alapo / literate-programming

This is the repository for the Literate Programming Workshop

Literate Programming

This is the official GitHub page for the workshop on Reproducible Science for Busy Researchers: How to save time using Literate Programming.

This repository will be updated as we progress through the workshop

Zoom Links

You should have received an email from REALISE once you registered with Zoom links for every module. Please make sure to check your SPAM folder. If you are still unable to find it, please visit the workshop's page on the REALISE website.

Survey

Please take time to fill out the Google Form to help me tailor content to you throughout the workshop.

Module Recordings

Links to the workshop's recordings will be posted here as they become available.

1. The advantages of Reproducible Science Workflows
2. Finding Help
3. Installation
   • Already have R Installed?
4. Essentials of RMarkdown
5. Introductory Statistics #1
   • Example Modifying for your data
6. Introductory Statistics #2
7. Data Wrangling
8. Plotting using the Grammar of Graphics (ggplot)

Installation Links

1. R
2. RStudio
3. RTools (Windows Only)
4. Git
5. Zotero
6. BetterBibTex
7. Download the MyProjectName folder from this repository and save it somewhere on your computer (remember where you put it)

literate-programming's Issues

Could not knit Word document in Mac

Describe the bug
Hi,

I am at the final step to knit the document in Rmarkdown in Mac OS X but a message saying "execution halted" keeps popping, the steps worked fine in Windows PC. I have R v4.0.2 and RStudio v1.4.1106.

Thankyou.

To Reproduce
Steps to reproduce the behavior:

1. Go to 'manuscript.rmd'
2. Click on 'Knit'
3. Scroll down to 'Knit to rdocx-document'
4. See error - Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared object '/Users/shrushtishah/systemfonts/libs/systemfonts.so':
   dlopen(/Users/shrushtishah/systemfonts/libs/systemfonts.so, 6): Symbol not found: _inflateValidate
   Referenced from: /Users/shrushtishah/systemfonts/libs/systemfonts.so (which was built for Mac OS X 10.13)
   Expected in: /usr/lib/libz.1.dylib
   in /Users/shrushtishah/systemfonts/libs/systemfonts.so
   Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
   Execution halted

Expected behavior
I tried to follow Andrew's instruction to remove certain symbols (check mark, book emoji etc.) from main RMD file but no success and same error occured again.

Screenshots
Please see attached

devtools::session_info()

devtools::session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.2 (2020-06-22)
 os       macOS Sierra 10.12.6        
 system   x86_64, darwin17.0          
 ui       RStudio                     
 language (EN)                        
 collate  en_CA.UTF-8                 
 ctype    en_CA.UTF-8                 
 tz       America/Edmonton            
 date     2021-03-23                  

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────
 ! package       * version date       lib source        
   abind           1.4-5   2016-07-21 [1] CRAN (R 4.0.2)
   addinslist    * 0.4.0   2021-01-10 [1] CRAN (R 4.0.2)
   arsenal       * 3.6.2   2021-02-17 [1] CRAN (R 4.0.2)
   askpass         1.1     2019-01-13 [1] CRAN (R 4.0.2)
   assertthat      0.2.1   2019-03-21 [1] CRAN (R 4.0.2)
   backports       1.2.0   2020-11-02 [1] CRAN (R 4.0.2)
   bayestestR      0.8.2   2021-01-26 [1] CRAN (R 4.0.2)
   BiocManager     1.30.10 2019-11-16 [1] CRAN (R 4.0.2)
   broom           0.7.5   2021-02-19 [1] CRAN (R 4.0.2)
   bslib           0.2.4   2021-01-25 [1] CRAN (R 4.0.2)
   cachem          1.0.4   2021-02-13 [1] CRAN (R 4.0.2)
   callr           3.5.1   2020-10-13 [1] CRAN (R 4.0.2)
   car             3.0-10  2020-09-29 [1] CRAN (R 4.0.2)
   carData         3.0-4   2020-05-22 [1] CRAN (R 4.0.2)
   cellranger      1.1.0   2016-07-27 [1] CRAN (R 4.0.2)
   cgwtools      * 3.3     2021-01-06 [1] CRAN (R 4.0.2)
   cli             2.1.0   2020-10-12 [1] CRAN (R 4.0.2)
   colorspace      2.0-0   2020-11-11 [1] CRAN (R 4.0.2)
   colourpicker  * 1.1.0   2020-09-14 [1] CRAN (R 4.0.2)
   crayon          1.3.4   2017-09-16 [1] CRAN (R 4.0.2)
   credentials     1.3.0   2020-07-21 [1] CRAN (R 4.0.2)
   curl            4.3     2019-12-02 [1] CRAN (R 4.0.1)
   data.table      1.13.2  2020-10-19 [1] CRAN (R 4.0.2)
   DBI             1.1.0   2019-12-15 [1] CRAN (R 4.0.2)
   dbplyr          2.0.0   2020-11-03 [1] CRAN (R 4.0.2)
   desc            1.3.0   2021-03-05 [1] CRAN (R 4.0.2)
   devtools        2.3.2   2020-09-18 [1] CRAN (R 4.0.2)
   digest          0.6.27  2020-10-24 [1] CRAN (R 4.0.2)
   dplyr           1.0.2   2020-08-18 [1] CRAN (R 4.0.2)
   ellipsis        0.3.1   2020-05-15 [1] CRAN (R 4.0.2)
   esquisse      * 0.3.1   2020-09-27 [1] CRAN (R 4.0.2)
   evaluate        0.14    2019-05-28 [1] CRAN (R 4.0.1)
   fansi           0.4.1   2020-01-08 [1] CRAN (R 4.0.2)
   fastmap         1.1.0   2021-01-25 [1] CRAN (R 4.0.2)
   forcats         0.5.0   2020-03-01 [1] CRAN (R 4.0.2)
   foreign         0.8-80  2020-05-24 [2] CRAN (R 4.0.2)
   formatR         1.8     2021-03-12 [1] CRAN (R 4.0.2)
   Formula       * 1.2-4   2020-10-16 [1] CRAN (R 4.0.2)
   fs              1.5.0   2020-07-31 [1] CRAN (R 4.0.2)
   gargle          1.0.0   2021-03-03 [1] CRAN (R 4.0.2)
   generics        0.1.0   2020-10-31 [1] CRAN (R 4.0.2)
 V ggplot2         3.3.2   2020-12-30 [1] CRAN (R 4.0.2)
   ggThemeAssist * 0.1.5   2016-08-13 [1] CRAN (R 4.0.2)
   glue            1.4.2   2020-08-27 [1] CRAN (R 4.0.2)
   gmp             0.6-2   2021-01-07 [1] CRAN (R 4.0.2)
   googledrive     1.0.1   2020-05-05 [1] CRAN (R 4.0.2)
   googlesheets4 * 0.3.0   2021-03-04 [1] CRAN (R 4.0.2)
   gtable          0.3.0   2019-03-25 [1] CRAN (R 4.0.2)
   hablar        * 0.3.0   2020-03-19 [1] CRAN (R 4.0.2)
   haven           2.3.1   2020-06-01 [1] CRAN (R 4.0.2)
   hms             0.5.3   2020-01-08 [1] CRAN (R 4.0.2)
   htmltools       0.5.1.1 2021-01-22 [1] CRAN (R 4.0.2)
   htmlwidgets     1.5.2   2020-10-03 [1] CRAN (R 4.0.2)
   httpuv          1.5.5   2021-01-13 [1] CRAN (R 4.0.2)
   httr            1.4.2   2020-07-20 [1] CRAN (R 4.0.2)
   insight         0.13.1  2021-02-22 [1] CRAN (R 4.0.2)
   janitor         2.1.0   2021-01-05 [1] CRAN (R 4.0.2)
   jquerylib       0.1.3   2020-12-17 [1] CRAN (R 4.0.2)
   jsonlite        1.7.2   2020-12-09 [1] CRAN (R 4.0.2)
   jtools        * 2.1.3   2021-03-12 [1] CRAN (R 4.0.2)
   knitr           1.31    2021-01-27 [1] CRAN (R 4.0.2)
   later           1.1.0.1 2020-06-05 [1] CRAN (R 4.0.2)
   lattice       * 0.20-41 2020-04-02 [2] CRAN (R 4.0.2)
   lifecycle       0.2.0   2020-03-06 [1] CRAN (R 4.0.2)
   lubridate       1.7.9.2 2020-11-13 [1] CRAN (R 4.0.2)
 V magrittr        1.5     2020-11-17 [1] CRAN (R 4.0.2)
   MASS            7.3-53  2020-09-09 [2] CRAN (R 4.0.2)
   Matrix          1.2-18  2019-11-27 [2] CRAN (R 4.0.2)
   memoise         2.0.0   2021-01-26 [1] CRAN (R 4.0.2)
   mime            0.10    2021-02-13 [1] CRAN (R 4.0.2)
   miniUI          0.1.1.1 2018-05-18 [1] CRAN (R 4.0.2)
   modelr          0.1.8   2020-05-19 [1] CRAN (R 4.0.2)
   munsell         0.5.0   2018-06-12 [1] CRAN (R 4.0.2)
   officer       * 0.3.17  2021-03-05 [1] CRAN (R 4.0.2)
   openssl         1.4.3   2020-09-18 [1] CRAN (R 4.0.2)
   openxlsx        4.2.3   2020-10-27 [1] CRAN (R 4.0.2)
   pacman          0.5.1   2019-03-11 [1] CRAN (R 4.0.2)
   pander          0.6.3   2018-11-06 [1] CRAN (R 4.0.2)
   pillar          1.4.6   2020-07-10 [1] CRAN (R 4.0.2)
   pkgbuild        1.1.0   2020-07-13 [1] CRAN (R 4.0.2)
   pkgconfig       2.0.3   2019-09-22 [1] CRAN (R 4.0.2)
   pkgload         1.1.0   2020-05-29 [1] CRAN (R 4.0.2)
   plyr          * 1.8.6   2020-03-03 [1] CRAN (R 4.0.2)
   prettyunits     1.1.1   2020-01-24 [1] CRAN (R 4.0.2)
   processx        3.4.4   2020-09-03 [1] CRAN (R 4.0.2)
   promises        1.1.1   2020-06-09 [1] CRAN (R 4.0.2)
   ps              1.4.0   2020-10-07 [1] CRAN (R 4.0.2)
   purrr           0.3.4   2020-04-17 [1] CRAN (R 4.0.2)
   R6              2.5.0   2020-10-28 [1] CRAN (R 4.0.2)
 V Rcpp            1.0.5   2021-01-15 [1] CRAN (R 4.0.2)
   readr           1.4.0   2020-10-05 [1] CRAN (R 4.0.2)
   readxl          1.3.1   2019-03-13 [1] CRAN (R 4.0.2)
   remotes         2.2.0   2020-07-21 [1] CRAN (R 4.0.2)
   reprex          0.3.0   2019-05-16 [1] CRAN (R 4.0.2)
   rio           * 0.5.26  2021-03-01 [1] CRAN (R 4.0.2)
   rlang           0.4.10  2020-12-30 [1] CRAN (R 4.0.2)
   rmarkdown       2.7     2021-02-19 [1] CRAN (R 4.0.2)
   Rmisc         * 1.5     2013-10-22 [1] CRAN (R 4.0.2)
   rprojroot       2.0.2   2020-11-15 [1] CRAN (R 4.0.2)
   rstatix         0.7.0   2021-02-13 [1] CRAN (R 4.0.2)
   rstudioapi      0.13    2020-11-12 [1] CRAN (R 4.0.2)
   rvest           0.3.6   2020-07-25 [1] CRAN (R 4.0.2)
   sass            0.3.1   2021-01-24 [1] CRAN (R 4.0.2)
   scales          1.1.1   2020-05-11 [1] CRAN (R 4.0.2)
   sessioninfo     1.1.1   2018-11-05 [1] CRAN (R 4.0.2)
   shiny           1.6.0   2021-01-25 [1] CRAN (R 4.0.2)
   shinyWidgets    0.6.0   2021-03-15 [1] CRAN (R 4.0.2)
   sjlabelled      1.1.7   2020-09-24 [1] CRAN (R 4.0.2)
   sjmisc          2.8.6   2021-01-07 [1] CRAN (R 4.0.2)
   snakecase       0.11.0  2019-05-25 [1] CRAN (R 4.0.2)
   stringi         1.5.3   2020-09-09 [1] CRAN (R 4.0.2)
   stringr         1.4.0   2019-02-10 [1] CRAN (R 4.0.2)
   survival      * 3.2-7   2020-09-28 [2] CRAN (R 4.0.2)
   sys             3.4     2020-07-23 [1] CRAN (R 4.0.2)
   testthat        3.0.0   2020-10-31 [1] CRAN (R 4.0.2)
   tibble          3.0.4   2020-10-12 [1] CRAN (R 4.0.2)
   tidyr           1.1.2   2020-08-27 [1] CRAN (R 4.0.2)
   tidyselect      1.1.0   2020-05-11 [1] CRAN (R 4.0.2)
   tidyverse       1.3.0   2019-11-21 [1] CRAN (R 4.0.2)
 V tinytex         0.27    2021-03-04 [1] CRAN (R 4.0.2)
   usethis         1.6.3   2020-09-17 [1] CRAN (R 4.0.2)
   uuid            0.1-4   2020-02-26 [1] CRAN (R 4.0.2)
   vctrs           0.3.4   2020-08-29 [1] CRAN (R 4.0.2)
   withr           2.3.0   2020-09-22 [1] CRAN (R 4.0.2)
 V xfun            0.19    2021-03-11 [1] CRAN (R 4.0.2)
   xml2            1.3.2   2020-04-23 [1] CRAN (R 4.0.2)
   xtable          1.8-4   2019-04-21 [1] CRAN (R 4.0.2)
   yaml            2.2.1   2020-02-01 [1] CRAN (R 4.0.2)
   zip             2.1.1   2020-08-27 [1] CRAN (R 4.0.2)

[1] /Users/shrushtishah
[2] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

 V ── Loaded and on-disk version mismatch.

Error in import("raw/data.xlsx", which = "MRI-data") : could not find function "import"

Hello,

Im doing module 7 right now and im having trouble running lines 70-80. I keep getting the error from line 76-80: Error in import("raw/data.xlsx", which = "MRI-data") : could not find function "import".
I made sure I have the data.xlsx in my raw folder and can see the MRI-data section. I also looked up the error but couldn't find a solution there. I was able to run the first portion of the lines fine, but when I added the second portion it caused the error. Im not sure what the issue is, could it be related to the file itself?

Thanks!

# Load your data ----------
df.demo <- rio::import("raw/data.xlsx", which = "demographics") %>% # Imports the sheet with demographic data
  janitor::clean_names() %>% # Clean the column names
  dplyr::rename(
    "ID" = "study_id",
    "Group" = "group"
  )

df.mri <- import("raw/data.xlsx", which = "MRI-data") %>%
  janitor::clean_names() %>%                             # clean column names
  janitor::remove_empty(c("rows", "cols")) %>%           # remove the empty rows and columns
  janitor::remove_constant(na.rm = TRUE, quiet = FALSE)  # remove the column of all "Yes" values 

Unable to add exported .bib to YAML and insert a figure

Hello,

Im trying to add my own exported .bib file to the YAML as shown in the video, so that I can link it to the document, but I get an error when trying to knit. My exported Zotero bibliography is called Test2.bib, I have it on my desktop which I thought might be an issue but when I moved it to my documents I got the same error. Ive looked for solutions online and made sure the directory was the same.

This is my YAML:

date: "`r Sys.Date()`"
author: "Danika Walsh"
title: "My project test 1"
output: 
  officedown::rdocx_document:
    reference_docx: styles/template.docx                  # This is the template that will style my document when its knit
link-citations: yes 
bibliography: styles/Test2.bib
#bibliography: G:/My Drive/ZoteroRPlugin/My Library.bib
zotero: TRUE
csl: styles/Citation Styles/american-physiological-society.csl      # This sets the style of formatting for references in text and bibliography

This is the error I got when pressing knit:

File styles/Test2.bib not found in resource path
Error: pandoc document conversion failed with error 99
Execution halted

When trying to add a figure as well:

{r knit-citations, fig.cap = "Awesome cartoon of knitting citations.", fig.asp=1748/2480, fig.height=6.5} knitr::include_graphics("images/RMarkdown - Citations.png")

I get a similar error, but in the document itself:

Figure [Error! Reference source not found.]

It likely a problem with the directory but I can't seem to figure out what to change. I can see the .bib file il my my files in RStudio Im still learning so I would really appreciate the help.

Thank you so much!

**sessionInfo()**

<img width="976" alt="Screenshot 2024-01-29 at 10 14 02 AM" src="https://github.com/alapo/Literate-Programming/assets/157257679/f8c34bcb-0555-4003-9bfe-0648719fcd7b">
<img width="904" alt="Screenshot 2024-01-29 at 10 14 10 AM" src="https://github.com/alapo/Literate-Programming/assets/157257679/1e404c30-21a7-4e8f-8feb-bcb1d8998788">

Problem with turning a numeric variable into a factor

Hi Andrew,

I'm trying out the skills from module 05 with some birth data that I imported from a Stata file. I have a four-level categorical variable for maternal age (age 15-19, 20s, 30s, or age 40+) that was a "numeric" type and I tried to make it a "factor" instead. It looks like it worked, but then it won't let me group infant birth weight (tgrams) by this maternal age variable (mom_age_cat). It looks like all the mom_age_cat values are missing? But the dataset I imported had no missing data on this variable...

df <- rio::import("data/NC_birth_data_PGME_edited.dta") 
str(df)
'data.frame':	800 obs. of  15 variables:
 $ plural     : num  1 1 1 1 1 1 1 1 1 1 ...
  ..- attr(*, "label")= chr "plural"
  ..- attr(*, "format.stata")= chr "%10.0g"
 $ sex        : num  1 2 1 1 1 1 2 2 2 2 ...
  ..- attr(*, "label")= chr "sex"
  ..- attr(*, "format.stata")= chr "%10.0g"
 $ mage       : num  32 32 27 27 25 28 25 15 37 21 ...
  ..- attr(*, "label")= chr "mage"
  ..- attr(*, "format.stata")= chr "%10.0g"
 $ weeks      : num  40 37 39 39 39 43 39 42 41 39 ...
  ..- attr(*, "label")= chr "weeks"
  ..- attr(*, "format.stata")= chr "%10.0g"
 $ marital    : num  1 1 1 1 1 1 1 2 1 1 ...
  ..- attr(*, "label")= chr "marital"
  ..- attr(*, "format.stata")= chr "%10.0g"
 $ racemom    : num  1 1 1 1 1 1 1 1 8 1 ...
  ..- attr(*, "label")= chr "racemom"
  ..- attr(*, "format.stata")= chr "%10.0g"
 $ hispmom    : chr  "N" "N" "N" "N" ...
  ..- attr(*, "label")= chr "hispmom"
  ..- attr(*, "format.stata")= chr "%9s"
 $ gained     : num  38 34 12 15 32 32 75 25 31 28 ...
  ..- attr(*, "label")= chr "gained"
  ..- attr(*, "format.stata")= chr "%10.0g"
 $ smoke      : num  0 0 0 0 0 0 0 0 0 0 ...
  ..- attr(*, "label")= chr "smoke"
  ..- attr(*, "format.stata")= chr "%10.0g"
 $ drink      : num  0 0 0 0 0 0 0 0 0 0 ...
  ..- attr(*, "label")= chr "drink"
  ..- attr(*, "format.stata")= chr "%10.0g"
 $ tounces    : num  111 116 138 136 121 117 143 113 139 120 ...
  ..- attr(*, "label")= chr "tounces"
  ..- attr(*, "format.stata")= chr "%10.0g"
 $ tgrams     : num  3147 3289 3912 3856 3430 ...
  ..- attr(*, "label")= chr "tgrams"
  ..- attr(*, "format.stata")= chr "%10.0g"
 $ low        : num  0 0 0 0 0 0 0 0 0 0 ...
  ..- attr(*, "label")= chr "low"
  ..- attr(*, "format.stata")= chr "%10.0g"
 $ premie     : num  0 0 0 0 0 0 0 0 0 0 ...
  ..- attr(*, "label")= chr "premie"
  ..- attr(*, "format.stata")= chr "%10.0g"
 $ mom_age_cat: num  2 2 1 1 1 1 1 0 2 1 ...
  ..- attr(*, "format.stata")= chr "%10.0g"
  ..- attr(*, "labels")= Named num [1:4] 0 1 2 3
  .. ..- attr(*, "names")= chr [1:4] "Aged 15-19" "Aged 20-29" "Aged 30-39" "Aged 40+"

Trying to turn it into a factor

df$mom_age_cat <- factor(df$mom_age_cat, levels=c("15-19", "20-29", "30-39", "40+"), ordered=TRUE) # Data is imported type "character" we need to change that to factors before running statistics.
levels(df$mom_age_cat) # Confirm that our data is ordered properly.

[1] "15-19" "20-29" "30-39" "40+"  

df %>%
+   group_by(mom_age_cat) %>%
+   get_summary_stats(tgrams, type = "mean_sd")
# A tibble: 1 x 5
  mom_age_cat variable     n  mean    sd
  <ord>       <chr>    <dbl> <dbl> <dbl>
1 NA          tgrams     800 3299.  639.

ggboxplot(df, x = "mom_age_cat", y = "tgrams")

Where can we download the "MyProjectName.Rproj" file?

Hi there,

I followed along with the "Workshop 03 - Installation" YouTube video up until minute 8:20 where Andrew opens up the "MyProjectName.Rproj" file. Were we sent that file previously? Or can we download this file from GitHub? If so, how? I can open that folder, but it just shows me all the individual files...

Please help!

-Chelsea

Could not find function `describe.aov`

Describe the bug
Hi,
I am at the final step to knit the document in Rmarkdown in Windows 10 and I got a message saying "execution halted" in Line 81 (which is empty) I have R version 4.0.4 and RStudio v1.4.1106.

Thank you.

To Reproduce
Steps to reproduce the behavior:

1. Go to 'manuscript.rmd'
2. Click on 'Knit'
3. Scroll down to 'Knit to rdocx-document'
4. See error in RMarkdown - Error in describe-aov(model, “Group”) : could not find function “describe.aov” calls: … inline_exec -> hook_eval -> withVisible -> eval -> eval Execution halted

Additionally, I wasn't able to install easystats using the installR script. This is the error message I got:
Error: Failed to install 'easystats' from GitHub:
Failed to install 'modelbased' from GitHub:
(converted from warning) installation of package ‘C:/Users/lucia/AppData/Local/Temp/Rtmp8c4edV/file24485b91473d/modelbased_0.5.9.tar.gz’ had non-zero exit status

Expected behavior
As explained in the video, the word document should open, but nothing happens.

Screenshots

devtools::session_info()
In your Console, type devtools::session_info() and paste it in the code section below. This allows me to evaluate your R environment for any issues.

# REMOVE THIS LINE AND PASTE OUTPUT FROM 
devtools::session_info()

devtools::session_info()

devtools::session_info()
- Session info -----------------------------------------------
 setting  value                       
 version  R version 4.0.4 (2021-02-15)
 os       Windows 10 x64              
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  English_United States.1252  
 ctype    English_United States.1252  
 tz       America/Denver              
 date     2021-03-24                  

- Packages ---------------------------------------------------
 package     * version date       lib
 askpass       1.1     2019-01-13 [1]
 assertthat    0.2.1   2019-03-21 [1]
 cachem        1.0.4   2021-02-13 [1]
 callr         3.5.1   2020-10-13 [1]
 cellranger    1.1.0   2016-07-27 [1]
 cli           2.3.1   2021-02-23 [1]
 crayon        1.4.1   2021-02-08 [1]
 credentials   1.3.0   2020-07-21 [1]
 curl          4.3     2019-12-02 [1]
 data.table    1.14.0  2021-02-21 [1]
 desc          1.3.0   2021-03-05 [1]
 devtools      2.3.2   2020-09-18 [1]
 digest        0.6.27  2020-10-24 [1]
 ellipsis      0.3.1   2020-05-15 [1]
 evaluate      0.14    2019-05-28 [1]
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[1] C:/Users/lucia/Documents/R/win-library/4.0
[2] C:/Program Files/R/R-4.0.4/library

Issues with RMarkdown with Module05.Rmd

Hello! I am having issues with the RMarkdown from last workshop. I ran lines 49-53 as stated in the Module05.Rmd script.

i```
f (!require("pacman")) install.packages("pacman") # if pacman is not installed, the install it.
pacman::p_load(effectsize, ggpubr, ggstatsplot, googlesheets4, janitor, jtools, knitr, parameters, rio, remotes, report, rstatix, tidyverse, see, sjPlot, sjmisc) # load/install required packages

Load your data ----------

df <- read_sheet("https://docs.google.com/spreadsheets/d/1fFVmBFpdAKxzLMT8dx7pZm48mo9CE3kIwYhrkaZj7NM", sheet = "1")

This worked fine. However when I tried to knit the document, I got several error messages. The final one being as follows:

sjmisc installed
Quitting from lines 48-55 (Module05.Rmd) 
Error in read_sheet("https://docs.google.com/spreadsheets/d/1fFVmBFpdAKxzLMT8dx7pZm48mo9CE3kIwYhrkaZj7NM",  : 
  could not find function "read_sheet"
Calls: <Anonymous> ... handle -> withCallingHandlers -> withVisible -> eval -> eval
In addition: There were 15 warnings (use warnings() to see them)

Execution halted

devtools::session_info()
> devtools::session_info()
- Session info ------------------------------------------------------------------------
 setting  value                       
 version  R version 4.0.0 (2020-04-24)
 os       Windows 10 x64              
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  English_Canada.1252         
 ctype    English_Canada.1252         
 tz       America/Denver              
 date     2021-04-06                  

- Packages ----------------------------------------------------------------------------
 ! package             * version    date       lib
   abind                 1.4-5      2016-07-21 [1]
   apastats            * 0.3        2021-03-16 [1]
   askpass               1.1        2019-01-13 [1]
   assertthat            0.2.1      2019-03-21 [1]
   backports             1.2.1      2020-12-09 [1]
   BayesFactor           0.9.12-4.2 2018-05-19 [1]
   bayestestR            0.8.2      2021-01-26 [1]
   BiocManager           1.30.10    2019-11-16 [1]
   boot                  1.3-24     2019-12-20 [2]
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   BWStest               0.2.2      2018-10-18 [1]
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   callr                 3.5.1      2020-10-13 [1]
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   prettyunits           1.1.1      2020-01-24 [1]
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   reprex                1.0.0      2021-01-27 [1]
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 CRAN (R 4.0.4)                        
 CRAN (R 4.0.4)                        
 CRAN (R 4.0.3)                        
 CRAN (R 4.0.4)                        
 CRAN (R 4.0.4)                        

[1] C:/Users/charl/Documents/R/win-library/4.0
[2] C:/Program Files/R/R-4.0.0/library

 R -- Package was removed from disk.


Comment: Please advise on how I can fix this. Thank you.

API limit exceeded

Describe the bug
While trying to install the different packages in the Install.R file, I ran into the following error:

To Reproduce
When trying to run the code that requires Github, something went wrong with the token. I ran this code:

remotes::install_github("easystats/easystats")
remotes::install_github("easystats/report")  # You only need to do that once
remotes::install_github("easystats/correlation")
remotes::install_github("davidgohel/officedown")

devtools::install_github('achetverikov/apastats', subdir='apastats')
devtools::install_github("benmarwick/wordcountaddin", type = "source", dependencies = TRUE)
devtools::install_github('rstudio/rmarkdown')

I got this error:
Error: Failed to install 'rmarkdown' from GitHub:
HTTP error 403.
API rate limit exceeded for 172.103.181.16. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)

Rate limit remaining: 0/60
Rate limit reset at: 2021-03-23 18:10:44 UTC

To increase your GitHub API rate limit

• Use usethis::browse_github_pat() to create a Personal Access Token.
• Use usethis::edit_r_environ() and add the token as GITHUB_PAT.

usethis::browse_github_pat()
Error: browse_github_pat() was deprecated in usethis 2.0.0 and is now defunct.
Please use create_github_token() instead.
create_github_token()
Error in create_github_token() :
could not find function "create_github_token"

Expected behavior
In the video Adam showed, he got prompted to sign into github and that never happened for me, which is why I might be getting this error.

Screenshots
see attached

devtools::session_info()
In your Console, type devtools::session_info() and paste it in the code section below. This allows me to evaluate your R environment for any issues.

# REMOVE THIS LINE AND PASTE OUTPUT FROM 
 Session info --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 4.0.4 (2021-02-15)
 os       Windows 10 x64              
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  English_United States.1252  
 ctype    English_United States.1252  
 tz       America/Denver              
 date     2021-03-23                  

- Packages ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 package     * version date       lib source                                
 assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.0.4)                        
 cachem        1.0.4   2021-02-13 [1] CRAN (R 4.0.4)                        
 callr         3.5.1   2020-10-13 [1] CRAN (R 4.0.4)                        
 cellranger    1.1.0   2016-07-27 [1] CRAN (R 4.0.4)                        
 cli           2.3.1   2021-02-23 [1] CRAN (R 4.0.4)                        
 crayon        1.4.1   2021-02-08 [1] CRAN (R 4.0.4)                        
 curl          4.3     2019-12-02 [1] CRAN (R 4.0.4)                        
 data.table    1.14.0  2021-02-21 [1] CRAN (R 4.0.4)                        
 desc          1.3.0   2021-03-05 [1] CRAN (R 4.0.4)                        
 devtools      2.3.2   2020-09-18 [1] CRAN (R 4.0.4)                        
 digest        0.6.27  2020-10-24 [1] CRAN (R 4.0.4)                        
 ellipsis      0.3.1   2020-05-15 [1] CRAN (R 4.0.4)                        
 evaluate      0.14    2019-05-28 [1] CRAN (R 4.0.4)                        
 fansi         0.4.2   2021-01-15 [1] CRAN (R 4.0.4)                        
 fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.0.4)                        
 forcats       0.5.1   2021-01-27 [1] CRAN (R 4.0.4)                        
 foreign       0.8-81  2020-12-22 [2] CRAN (R 4.0.4)                        
 fs            1.5.0   2020-07-31 [1] CRAN (R 4.0.4)                        
 gdtools       0.2.3   2021-01-06 [1] CRAN (R 4.0.4)                        
 glue          1.4.2   2020-08-27 [1] CRAN (R 4.0.4)                        
 haven         2.3.1   2020-06-01 [1] CRAN (R 4.0.4)                        
 hms           1.0.0   2021-01-13 [1] CRAN (R 4.0.4)                        
 htmltools     0.5.1.1 2021-01-22 [1] CRAN (R 4.0.4)                        
 knitr         1.31    2021-01-27 [1] CRAN (R 4.0.4)                        
 lifecycle     1.0.0   2021-02-15 [1] CRAN (R 4.0.4)                        
 magrittr      2.0.1   2020-11-17 [1] CRAN (R 4.0.4)                        
 memoise       2.0.0   2021-01-26 [1] CRAN (R 4.0.4)                        
 officedown    0.2.1   2021-02-01 [1] CRAN (R 4.0.4)                        
 officer       0.3.17  2021-03-05 [1] CRAN (R 4.0.4)                        
 openxlsx      4.2.3   2020-10-27 [1] CRAN (R 4.0.4)                        
 pacman        0.5.1   2019-03-11 [1] CRAN (R 4.0.4)                        
 pillar        1.5.1   2021-03-05 [1] CRAN (R 4.0.4)                        
 pkgbuild      1.2.0   2020-12-15 [1] CRAN (R 4.0.4)                        
 pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.0.4)                        
 pkgload       1.2.0   2021-02-23 [1] CRAN (R 4.0.4)                        
 prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.0.4)                        
 processx      3.4.5   2020-11-30 [1] CRAN (R 4.0.4)                        
 ps            1.6.0   2021-02-28 [1] CRAN (R 4.0.4)                        
 purrr         0.3.4   2020-04-17 [1] CRAN (R 4.0.4)                        
 R6            2.5.0   2020-10-28 [1] CRAN (R 4.0.4)                        
 Rcpp          1.0.6   2021-01-15 [1] CRAN (R 4.0.4)                        
 readxl        1.3.1   2019-03-13 [1] CRAN (R 4.0.4)                        
 remotes       2.2.0   2020-07-21 [1] CRAN (R 4.0.4)                        
 rio           0.5.26  2021-03-01 [1] CRAN (R 4.0.4)                        
 rlang         0.4.10  2020-12-30 [1] CRAN (R 4.0.4)                        
 rmarkdown     2.7     2021-02-19 [1] CRAN (R 4.0.4)                        
 rprojroot     2.0.2   2020-11-15 [1] CRAN (R 4.0.4)                        
 rscodeio      0.1.0   2021-03-19 [1] Github (anthonynorth/rscodeio@88a1a37)
 rstudioapi    0.13    2020-11-12 [1] CRAN (R 4.0.4)                        
 rvg           0.2.5   2020-06-30 [1] CRAN (R 4.0.4)                        
 sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 4.0.4)                        
 stringi       1.5.3   2020-09-09 [1] CRAN (R 4.0.3)                        
 systemfonts   1.0.1   2021-02-09 [1] CRAN (R 4.0.4)                        
 testthat      3.0.2   2021-02-14 [1] CRAN (R 4.0.4)                        
 tibble        3.1.0   2021-02-25 [1] CRAN (R 4.0.4)                        
 usethis       2.0.1   2021-02-10 [1] CRAN (R 4.0.4)                        
 utf8          1.1.4   2018-05-24 [1] CRAN (R 4.0.4)                        
 uuid          0.1-4   2020-02-26 [1] CRAN (R 4.0.3)                        
 vctrs         0.3.6   2020-12-17 [1] CRAN (R 4.0.4)                        
 withr         2.4.1   2021-01-26 [1] CRAN (R 4.0.4)                        
 xfun          0.22    2021-03-11 [1] CRAN (R 4.0.4)                        
 xml2          1.3.2   2020-04-23 [1] CRAN (R 4.0.4)                        
 yaml          2.2.1   2020-02-01 [1] CRAN (R 4.0.3)                        
 zip           2.1.1   2020-08-27 [1] CRAN (R 4.0.4)                        

[1] C:/Users/racin/Documents/R/win-library/4.0
[2] C:/Program Files/R/R-4.0.4/library
> 



**Additional context**
Add any other context about the problem here.
![Capture](https://user-images.githubusercontent.com/80359264/112193223-4d843a80-8bcd-11eb-99db-3639aeabd493.PNG)

Downloading easystats suite fails

Describe the bug
When attempting to download the easystats suite the download fails and produces the following error.

"Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  download from 'https://api.github.com/repos/easystats/easystats/tarball/HEAD' failed" 

To Reproduce
I followed the correct steps in the installation video with the only difference being I had to generate a PAT for GitHub as there was no login prompt for Mac.

Expected behavior
I expected the download to work perfectly as in the video.

Screenshots
N/A

sessionInfo()

R version 4.0.4 (2021-02-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] zip_2.1.1         Rcpp_1.0.6        cellranger_1.1.0  pillar_1.5.0      compiler_4.0.4    prettyunits_1.1.1 forcats_0.5.1     remotes_2.2.0    
 [9] sys_3.4           tools_4.0.4       testthat_3.0.2    pkgbuild_1.2.0    pkgload_1.2.0     jsonlite_1.7.2    tibble_3.1.0      memoise_2.0.0    
[17] lifecycle_1.0.0   pkgconfig_2.0.3   rlang_0.4.10      openxlsx_4.2.3    cli_2.3.1         curl_4.3          haven_2.3.1       rio_0.5.26       
[25] fastmap_1.1.0     withr_2.4.1       hms_1.0.0         desc_1.2.0        fs_1.5.0          vctrs_0.3.6       askpass_1.1       devtools_2.3.2   
[33] rprojroot_2.0.2   glue_1.4.2        data.table_1.14.0 R6_2.5.0          processx_3.4.5    fansi_0.4.2       readxl_1.3.1      foreign_0.8-81   
[41] pacman_0.5.1      sessioninfo_1.1.1 rscodeio_0.1.0    callr_3.5.1       purrr_0.3.4       magrittr_2.0.1    ps_1.6.0          credentials_1.3.0
[49] ellipsis_0.3.1    usethis_2.0.1     assertthat_0.2.1  utf8_1.1.4        stringi_1.5.3     openssl_1.4.3     cachem_1.0.4      crayon_1.4.1   

Additional context
Tried to install from source, also did not work and produced the following error:

Error: package or namespace load failed for ‘easystats’:
 .onAttach failed in attachNamespace() for 'easystats', details:
  call: NULL
  error: 'color_theme' is not an exported object from 'namespace:insight'
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/parkersmith/Library/R/4.0/library/easystats’

Can't find Zoom links for workshop

Before you ask a question

• Have you searched other issues on this repository?
• Have you watched the YouTube videos for an answer?
• Have you checked the main page on the repo?

Describe your administrative issue below
Hi there,

I registered for the workshop but never got the email with the Zoom links in order to attend it live. Can anyone direct me to where I can obtain the links?

LanguageToolR installation issue

If I type into my consol:

install.packages("LanguageToolR")

I get the message:

Warning in install.packages :
package ‘LanguageToolR’ is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

When I tried to look on cran I couldn't find LanguageTools. Does anyone know where I could find a version that will work for me?

Thank you!

Errors while running unchanged code Mod7

Hello,

Im having trouble running this line of code from module 7:

df.mri <- df.mri %>% dplyr::rename( # "NewName" = "OldName" "completed_mri" ="completed_mri_1_yes_0_no") %>% filter(site_mri == "Calgary" & completed_mri == "1") %>% # remove all data that is not from Calgary and those who did not complete an MRI filter(id %in% unique(df.demo$ID)) %>% # I only want IDs that are in present in df.demo suppressWarnings(hablar::convert(num(left_af:right_uf))) %>% # Converts some of the columns into numeric -- requires hablar library gather(mriloc, dti_value, left_cst:right_uf) %>% dplyr::arrange(id) %>% mutate(hemisphere = case_when( str_contains(mriloc, "left") == TRUE ~ "Left", str_contains(mriloc, "left") == FALSE ~ "Right" ))

Its the exact same code as you have in the video and im able to knit the document but when I try to run the chunk itself (after having run all the lines before without issue) I get the following error:

Error in dplyr::rename():
! Can't rename columns that don't exist.
✖ Column completed_mri_1_yes_0_no doesn't exist.
Backtrace:

1. ... %>% ...
2. dplyr:::rename.data.frame(., completed_mri = "completed_mri_1_yes_0_no")
   Error in dplyr::rename(., completed_mri = "completed_mri_1_yes_0_no")

In the video there's an issue with this line but the steps to remove it are already done to the code so I don't think it's the same issue. I believe we changed the name of the MRI column previously in the module so could that be the reason behind the error? Im getting some errors while running lines after this one so im not sure if these are related.

Thanks for your help!

Danika

LanguageToolR::lato_quick_setup() not working for me

Describe the bug
When I try to run the following line of code (line 34 in the InstallR script)

LanguageToolR::lato_quick_setup()

I get the following error:

Error in system2("java", c("-XshowSettings:properties", "-version"), stderr = TRUE,  : 
  '"java"' not found

To Reproduce
Steps to reproduce the behavior:
When I first tried installing the R packages, I forgot to install RTools and had gotten stuck on line 28 (Wordcountaddin) so I tried re-installing R and R studio and then figured out that I had missed RTools so did it in the right order. So this time I went line by line like in your video (after installing ALL of the other software) and I got through line 28 no problem.
Everything worked OK until line 34 when I got this error.

Expected behavior
I expected it to run like in your video.

Screenshots

devtools::session_info()
In your Console, type devtools::session_info() and paste it in the code section below. This allows me to evaluate your R environment for any issues.

setting  value                       
 version  R version 4.0.4 (2021-02-15)
 os       Windows 10 x64              
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  English_Canada.1252         
 ctype    English_Canada.1252         
 tz       America/Denver              
 date     2021-03-17                  

- Packages ----------------------------------------------------------------------
 package       * version  date       lib source                                
 askpass         1.1      2019-01-13 [1] CRAN (R 4.0.4)                        
 assertthat      0.2.1    2019-03-21 [1] CRAN (R 4.0.4)                        
 cachem          1.0.4    2021-02-13 [1] CRAN (R 4.0.4)                        
 callr           3.5.1    2020-10-13 [1] CRAN (R 4.0.4)                        
 cellranger      1.1.0    2016-07-27 [1] CRAN (R 4.0.4)                        
 cli             2.3.1    2021-02-23 [1] CRAN (R 4.0.4)                        
 crayon          1.4.1    2021-02-08 [1] CRAN (R 4.0.4)                        
 credentials     1.3.0    2020-07-21 [1] CRAN (R 4.0.4)                        
 curl            4.3      2019-12-02 [1] CRAN (R 4.0.4)                        
 data.table      1.14.0   2021-02-21 [1] CRAN (R 4.0.4)                        
 desc            1.3.0    2021-03-05 [1] CRAN (R 4.0.4)                        
 devtools        2.3.2    2020-09-18 [1] CRAN (R 4.0.4)                        
 easystats       0.3.0    2021-03-18 [1] Github (easystats/easystats@a56b091)  
 ellipsis        0.3.1    2020-05-15 [1] CRAN (R 4.0.4)                        
 fansi           0.4.2    2021-01-15 [1] CRAN (R 4.0.4)                        
 fastmap         1.1.0    2021-01-25 [1] CRAN (R 4.0.4)                        
 forcats         0.5.1    2021-01-27 [1] CRAN (R 4.0.4)                        
 foreign         0.8-81   2020-12-22 [2] CRAN (R 4.0.4)                        
 fs              1.5.0    2020-07-31 [1] CRAN (R 4.0.4)                        
 glue            1.4.2    2020-08-27 [1] CRAN (R 4.0.4)                        
 haven           2.3.1    2020-06-01 [1] CRAN (R 4.0.4)                        
 hms             1.0.0    2021-01-13 [1] CRAN (R 4.0.4)                        
 httr            1.4.2    2020-07-20 [1] CRAN (R 4.0.4)                        
 insight         0.13.1.1 2021-03-18 [1] Github (easystats/insight@e70a46a)    
 jsonlite        1.7.2    2020-12-09 [1] CRAN (R 4.0.4)                        
 LanguageToolR   0.1.3    2021-03-18 [1] Github (nevrome/LanguageToolR@7a6ca3a)
 lifecycle       1.0.0    2021-02-15 [1] CRAN (R 4.0.4)                        
 magrittr        2.0.1    2020-11-17 [1] CRAN (R 4.0.4)                        
 memoise         2.0.0    2021-01-26 [1] CRAN (R 4.0.4)                        
 openssl         1.4.3    2020-09-18 [1] CRAN (R 4.0.4)                        
 openxlsx        4.2.3    2020-10-27 [1] CRAN (R 4.0.4)                        
 pacman          0.5.1    2019-03-11 [1] CRAN (R 4.0.4)                        
 pillar          1.5.1    2021-03-05 [1] CRAN (R 4.0.4)                        
 pkgbuild        1.2.0    2020-12-15 [1] CRAN (R 4.0.4)                        
 pkgconfig       2.0.3    2019-09-22 [1] CRAN (R 4.0.4)                        
 pkgload         1.2.0    2021-02-23 [1] CRAN (R 4.0.4)                        
 prettyunits     1.1.1    2020-01-24 [1] CRAN (R 4.0.4)                        
 processx        3.4.5    2020-11-30 [1] CRAN (R 4.0.4)                        
 ps              1.6.0    2021-02-28 [1] CRAN (R 4.0.4)                        
 purrr           0.3.4    2020-04-17 [1] CRAN (R 4.0.4)                        
 R6              2.5.0    2020-10-28 [1] CRAN (R 4.0.4)                        
 Rcpp            1.0.6    2021-01-15 [1] CRAN (R 4.0.4)                        
 readxl          1.3.1    2019-03-13 [1] CRAN (R 4.0.4)                        
 remotes         2.2.0    2020-07-21 [1] CRAN (R 4.0.4)                        
 rio             0.5.26   2021-03-01 [1] CRAN (R 4.0.4)                        
 rlang           0.4.10   2020-12-30 [1] CRAN (R 4.0.4)                        
 rprojroot       2.0.2    2020-11-15 [1] CRAN (R 4.0.4)                        
 rscodeio        0.1.0    2021-03-18 [1] Github (anthonynorth/rscodeio@88a1a37)
 rstudioapi      0.13     2020-11-12 [1] CRAN (R 4.0.4)                        
 rvest           1.0.0    2021-03-09 [1] CRAN (R 4.0.4)                        
 sessioninfo     1.1.1    2018-11-05 [1] CRAN (R 4.0.4)                        
 stringi         1.5.3    2020-09-09 [1] CRAN (R 4.0.3)                        
 sys             3.4      2020-07-23 [1] CRAN (R 4.0.4)                        
 testthat        3.0.2    2021-02-14 [1] CRAN (R 4.0.4)                        
 tibble          3.1.0    2021-02-25 [1] CRAN (R 4.0.4)                        
 usethis         2.0.1    2021-02-10 [1] CRAN (R 4.0.4)                        
 utf8            1.2.1    2021-03-12 [1] CRAN (R 4.0.4)                        
 vctrs           0.3.6    2020-12-17 [1] CRAN (R 4.0.4)                        
 withr           2.4.1    2021-01-26 [1] CRAN (R 4.0.4)                        
 xml2            1.3.2    2020-04-23 [1] CRAN (R 4.0.4)                        
 zip             2.1.1    2020-08-27 [1] CRAN (R 4.0.4)                        

[1] C:/Users/zipre/Documents/R/win-library/4.0
[2] C:/Program Files/R/R-4.0.4/library

Additional context
I tried to Google the problem first and came across responses to try installing 64-bit Java, which I did, but I still got the same error anyways.

Error installing Rio package

Describe the bug
I get the following error at this step: "Error: package ‘utf8’ does not have a namespace"

To Reproduce
Steps to reproduce the behavior:
In the MyProjectName installer file, click the line: rio::install_formats() # will install packages required by rio to function
Hit CTRL-ENTER to install

Expected behavior
I expected this package to install without errors. I've also captured in the screen shot a message that accompanied the Tidyverse installation; I don't know whether these things that failed to install/load are a problem or not, as the overall Tidyverse package installed.

Screenshots

devtools::session_info()
In your Console, type devtools::session_info() and paste it in the code section below. This allows me to evaluate your R environment for any issues.

- Session info ---------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 4.0.4 (2021-02-15)
 os       Windows 10 x64              
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  English_Canada.1252         
 ctype    English_Canada.1252         
 tz       America/Denver              
 date     2021-03-19                  

- Packages -------------------------------------------------------------------------------------------------------------
 package       * version date       lib source                                
 addinslist    * 0.4.0   2021-01-10 [1] CRAN (R 4.0.4)                        
 arsenal       * 3.6.2   2021-02-17 [1] CRAN (R 4.0.4)                        
 askpass         1.1     2019-01-13 [1] CRAN (R 4.0.4)                        
 assertthat      0.2.1   2019-03-21 [1] CRAN (R 4.0.4)                        
 bayestestR    * 0.8.2   2021-01-26 [1] CRAN (R 4.0.4)                        
 BiocManager     1.30.10 2019-11-16 [1] CRAN (R 4.0.4)                        
 cachem          1.0.4   2021-02-13 [1] CRAN (R 4.0.4)                        
 callr           3.5.1   2020-10-13 [1] CRAN (R 4.0.4)                        
 cellranger      1.1.0   2016-07-27 [1] CRAN (R 4.0.4)                        
 cgwtools      * 3.3     2021-01-06 [1] CRAN (R 4.0.4)                        
 cli             2.3.1   2021-02-23 [1] CRAN (R 4.0.4)                        
 coda            0.19-4  2020-09-30 [1] CRAN (R 4.0.4)                        
 colorspace      2.0-0   2020-11-11 [1] CRAN (R 4.0.4)                        
 colourpicker  * 1.1.0   2020-09-14 [1] CRAN (R 4.0.4)                        
 crayon          1.4.1   2021-02-08 [1] CRAN (R 4.0.4)                        
 credentials     1.3.0   2020-07-21 [1] CRAN (R 4.0.4)                        
 curl            4.3     2019-12-02 [1] CRAN (R 4.0.4)                        
 data.table      1.14.0  2021-02-21 [1] CRAN (R 4.0.4)                        
 desc            1.3.0   2021-03-05 [1] CRAN (R 4.0.4)                        
 devtools        2.3.2   2020-09-18 [1] CRAN (R 4.0.4)                        
 digest          0.6.27  2020-10-24 [1] CRAN (R 4.0.4)                        
 easystats     * 0.3.0   2021-03-16 [1] Github (easystats/easystats@e795908)  
 ellipsis        0.3.1   2020-05-15 [1] CRAN (R 4.0.4)                        
 emmeans         1.5.4   2021-02-03 [1] CRAN (R 4.0.4)                        
 estimability    1.3     2018-02-11 [1] CRAN (R 4.0.3)                        
 fansi           0.4.2   2021-01-15 [1] CRAN (R 4.0.4)                        
 fastmap         1.1.0   2021-01-25 [1] CRAN (R 4.0.4)                        
 forcats         0.5.1   2021-01-27 [1] CRAN (R 4.0.4)                        
 foreign         0.8-81  2020-12-22 [2] CRAN (R 4.0.4)                        
 formatR         1.8     2021-03-12 [1] CRAN (R 4.0.4)                        
 Formula       * 1.2-4   2020-10-16 [1] CRAN (R 4.0.3)                        
 fs              1.5.0   2020-07-31 [1] CRAN (R 4.0.4)                        
 generics        0.1.0   2020-10-31 [1] CRAN (R 4.0.4)                        
 glue            1.4.2   2020-08-27 [1] CRAN (R 4.0.4)                        
 gmp             0.6-2   2021-01-07 [1] CRAN (R 4.0.4)                        
 gtable          0.3.0   2019-03-25 [1] CRAN (R 4.0.4)                        
 hms             1.0.0   2021-01-13 [1] CRAN (R 4.0.4)                        
 htmltools       0.5.1.1 2021-01-22 [1] CRAN (R 4.0.4)                        
 htmlwidgets     1.5.3   2020-12-10 [1] CRAN (R 4.0.4)                        
 httpuv          1.5.5   2021-01-13 [1] CRAN (R 4.0.4)                        
 httr            1.4.2   2020-07-20 [1] CRAN (R 4.0.4)                        
 insight       * 0.13.1  2021-02-22 [1] CRAN (R 4.0.4)                        
 LanguageToolR   0.1.3   2021-03-16 [1] Github (nevrome/LanguageToolR@7a6ca3a)
 later           1.1.0.1 2020-06-05 [1] CRAN (R 4.0.4)                        
 lattice       * 0.20-41 2020-04-02 [2] CRAN (R 4.0.4)                        
 lifecycle       1.0.0   2021-02-15 [1] CRAN (R 4.0.4)                        
 magrittr        2.0.1   2020-11-17 [1] CRAN (R 4.0.4)                        
 Matrix          1.3-2   2021-01-06 [2] CRAN (R 4.0.4)                        
 memoise         2.0.0   2021-01-26 [1] CRAN (R 4.0.4)                        
 mime            0.10    2021-02-13 [1] CRAN (R 4.0.4)                        
 miniUI          0.1.1.1 2018-05-18 [1] CRAN (R 4.0.4)                        
 munsell         0.5.0   2018-06-12 [1] CRAN (R 4.0.4)                        
 mvtnorm         1.1-1   2020-06-09 [1] CRAN (R 4.0.3)                        
 officer       * 0.3.17  2021-03-05 [1] CRAN (R 4.0.4)                        
 openssl         1.4.3   2020-09-18 [1] CRAN (R 4.0.4)                        
 pacman        * 0.5.1   2019-03-11 [1] CRAN (R 4.0.4)                        
 parameters    * 0.12.0  2021-02-21 [1] CRAN (R 4.0.4)                        
 performance   * 0.7.0   2021-02-03 [1] CRAN (R 4.0.4)                        
 pkgbuild        1.2.0   2020-12-15 [1] CRAN (R 4.0.4)                        
 pkgconfig       2.0.3   2019-09-22 [1] CRAN (R 4.0.4)                        
 pkgload         1.2.0   2021-02-23 [1] CRAN (R 4.0.4)                        
 plyr          * 1.8.6   2020-03-03 [1] CRAN (R 4.0.4)                        
 prettyunits     1.1.1   2020-01-24 [1] CRAN (R 4.0.4)                        
 processx        3.4.5   2020-11-30 [1] CRAN (R 4.0.4)                        
 promises        1.2.0.1 2021-02-11 [1] CRAN (R 4.0.4)                        
 ps              1.6.0   2021-02-28 [1] CRAN (R 4.0.4)                        
 purrr           0.3.4   2020-04-17 [1] CRAN (R 4.0.4)                        
 R6              2.5.0   2020-10-28 [1] CRAN (R 4.0.4)                        
 Rcpp            1.0.6   2021-01-15 [1] CRAN (R 4.0.4)                        
 remotes         2.2.0   2020-07-21 [1] CRAN (R 4.0.4)                        
 rlang           0.4.10  2020-12-30 [1] CRAN (R 4.0.4)                        
 Rmisc         * 1.5     2013-10-22 [1] CRAN (R 4.0.4)                        
 rprojroot       2.0.2   2020-11-15 [1] CRAN (R 4.0.4)                        
 rscodeio        0.1.0   2021-03-16 [1] Github (anthonynorth/rscodeio@88a1a37)
 rvest           1.0.0   2021-03-09 [1] CRAN (R 4.0.4)                        
 scales          1.1.1   2020-05-11 [1] CRAN (R 4.0.4)                        
 sessioninfo     1.1.1   2018-11-05 [1] CRAN (R 4.0.4)                        
 shiny           1.6.0   2021-01-25 [1] CRAN (R 4.0.4)                        
 survival      * 3.2-7   2020-09-28 [2] CRAN (R 4.0.4)                        
 sys             3.4     2020-07-23 [1] CRAN (R 4.0.4)                        
 testthat        3.0.2   2021-02-14 [1] CRAN (R 4.0.4)                        
 tinytex         0.30    2021-03-04 [1] CRAN (R 4.0.4)                        
 usethis         2.0.1   2021-02-10 [1] CRAN (R 4.0.4)                        
 uuid            0.1-4   2020-02-26 [1] CRAN (R 4.0.3)                        
 vctrs           0.3.6   2020-12-17 [1] CRAN (R 4.0.4)                        
 withr           2.4.1   2021-01-26 [1] CRAN (R 4.0.4)                        
 xfun            0.22    2021-03-11 [1] CRAN (R 4.0.4)                        
 xml2            1.3.2   2020-04-23 [1] CRAN (R 4.0.4)                        
 xtable          1.8-4   2019-04-21 [1] CRAN (R 4.0.4)                        
 zip             2.1.1   2020-08-27 [1] CRAN (R 4.0.4)                        

[1] C:/Users/hgans/OneDrive/Documents/R/win-library/4.0
[2] C:/Program Files/R/R-4.0.4/library

Additional context
Add any other context about the problem here.

Unable to Connect RStudio to Google Sheets

From Module 5, I opened Module05.Rmd in RStudio and tried to run line 49 to 50 like Andrew said:

if (!require("pacman")) install.packages("pacman") # if pacman is not installed, the install it.
pacman::p_load(effectsize, ggpubr, ggstatsplot, googlesheets4, janitor, jtools, knitr, parameters, rio, remotes, report, rstatix, tidyverse,  see, sjPlot, sjmisc) # load/install required packages

# Load your data ----------
df <- read_sheet("https://docs.google.com/spreadsheets/d/1fFVmBFpdAKxzLMT8dx7pZm48mo9CE3kIwYhrkaZj7NM", sheet = "1")  

The first time, it opened google sheets and I was able to connect my RStudio to my Gmail account. DF was supposed to appear in my environment but it did not. I tried to re-run lines 49-50 but just get the error seen in the image below.

I'm not sure how to proceed now.