This is a repeat of a question asked on stackoverflow (https://stackoverflow.com/questions/63250597/), the responder didn't have an answer and suggested I ask here.
I have a Rmd file saved in a folder one below my project([path]/scripts), and the data is in a parallel folder ([path]/data) and I can't seem to set the working directory and access the data when running the chunks. I use the setup chunk, as below, and then run code in a following chunk. If I knit the whole document it works fine but if I run the 2nd chunk on its own I get "Error: 'data/warriner_2013_emotional_valence.csv' does not exist in current working directory ('[path]/scripts')" .
If I create a chunk with the command getwd() I get [path]/scripts if I manually run the chunks. If I knit them, I get [path] - which is where I want it. This seems to corroborate it being a run vs knit issue.
```{r setup, include=FALSE}
require("knitr")
opts_chunk$set(echo = TRUE)
opts_knit$set(root.dir = "..")
```
```{r}
library(tidyverse)
war <- read_csv('data/warriner_2013_emotional_valence.csv')
```
Other solutions I've found say to run the code in a separate chunk to the setup, which I'm doing.
I've also tried changing the R Markdown Global Options "Evaluate chunks in directory: 'Project'" - which has no effect.
>sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils
[5] datasets methods base
other attached packages:
[1] broom_0.7.0 forcats_0.5.0
[3] stringr_1.4.0 dplyr_1.0.1
[5] purrr_0.3.4 readr_1.3.1
[7] tidyr_1.1.1 tibble_3.0.3
[9] ggplot2_3.3.2 tidyverse_1.3.0
[11] knitr_1.29
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 cellranger_1.1.0
[3] pillar_1.4.6 compiler_4.0.2
[5] dbplyr_1.4.4 tools_4.0.2
[7] digest_0.6.25 lubridate_1.7.9
[9] jsonlite_1.7.0 evaluate_0.14
[11] lifecycle_0.2.0 gtable_0.3.0
[13] pkgconfig_2.0.3 rlang_0.4.7
[15] reprex_0.3.0 cli_2.0.2
[17] DBI_1.1.0 rstudioapi_0.11
[19] yaml_2.2.1 haven_2.3.1
[21] xfun_0.16 withr_2.2.0
[23] xml2_1.3.2 httr_1.4.2
[25] fs_1.5.0 generics_0.0.2
[27] vctrs_0.3.2 hms_0.5.3
[29] grid_4.0.2 tidyselect_1.1.0
[31] glue_1.4.1 R6_2.4.1
[33] fansi_0.4.1 readxl_1.3.1
[35] rmarkdown_2.3 modelr_0.1.8
[37] blob_1.2.1 magrittr_1.5
[39] backports_1.1.7 scales_1.1.1
[41] ellipsis_0.3.1 htmltools_0.5.0
[43] rvest_0.3.6 assertthat_0.2.1
[45] colorspace_1.4-1 stringi_1.4.6
[47] munsell_0.5.0 crayon_1.3.4
