This question already has answers here:
Error: could not find function ... in R
(10 answers)
Closed 7 months ago.
I installed a R package named "GeoTcgaData", libraried it and wanted to use the function "fpkmToTPM_matrix" to convert my data. But this message came out:
Error in fpkmToTpm_matrix(J_Rseq) :
could not find function "fpkmToTpm_matrix"
Wondering where the problem is.
(The version of the package is 1.1.0)
You may need to install some of the dependencies separately via Bioconductor. If you install the packages using:
install.packages("BiocManager")
BiocManager::install(pkgs = c('DESeq2', 'impute', 'edgeR', 'cqn', 'topconfects', 'ChAMP', 'clusterProfiler',
'org.Hs.eg.db', 'minfi', 'IlluminaHumanMethylation450kanno.ilmn12.hg19',
'dearseq', 'NOISeq'))
You can then (hopefully) install and run GeoTcgaData as expected:
install.packages("GeoTcgaData", type = "source")
library(GeoTcgaData)
#> =============================================================
#> Hello, friend! welcome to use GeoTcgaData!
#> -------------------------------------------------------------
#> Version:1.1.0
#> =============================================================
lung_squ_count2 <- matrix(c(0.11,0.22,0.43,0.14,0.875,0.66,0.77,0.18,0.29),ncol=3)
rownames(lung_squ_count2) <- c("DISC1","TCOF1","SPPL3")
colnames(lung_squ_count2) <- c("sample1","sample2","sample3")
lung_squ_count2
#> sample1 sample2 sample3
#> DISC1 0.11 0.140 0.77
#> TCOF1 0.22 0.875 0.18
#> SPPL3 0.43 0.660 0.29
result <- fpkmToTpm_matrix(lung_squ_count2)
result
#> sample1 sample2 sample3
#> DISC1 144736.8 83582.09 620967.7
#> TCOF1 289473.7 522388.06 145161.3
#> SPPL3 565789.5 394029.85 233871.0
sessionInfo()
#> R version 4.1.3 (2022-03-10)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur/Monterey 10.16
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] GeoTcgaData_1.1.0
#>
#> loaded via a namespace (and not attached):
#> [1] Rcpp_1.0.9 plyr_1.8.7 pillar_1.8.0 compiler_4.1.3
#> [5] highr_0.9 R.methodsS3_1.8.2 R.utils_2.12.0 tools_4.1.3
#> [9] digest_0.6.29 evaluate_0.15 lifecycle_1.0.1 tibble_3.1.8
#> [13] R.cache_0.16.0 pkgconfig_2.0.3 rlang_1.0.4 reprex_2.0.1
#> [17] DBI_1.1.3 cli_3.3.0 rstudioapi_0.13 yaml_2.3.5
#> [21] xfun_0.31 fastmap_1.1.0 withr_2.5.0 styler_1.7.0
#> [25] stringr_1.4.0 dplyr_1.0.9 knitr_1.39 generics_0.1.3
#> [29] fs_1.5.2 vctrs_0.4.1 tidyselect_1.1.2 glue_1.6.2
#> [33] R6_2.5.1 fansi_1.0.3 rmarkdown_2.14 purrr_0.3.4
#> [37] magrittr_2.0.3 htmltools_0.5.3 splines_4.1.3 assertthat_0.2.1
#> [41] utf8_1.2.2 nor1mix_1.3-0 stringi_1.7.8 cqn_1.38.0
#> [45] R.oo_1.25.0
Created on 2022-08-08 by the reprex package (v2.0.1)
If installing the dependencies separately doesn't solve the issue, another potential alternative is to define the function yourself. From the source code:
fpkmToTpm <- function(fpkm)
{
exp(log(fpkm) - log(sum(fpkm)) + log(1e6))
}
fpkmToTpm_matrix <- function(fpkm_matrix) {
fpkm_matrix_new <- apply(fpkm_matrix, 2, fpkmToTpm)
}
fpkmToTpm_matrix(J_Rseq)
Does this work?
Also, please edit your question to include the output of the command sessionInfo()
Related
Please have a look at the reprex at the end of the post.
I generate some lognormally distributed values and then I bin the distribution using a non-uniform bin (the grid is evenly spaced if I take its logarithm).
The point is not the maths, but the fact that, using annotation_logticks
( see
https://ggplot2.tidyverse.org/reference/annotation_logticks.html
) I cannot add the ticks to the plot.
Does anybody understand what goes wrong?
Thanks a lot!
library(tidyverse)
library(scales)
#>
#> Attaching package: 'scales'
#> The following object is masked from 'package:purrr':
#>
#> discard
#> The following object is masked from 'package:readr':
#>
#> col_factor
## auxiliary functions
scale_x_log10nice <- function(name=NULL,omag=seq(-20,20),...) {
breaks10 <- 10^omag
scale_x_log10(name,breaks=breaks10,
labels=scales::trans_format("log10", scales::math_format(10^.x)),...)
}
log_binning <- function(x_min,x_max,n_bin){
x_max <- x_max
m <- n_bin-1
r <- (x_max/x_min)^(1/m)
my_seq <- seq(0,m,by=1)
grid <- x_min*r^my_seq
}
##################################################à
set.seed(1234)
n_bins <- 10
df <- tibble(x=rlnorm(10e4, sdlog=2))
my_breaks2 <- log_binning(min(df$x),
max(df$x), n_bins)
gpl <- ggplot(df, aes(x=x )) +
theme_bw()+
geom_histogram(## binwidth=10e3,
colour="black", fill="blue"## , boundary=0
, breaks=my_breaks2
)+
scale_x_log10nice("x values")
gpl
gpl2 <- gpl+
annotation_logticks(sides="b", outside=T)
## where are the logticks?
gpl2
sessionInfo()
#> R version 4.2.2 (2022-10-31)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Debian GNU/Linux 11 (bullseye)
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
#>
#> locale:
#> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
#> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
#> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] scales_1.2.1 forcats_0.5.2 stringr_1.5.0 dplyr_1.0.99.9000
#> [5] purrr_1.0.0 readr_2.1.3 tidyr_1.2.1 tibble_3.1.8
#> [9] ggplot2_3.4.0 tidyverse_1.3.2
#>
#> loaded via a namespace (and not attached):
#> [1] tidyselect_1.2.0 xfun_0.36 haven_2.5.1
#> [4] gargle_1.2.1 colorspace_2.0-3 vctrs_0.5.1
#> [7] generics_0.1.3 htmltools_0.5.4 yaml_2.3.6
#> [10] utf8_1.2.2 rlang_1.0.6 pillar_1.8.1
#> [13] glue_1.6.2 withr_2.5.0 DBI_1.1.3
#> [16] dbplyr_2.2.1 readxl_1.4.1 modelr_0.1.10
#> [19] lifecycle_1.0.3 munsell_0.5.0 gtable_0.3.1
#> [22] cellranger_1.1.0 rvest_1.0.3 evaluate_0.19
#> [25] labeling_0.4.2 knitr_1.41 tzdb_0.3.0
#> [28] fastmap_1.1.0 fansi_1.0.3 highr_0.10
#> [31] broom_1.0.2 backports_1.4.1 googlesheets4_1.0.1
#> [34] jsonlite_1.8.4 farver_2.1.1 fs_1.5.2
#> [37] hms_1.1.2 digest_0.6.31 stringi_1.7.8
#> [40] grid_4.2.2 cli_3.6.0 tools_4.2.2
#> [43] magrittr_2.0.3 crayon_1.5.2 pkgconfig_2.0.3
#> [46] ellipsis_0.3.2 xml2_1.3.3 reprex_2.0.2
#> [49] googledrive_2.0.0 lubridate_1.9.0 timechange_0.1.1
#> [52] assertthat_0.2.1 rmarkdown_2.19 httr_1.4.4
#> [55] R6_2.5.1 compiler_4.2.2
Created on 2023-01-17 with reprex v2.0.2
If you want to use outside = TRUE in annotation_logticks, you also need to turn clipping off.
From the docs for ?annotation_logticks
outside logical that controls whether to move the log ticks outside of the plot area. Default is off (FALSE). You will also need to use coord_cartesian(clip = "off")
gpl +
annotation_logticks(sides="b", outside = TRUE) +
coord_cartesian(clip = "off")
Please have a look at the reprex at the end of the post.
I need to read a column as a string, perform several manipulations and then save convert it to a numerical column.
The blanks ("") in the string column give me a headache because arrow does not convert them to numerical missing values NA.
Does anybody know how to achieve that?
Many thanks
library(tidyverse)
library(arrow)
#> Some features are not enabled in this build of Arrow. Run `arrow_info()` for more information.
#>
#> Attaching package: 'arrow'
#> The following object is masked from 'package:utils':
#>
#> timestamp
df <- tibble(x=rep(c("4000 -", "6000 -", "", "8000 - "), 10),
y=seq(1,10, length=40))
write_csv(df, "test_string.csv")
data <- open_dataset("test_string.csv",
format="csv",
skip=1,
schema=schema(x=string(), y=double()))
data2 <- data |>
mutate(x= sub(" -.*", "", x) ) |>
mutate(x2=as.numeric(x)) |>
collect() ## how to convert the blank to a numeric NA ?
#> Error in `collect()`:
#> ! Invalid: Failed to parse string: '' as a scalar of type double
#> Backtrace:
#> ▆
#> 1. ├─dplyr::collect(mutate(mutate(data, x = sub(" -.*", "", x)), x2 = as.numeric(x)))
#> 2. └─arrow:::collect.arrow_dplyr_query(mutate(mutate(data, x = sub(" -.*", "", x)), x2 = as.numeric(x)))
#> 3. └─base::tryCatch(...)
#> 4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#> 5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#> 6. └─value[[3L]](cond)
#> 7. └─arrow:::augment_io_error_msg(e, call, schema = x$.data$schema)
#> 8. └─rlang::abort(msg, call = call)
sessionInfo()
#> R version 4.2.2 (2022-10-31)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Debian GNU/Linux 11 (bullseye)
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.13.so
#>
#> locale:
#> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
#> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
#> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] arrow_10.0.0 forcats_0.5.2 stringr_1.4.1 dplyr_1.0.10
#> [5] purrr_0.3.5 readr_2.1.3 tidyr_1.2.1 tibble_3.1.8
#> [9] ggplot2_3.4.0 tidyverse_1.3.2
#>
#> loaded via a namespace (and not attached):
#> [1] lubridate_1.9.0 assertthat_0.2.1 digest_0.6.30
#> [4] utf8_1.2.2 R6_2.5.1 cellranger_1.1.0
#> [7] backports_1.4.1 reprex_2.0.2 evaluate_0.17
#> [10] httr_1.4.4 highr_0.9 pillar_1.8.1
#> [13] rlang_1.0.6 googlesheets4_1.0.1 readxl_1.4.1
#> [16] R.utils_2.12.1 R.oo_1.25.0 rmarkdown_2.17
#> [19] styler_1.8.0 googledrive_2.0.0 bit_4.0.4
#> [22] munsell_0.5.0 broom_1.0.1 compiler_4.2.2
#> [25] modelr_0.1.9 xfun_0.34 pkgconfig_2.0.3
#> [28] htmltools_0.5.3 tidyselect_1.2.0 fansi_1.0.3
#> [31] crayon_1.5.2 tzdb_0.3.0 dbplyr_2.2.1
#> [34] withr_2.5.0 R.methodsS3_1.8.2 grid_4.2.2
#> [37] jsonlite_1.8.3 gtable_0.3.1 lifecycle_1.0.3
#> [40] DBI_1.1.3 magrittr_2.0.3 scales_1.2.1
#> [43] vroom_1.6.0 cli_3.4.1 stringi_1.7.8
#> [46] fs_1.5.2 xml2_1.3.3 ellipsis_0.3.2
#> [49] generics_0.1.3 vctrs_0.5.0 tools_4.2.2
#> [52] bit64_4.0.5 R.cache_0.16.0 glue_1.6.2
#> [55] hms_1.1.2 parallel_4.2.2 fastmap_1.1.0
#> [58] yaml_2.3.6 timechange_0.1.1 colorspace_2.0-3
#> [61] gargle_1.2.1 rvest_1.0.3 knitr_1.40
#> [64] haven_2.5.1
Created on 2022-11-07 with reprex v2.0.2
ifelse works here when all classes are correct (and not double()); if_else enforces this already, so we can use either.
data |>
mutate(x = sub(" -.*", "", x)) |>
mutate(
x = ifelse(x == "", NA_character_, x), # also if_else works
x2 = as.numeric(x)
) |>
collect()
# # A tibble: 40 x 3
# x y x2
# <chr> <dbl> <dbl>
# 1 4000 1 4000
# 2 6000 1.23 6000
# 3 NA 1.46 NA
# 4 8000 1.69 8000
# 5 4000 1.92 4000
# 6 6000 2.15 6000
# 7 NA 2.38 NA
# 8 8000 2.62 8000
# 9 4000 2.85 4000
# 10 6000 3.08 6000
# # ... with 30 more rows
Try using the read_csv instead of open_dataset
library(readr)
data <- read_csv("test_string.csv")
I am using Rstudio on a Windows machine and try to do some string matching with Chinese characters. I am not familiar with encoding settings on windows so I check some tutorials and make sure that the result of Sys.getlocale() should be the right one.
When executing str_detect() within dataframe, the matching fails. But it works on a vector level. Also, df_edu_village %>% filter(str_detect(village, "糖")) show a different result with df_edu_village %>% filter(str_detect(village, curl::curl_escape("糖") %>% curl::curl_unescape())).
Below I try to reproduce the result but reprex() isn't working, and the problem may be due to copy-paste so I knit the result into HTML with Rmd myself. Thanks for any help.
# devtools::install_github("ntupsc/pscdata")
library(pscdata)
library(tidyverse)
## -- Attaching packages --------------------------------------- tidyverse 1.3.1 --
## v ggplot2 3.3.5 v purrr 0.3.4
## v tibble 3.1.4 v dplyr 1.0.7
## v tidyr 1.1.3 v stringr 1.4.0
## v readr 2.0.1 v forcats 0.5.1
## -- Conflicts ------------------------------------------ tidyverse_conflicts() --
## x dplyr::filter() masks stats::filter()
## x dplyr::lag() masks stats::lag()
df_edu_village <- pscdata::edu_village_original %>% as_tibble() %>% distinct(village)
df_edu_village %>% filter(str_detect(village, "糖"))
## Error: Problem with `filter()` input `..1`.
## i Input `..1` is `str_detect(village, "糖")`.
## x Syntax error in regex pattern. (U_REGEX_RULE_SYNTAX, context=`聶}`)
df_edu_village %>% filter(str_detect(village, curl::curl_escape("糖") %>% curl::curl_unescape()))
## # A tibble: 3 x 1
## village
## <chr>
## 1 糖<U+5ECD>里
## 2 糖友里
## 3 大糖里
df_edu_village %>% filter(str_detect(village, "里"))
## # A tibble: 0 x 1
## # ... with 1 variable: village <chr>
str_detect(df_edu_village$village[1], "里")
## [1] FALSE
grepl(df_edu_village$village[1], "里")
## [1] FALSE
str_detect("留侯里", "里")
## [1] TRUE
Sys.getlocale()
## [1] "LC_COLLATE=Chinese (Traditional)_Taiwan.950;LC_CTYPE=Chinese (Traditional)_Taiwan.950;LC_MONETARY=Chinese (Traditional)_Taiwan.950;LC_NUMERIC=C;LC_TIME=Chinese (Traditional)_Taiwan.950"
sessionInfo()
## R version 4.1.1 (2021-08-10)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 18362)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=Chinese (Traditional)_Taiwan.950
## [2] LC_CTYPE=Chinese (Traditional)_Taiwan.950
## [3] LC_MONETARY=Chinese (Traditional)_Taiwan.950
## [4] LC_NUMERIC=C
## [5] LC_TIME=Chinese (Traditional)_Taiwan.950
## system code page: 1252
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
## [5] readr_2.0.1 tidyr_1.1.3 tibble_3.1.4 ggplot2_3.3.5
## [9] tidyverse_1.3.1 pscdata_0.1.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.1.1 xfun_0.26 haven_2.4.3 colorspace_2.0-2
## [5] vctrs_0.3.8 generics_0.1.0 htmltools_0.5.2 yaml_2.2.1
## [9] utf8_1.2.2 rlang_0.4.11 jquerylib_0.1.4 pillar_1.6.2
## [13] withr_2.4.2 glue_1.4.2 DBI_1.1.1 dbplyr_2.1.1
## [17] modelr_0.1.8 readxl_1.3.1 lifecycle_1.0.0 munsell_0.5.0
## [21] gtable_0.3.0 cellranger_1.1.0 rvest_1.0.1 evaluate_0.14
## [25] knitr_1.34 tzdb_0.1.2 fastmap_1.1.0 curl_4.3.2
## [29] fansi_0.5.0 broom_0.7.9 Rcpp_1.0.7 backports_1.2.1
## [33] scales_1.1.1 jsonlite_1.7.2 fs_1.5.0 hms_1.1.0
## [37] digest_0.6.27 stringi_1.7.4 grid_4.1.1 cli_3.0.1
## [41] tools_4.1.1 magrittr_2.0.1 crayon_1.4.1 pkgconfig_2.0.3
## [45] ellipsis_0.3.2 xml2_1.3.2 reprex_2.0.1 lubridate_1.7.10
## [49] rstudioapi_0.13 assertthat_0.2.1 rmarkdown_2.11 httr_1.4.2
## [53] R6_2.5.1 compiler_4.1.1
I am absolutely puzzled at what I see.
I read an excel file and when I look at the unique values in a column of strings, I do not understand the result.
I can reproduce this in a minimal reprex (see below): why dd has two unique elements, wheread dd2 has just one?
Any suggestion is appreciated.
dd <- c("Grant", "Grant")
dd2 <- c("Grant", "Grant")
unique(dd)
#> [1] "Grant" "Grant"
length(unique(dd))
#> [1] 2
unique(dd2)
#> [1] "Grant"
length(unique(dd2))
#> [1] 1
sessionInfo()
#> R version 4.1.1 (2021-08-10)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Debian GNU/Linux 11 (bullseye)
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
#>
#> locale:
#> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
#> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
#> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> loaded via a namespace (and not attached):
#> [1] knitr_1.33 magrittr_2.0.1 rlang_0.4.11 fansi_0.5.0
#> [5] stringr_1.4.0 styler_1.5.1 highr_0.9 tools_4.1.1
#> [9] xfun_0.25 utf8_1.2.2 withr_2.4.2 htmltools_0.5.1.1
#> [13] ellipsis_0.3.2 yaml_2.2.1 digest_0.6.27 tibble_3.1.3
#> [17] lifecycle_1.0.0 crayon_1.4.1 purrr_0.3.4 vctrs_0.3.8
#> [21] fs_1.5.0 glue_1.4.2 evaluate_0.14 rmarkdown_2.10
#> [25] reprex_2.0.1 stringi_1.7.3 compiler_4.1.1 pillar_1.6.2
#> [29] backports_1.2.1 pkgconfig_2.0.3
Created on 2021-09-13 by the reprex package (v2.0.1)
The raw values seems to be different, probably from copying
sapply(dd, charToRaw)
$`Grant`
[1] ef bb bf 47 72 61 6e 74
$Grant
[1] 47 72 61 6e 74
whereas with dd2, it is the same
sapply(dd2, charToRaw)
Grant Grant
[1,] 47 47
[2,] 72 72
[3,] 61 61
[4,] 6e 6e
[5,] 74 74
There seems to be an extra character in the first case
nchar(dd)
[1] 6 5
If we remove that first character, unique will be 1
unique(c(substring(dd[1],2), dd[2]))
[1] "Grant"
This has been asked several times in different forms, but here is a very simple example. I have used this function several times in the past, but apparently it fails miserably in the simplest case.
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
library(purrr)
bind_df_list <- function(ll){
res <- map_df(ll, bind_rows)
return(res)
}
ll<-list(seq(4), seq(4), seq(4))
dd<-bind_df_list(ll)
#> Error: Argument 1 must have names.
print(sessionInfo())
#> R version 4.0.4 (2021-02-15)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Debian GNU/Linux 10 (buster)
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so
#>
#> locale:
#> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
#> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
#> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] purrr_0.3.4 dplyr_1.0.4
#>
#> loaded via a namespace (and not attached):
#> [1] knitr_1.31 magrittr_2.0.1 tidyselect_1.1.0 R6_2.5.0
#> [5] rlang_0.4.10 stringr_1.4.0 styler_1.3.2 highr_0.8
#> [9] tools_4.0.4 xfun_0.21 DBI_1.1.1 htmltools_0.5.1.1
#> [13] ellipsis_0.3.1 assertthat_0.2.1 yaml_2.2.1 digest_0.6.27
#> [17] tibble_3.0.6 lifecycle_1.0.0 crayon_1.4.1 vctrs_0.3.6
#> [21] fs_1.5.0 glue_1.4.2 evaluate_0.14 rmarkdown_2.6
#> [25] reprex_1.0.0 stringi_1.5.3 compiler_4.0.4 pillar_1.4.7
#> [29] generics_0.1.0 backports_1.2.1 pkgconfig_2.0.3
Created on 2021-03-08 by the reprex package (v1.0.0)
Any idea about how to fix this?
Many thanks!
it is just a vector and ?bind_rows input should be a set of dataframes
... - Data frames to combine.
One option is to loop over the list, with map, convert to data.frame and append them by rows with _dfr
library(purrr)
map_dfr(ll, as.data.frame.list)
Or transpose and convert to data.frame
map_dfr(ll, ~ as.data.frame(t(.x)))
Or this can also be a named vector
map_dfr(ll, ~ setNames(.x, seq_along(.x)))
Or use rbind with do.call from base R as rbind have methods for matrix and data.frame
do.call(rbind, ll)
do.call(rbind.data.frame, ll)