Fortunately,

This could read "your needs, other options...".

Not necessary

referred

directory,

There should be a comma after this word.

The "its" after linux should be it's, but neither "its" is necessary.

Section 2.2 that the ...

; (?)

This sentence doesn't make sense.

Name is singular here, so this should be "it".

It's still I think general practice not to start a sentence with a conjunction.

expected, and then (?)

and then (?)

"and then"?

This should be "run and then".

Not necessary

, and

Fortunately,

and then (?)

treatment, and then

Not necessary

This should be something like "Second, we add treatment ...".

This should be something like "First, we plot treatment 1 data".

At some point,

To do this,

Maybe "details, but rather"?

I don't think this comma is necessary.

Ideally,

Next,

Not necessary

In such cases,

Not necessary

This link gives a "Page not Found."

originally called?

Not necessary

all-important

Should this be non-base?

This phrase should take a comma.

This comma isn't necessary.

I think this should be than

Missing period

For now,

loaded, and

I think there should be "and then" here since then isn't a conjunction.

There should be a comma after macOS and maybe one after Similarly.

Maybe this should be "character, and hence".

that the file

directory, and then

There should be a comma after this phrase and possibly between "macOS" and "when".

This isn't parallel. It could instead say "checks..., loads..., and continues...".

"RStudio, it" ?

I'm not sure this comma is necessary.

This could possibly take a comma?

console, and

This sentence doesn't quite make sense. Perhaps you want "Be careful as R is case sensitive."?

Missing comma.

Maybe this should read "appears and then"?

Should there be a comma after the parentheses?

A comma after this word makes the sentence clearer.

This should be "arguments, and you'll".

; ?

A comma after this word makes the sentence clearer.

I think this phrase could use a comma after it.

These two adjectives are similar enough that there should be a comma between them.

There should be a comma after this word.

Another missing URL

This should read "and then".

There should be a comma after this word.

This isn't joining two sentences, so it isn't necessary.

There's a missing comma after these parenthesis.

A comma between these two adjectives would help split them up.

A prepositional phrase at the start of a sentence usually takes a comma, but if they're short it isn't necessary. This one is probably borderline.

This comma isn't necessary.

I'm not sure, but maybe it should read "a data recording error"?

A comma makes sense here.

Comma?

I'm not sure what purpose these words serve here.

No comma is needed here.

There could be a comma after this word.

This comma should be moved to before "and"

These commas can be removed since the "and" only joins two things.

Technically, this comma doesn't need to be here, but it could be useful to set off the two parts of the sentence.

There should be a comma after the parenthesis to end the phrase of book titles.

This phrase often takes commas, but it seems to be up to the author.

"And" can be removed here. If it is, the comma after "analyst's time" should be removed as well.

This seem like it would fit better between professionals and assume.

These aren't really sentences as they lack a subject.

This sentence doesn't make grammatical sense.