Fix update-related issues

[anashen]

Hello! Here is an overview of the changes proposed in this pull request:

Changes proposed

1) Replace use of the deprecated function fct_explicit_na.

Why: Updating R results in an deprecated function error where fct_explicit_na is used, as documented in #19.

Fix: Replace fct_explicit_na with fct_na_value_to_level.

2) Replace use of the deprecated function aes_string.

Why: aes_string was deprecated in a recent version of ggplot.

Fix: Use the .data pronoun in the aes function where the aesthetics are specified in ggplot commands in the plot and legend functions.

3) Fix problems with use of external vectors in selecting functions.

Why: Using an external vector in selections was deprecated in a recent version of tidyselect.

Fix: Use all_of where vectors are used in theselect function; replace input in the group_by_at function with a character vector of column names.

4) Update package dependencies in vignettes.

Why: Packages forcats and tidyverse are required to be loaded in order for the Global Patterns Data and Human Microbiome Project 1 & 2 vignettes to run.

Fix: Add the necessary package load commands in the vignettes that require them.

---

Additionally: add a param comment to document recently added as_relative_abundance parameter in the prep_mdf function.

Checks

• Vignettes result in the same output with no changes.
• No new warnings or errors have been generated.

Thank you!

Best,
Anagha

[lakarstens]

Reviewed, thanks @anashen!