))
   . abort(bullets, class = "dplyr:::mutate_error", parent = skip_internal_condition(e),
   . bullets = bullets, call = error_call)
   . }, warning = function(w) {
   . if (check_muffled_warning(w)) {
   . maybe_restart("muffleWarning")
   . }
   . local_error_context(dots = dots, .index = i, mask = mask)
   . warn(c(cnd_bullet_header("computing"), i = cnd_header(w),
   . i = cnd_bullet_cur_group_label(what = "warning")))
   . maybe_restart("muffleWarning")
   . })
6. withCallingHandlers(mask$eval_all_mutate(quo), error = function(cnd) {
   . msg <- glue("Problem while computing column {quo_data$name_auto}.")
   . abort(msg, call = call("across"), parent = cnd)
   . })
7. mask$eval_all_mutate(quo)
8. (function (col)
   . {
   . na_if(col, "")
   . })(started_at)
9. na_if(col, "") # at line 8 of file
10. [<-(*tmp*, x == y, value = NA)
11. [<-.POSIXlt(*tmp*, x == y, value = NA)
12. ==.POSIXt(x, y)
13. as.POSIXct(e2)
14. as.POSIXct.default(e2)
15. as.POSIXct(as.POSIXlt(x, tz, ...), tz, ...)
16. as.POSIXlt(x, tz, ...)
17. as.POSIXlt.character(x, tz, ...)
18. stop("character string is not in a standard unambiguous format")
19. .handleSimpleError(function (cnd)
    . {
    . msg <- glue("Problem while computing column {quo_data$name_auto}.")
    . abort(msg, call = call("across"), parent = cnd)
    . }, "character string is not in a standard unambiguous format",
    . base::quote(as.POSIXlt.character(x, tz, ...)))
20. h(simpleError(msg, call))
21. abort(msg, call = call("across"), parent = cnd)
22. signal_abort(cnd, .file)
23. signalCondition(cnd)
24. (function (e)
    . {
    . local_error_context(dots = dots, .index = i, mask = mask)
    . bullets <- c(cnd_bullet_header("computing"), mutate_bullets(e))
    . abort(bullets, class = "dplyr:::mutate_error", parent = skip_internal_condition(e),
    . bullets = bullets, call = error_call)
    . })(structure(list(message = structure("Problem while computing column started_at.", class = c("glue",
    . "character")), trace = structure(list(call = list(IRkernel::main(),
    . kernel$run(), handle_shell(), executor$execute(msg), tryCatch(evaluate(request$content$code,
    . envir = .GlobalEnv, output_handler = oh, stop_on_error = 1L),
    . interrupt = function(cond) {
    . log_debug("Interrupt during execution")
    . interrupted <<- TRUE
    . }, error = .self$handle_error), tryCatchList(expr, classes,
    . parentenv, handlers), tryCatchOne(tryCatchList(expr,
    . names[-nh], parentenv, handlers[-nh]), names[nh], parentenv,
    . handlers[[nh]]), doTryCatch(return(expr), name, parentenv,
    . handler), tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
    . tryCatchOne(expr, names, parentenv, handlers[[1L]]), doTryCatch(return(expr),
    . name, parentenv, handler), evaluate(request$content$code,
    . envir = .GlobalEnv, output_handler = oh, stop_on_error = 1L),
    . evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
    . debug = debug, last = i == length(out), use_try = stop_on_error !=
    . 2L, keep_warning = keep_warning, keep_message = keep_message,
    . output_handler = output_handler, include_timing = include_timing),
    . timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,
    . envir, enclos, user_handlers)), warning = wHandler, error = eHandler,
    . message = mHandler))), handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,
    . envir, enclos, user_handlers)), warning = wHandler, error = eHandler,
    . message = mHandler)), try(f, silent = TRUE), tryCatch(expr,
    . error = function(e) {
    . call <- conditionCall(e)
    . if (!is.null(call)) {
    . if (identical(call[[1L]], quote(doTryCatch)))
    . call <- sys.call(-4L)
    . dcall <- deparse(call)[1L]
    . prefix <- paste("Error in", dcall, ": ")
    . LONG <- 75L
    . sm <- strsplit(conditionMessage(e), "\n")[[1L]]
    . w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L],
    . type = "w")
    . if (is.na(w))
    . w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
    . type = "b")
    . if (w > LONG)
    . prefix <- paste0(prefix, "\n ")
    . }
    . else prefix <- "Error : "
    . msg <- paste0(prefix, conditionMessage(e), "\n")
    . .Internal(seterrmessage(msg[1L]))
    . if (!silent && isTRUE(getOption("show.error.messages"))) {
    . cat(msg, file = outFile)
    . .Internal(printDeferredWarnings())
    . }
    . invisible(structure(msg, class = "try-error", condition = e))
    . }), tryCatchList(expr, classes, parentenv, handlers),
    . tryCatchOne(expr, names, parentenv, handlers[[1L]]), doTryCatch(return(expr),
    . name, parentenv, handler), withCallingHandlers(withVisible(eval_with_user_handlers(expr,
    . envir, enclos, user_handlers)), warning = wHandler, error = eHandler,
    . message = mHandler), withVisible(eval_with_user_handlers(expr,
    . envir, enclos, user_handlers)), eval_with_user_handlers(expr,
    . envir, enclos, user_handlers), eval(expr, envir, enclos),
    . eval(expr, envir, enclos), merged_tripdata %>% mutate(across(.cols = everything(),
    . .fns = function(col) {
    . na_if(col, "")
    . })), mutate(., across(.cols = everything(), .fns = function(col) {
    . na_if(col, "")
    . })), mutate.data.frame(., across(.cols = everything(), .fns = function(col) {
    . na_if(col, "")
    . })), mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env()),
    . withCallingHandlers({
    . for (i in seq_along(dots)) {
    . context_poke("column", old_current_column)
    . quosures <- expand_across(dots[[i]])
    . quosures_results <- vector(mode = "list", length = length(quosures))
    . for (k in seq_along(quosures)) {
    . quo <- quosures[[k]]
    . quo_data <- attr(quo, "dplyr:::data")
    . if (!is.null(quo_data$column)) {
    . context_poke("column", quo_data$column)
    . }
    . chunks <- NULL
    . result <- NULL
    . if (quo_is_symbol(quo)) {
    . name <- as_string(quo_get_expr(quo))
    . if (name %in% names(new_columns)) {
    . result <- new_columns[[name]]
    . chunks <- mask$resolve(name)
    . }
    . else if (name %in% names(.data)) {
    . result <- .data[[name]]
    . chunks <- mask$resolve(name)
    . }
    . if (inherits(.data, "rowwise_df") && vec_is_list(result)) {
    . sizes <- list_sizes(result)
    . wrong <- which(sizes != 1)
    . if (length(wrong)) {
    . group <- wrong[1L]
    . mask$set_current_group(group)
    . abort(class = c("dplyr:::mutate_incompatible_size",
    . "dplyr:::internal_error"), dplyr_error_data = list(result_size = sizes[group],
    . expected_size = 1))
    . }
    . }
    . }
    . else if (!quo_is_symbolic(quo) && !is.null(quo_get_expr(quo))) {
    . result <- quo_get_expr(quo)
    . result <- withCallingHandlers(vec_recycle(result,
    . vec_size(.data)), error = function(cnd) {
    . abort(class = c("dplyr:::mutate_constant_recycle_error",
    . "dplyr:::internal_error"), constant_size = vec_size(result),
    . data_size = vec_size(.data))
    . })
    . chunks <- vec_chop(result, rows)
    . }
    . if (is.null(chunks)) {
    . if (is.null(quo_data$column)) {
    . chunks <- mask$eval_all_mutate(quo)
    . }
    . else {
    . chunks <- withCallingHandlers(mask$eval_all_mutate(quo),
    . error = function(cnd) {
    . msg <- glue("Problem while computing column {quo_data$name_auto}.")
    . abort(msg, call = call("across"), parent = cnd)
    . })
    . }
    . }
    . if (is.null(chunks)) {
    . next
    . }
    . if (is.null(result)) {
    . if (length(rows) == 1) {
    . result <- chunks[[1]]
    . }
    . else {
    . chunks <- dplyr_vec_cast_common(chunks, quo_data$name_auto)
    . result <- vec_unchop(chunks, rows)
    . }
    . }
    . quosures_results[[k]] <- list(result = result,
    . chunks = chunks)
    . }
    . for (k in seq_along(quosures)) {
    . quo <- quosures[[k]]
    . quo_data <- attr(quo, "dplyr:::data")
    . quo_result <- quosures_results[[k]]
    . if (is.null(quo_result)) {
    . if (quo_data$is_named) {
    . name <- quo_data$name_given
    . new_columns[[name]] <- zap()
    . mask$remove(name)
    . }
    . next
    . }
    . result <- quo_result$result
    . chunks <- quo_result$chunks
    . if (!quo_data$is_named && is.data.frame(result)) {
    . types <- vec_ptype(result)
    . types_names <- names(types)
    . chunks_extracted <- .Call(dplyr_extract_chunks,
    . chunks, types)
    . for (j in seq_along(types)) {
    . mask$add_one(types_names[j], chunks_extracted[[j]],
    . result = result[[j]])
    . }
    . new_columns[types_names] <- result
    . }
    . else {
    . name <- quo_data$name_auto
    . mask$add_one(name = name, chunks = chunks,
    . result = result)
    . new_columns[[name]] <- result
    . }
    . }
    . }
    . }, error = function(e) {
    . local_error_context(dots = dots, .index = i, mask = mask)
    . bullets <- c(cnd_bullet_header("computing"), mutate_bullets(e))
    . abort(bullets, class = "dplyr:::mutate_error", parent = skip_internal_condition(e),
    . bullets = bullets, call = error_call)
    . }, warning = function(w) {
    . if (check_muffled_warning(w)) {
    . maybe_restart("muffleWarning")
    . }
    . local_error_context(dots = dots, .index = i, mask = mask)
    . warn(c(cnd_bullet_header("computing"), i = cnd_header(w),
    . i = cnd_bullet_cur_group_label(what = "warning")))
    . maybe_restart("muffleWarning")
    . }), withCallingHandlers(mask$eval_all_mutate(quo), error = function(cnd) {
    . msg <- glue("Problem while computing column {quo_data$name_auto}.")
    . abort(msg, call = call("across"), parent = cnd)
    . }), mask$eval_all_mutate(quo), <fn>(started_at), na_if(col,
    . ""), [<-(*tmp*, x == y, value = <lgl>), [<-.POSIXlt(*tmp*,
    . x == y, value = <lgl>), ==.POSIXt(x, y), as.POSIXct(e2),
    . as.POSIXct.default(e2), as.POSIXct(as.POSIXlt(x, tz, ...),
    . tz, ...), as.POSIXlt(x, tz, ...), as.POSIXlt.character(x,
    . tz, ...), stop("character string is not in a standard unambiguous format"),
    . .handleSimpleError(<fn>, "character string is not in a standard unambiguous format",
    . base::quote(as.POSIXlt.character(x, tz, ...))), h(simpleError(msg,
    . call)), abort(msg, call = call("across"), parent = cnd)),
    . parent = c(0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 6L, 9L, 10L, 4L,
    . 12L, 13L, 13L, 15L, 16L, 17L, 18L, 19L, 13L, 13L, 13L, 23L,
    . 24L, 0L, 0L, 0L, 28L, 29L, 29L, 29L, 0L, 33L, 34L, 34L, 34L,
    . 37L, 37L, 39L, 39L, 39L, 42L, 0L, 44L, 45L), visible = c(TRUE,
    . TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
    . TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
    . TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
    . TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
    . TRUE, TRUE, FALSE, FALSE, FALSE), namespace = c("IRkernel",
    . NA, "IRkernel", NA, "base", "base", "base", "base", "base",
    . "base", "base", "evaluate", "evaluate", "evaluate", "evaluate",
    . "base", "base", "base", "base", "base", "base", "base", "evaluate",
    . "base", "base", NA, "dplyr", "dplyr", "dplyr", "base", "base",
    . NA, NA, "dplyr", "base", "base", "lubridate", "base", "base",
    . "base", "base", "base", "base", "base", "dplyr", "rlang"),
    . scope = c("::", NA, "local", NA, "::", "local", "local",
    . "local", "local", "local", "local", "::", ":::", "local",
    . "local", "::", "::", "local", "local", "local", "::", "::",
    . ":::", "::", "::", NA, "::", ":::", ":::", "::", "::", NA,
    . NA, "::", "::", "::", "local", "::", "::", "::", "::", "::",
    . "::", "::", "local", "::")), row.names = c(NA, -46L), version = 2L, class = c("rlang_trace",
    . "rlib_trace", "tbl", "data.frame")), parent = structure(list(
    . message = "character string is not in a standard unambiguous format",
    . call = as.POSIXlt.character(x, tz, ...)), class = c("simpleError",
    . "error", "condition")), call = across(), use_cli_format = TRUE), class = c("rlang_error",
    . "error", "condition")))
25. abort(bullets, class = "dplyr:::mutate_error", parent = skip_internal_condition(e),
    . bullets = bullets, call = error_call)
26. signal_abort(cnd, .file)

[Sha1010]

@dvetsch75

If that doesn't work for you, can you please post a sample of your data?

Head(df) or str(df) is good?
it a huge dataset...

[dvetsch75]

dput(head(df, 100)) is usually sufficient.

[Sha1010]

@dvetsch75

dput(head(df, 100))

Thank you!

structure(list(ride_id = c("C2F7DD78E82EC875", "A6CF8980A652D272",
"BD0F91DFF741C66D", "CBB80ED419105406", "DDC963BFDDA51EEA", "A39C6F6CC0586C0B",
"BDC4AB637EDF981B", "81751A3186E59A6B", "154222B86A338ABD", "72DC25B2DD467EEF",
"F20394FE09C63DB2", "006D3F363CF9600B", "FB258EEBE89F4E17", "2EF51270B08DEE03",
"E119D4E6BF686601", "7DD70C4AA0F3EA7B", "0AA241497B970400", "F5E6D97D85BE8039",
"78168928DF06A497", "15C176B55C2BC059", "12D2B5AA545EF922", "1A185AF405E7B2DB",
"9D4AAF43A011FC59", "A209F8E0E84D49B4", "6D6B462903DCB23F", "DC809CD3B3F3BFC9",
"1C2362DAD4090D8A", "AB4032C2B151D137", "E6B6D4531ADC9F52", "81B423963BA2C10C",
"EC80F318604595AE", "80F0735AD7F23AD9", "59E50C91451F529C", "2A23ED3FECB72E5B",
"88543D9BC6760955", "E38E5318BDBC139A", "A184D11FDF48937A", "1EFB6377FE801DEF",
"0A5CD4848EB8CFE8", "74D8B5BC10B9E223", "3C07A7C383512251", "40C9DFE4CFB178A3",
"04EC503AB7123CCE", "ABA3DE288B9D9A10", "007070F5088EB3C0", "7117CF2AEFF29287",
"A3DCFB423064F830", "145739172978E774", "1EBF95B25BB5091A", "060598F8DA7E017B",
"9A7CC85A0C99CD19", "4498EE1461DCF780", "ED582A16A84658F3", "E65FE8D6EF398BAF",
"96EE9C6CBAB01FF5", "4C82D05AEAB243A2", "1060D99FAF5F5479", "9946705113D42A72",
"34C7E20D7F43EC1C", "4E79B5C58A342D04", "3505407FC37505BB", "E4C578629FD75DE6",
"DE75C65E97762100", "F26E4F5F00769CB6", "91DF55B30E0F8F30", "3D340D186F24FFA2",
"AAD4F48B225F73CD", "1D42868A4784FC60", "38A42898ED51CB39", "15D6F84CCB902A27"
), rideable_type = c("electric_bike", "electric_bike", "classic_bike",
"classic_bike", "classic_bike", "classic_bike", "classic_bike",
"classic_bike", "electric_bike", "classic_bike", "classic_bike",
"electric_bike", "classic_bike", "classic_bike", "electric_bike",
"classic_bike", "classic_bike", "classic_bike", "classic_bike",
"classic_bike", "classic_bike", "classic_bike", "electric_bike",
"classic_bike", "electric_bike", "classic_bike", "electric_bike",
"classic_bike", "classic_bike", "classic_bike", "electric_bike",
"electric_bike", "classic_bike", "electric_bike", "classic_bike",
"classic_bike", "classic_bike", "classic_bike", "electric_bike",
"classic_bike", "classic_bike", "classic_bike", "classic_bike",
"classic_bike", "classic_bike", "classic_bike", "classic_bike",
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[dvetsch75]

Thanks. I’ll take a look when I can get in front of a terminal in a couple hours.

[Sha1010]

OK, thank you very much!

I run 70 rows due to message limitation...