General cleanup of deprecated function calls

[serbinsh]

5: `qplot()` was deprecated in ggplot2 3.4.0.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated. 
6: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated. 
7: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

> lifecycle::last_lifecycle_warnings()
[[1]]
<warning/lifecycle_warning_deprecated>
Warning:
`qplot()` was deprecated in ggplot2 3.4.0.
---
Backtrace:
    ▆
 1. ├─base::source("~/Library/CloudStorage/OneDrive-NASA/Data/Github/spectratrait/inst/scripts/spectra-trait_neon_leafN_canopy_plsr_example.R")
 2. │ ├─base::withVisible(eval(ei, envir))
 3. │ └─base::eval(ei, envir)
 4. │   └─base::eval(ei, envir)
 5. └─ggplot2::qplot(...) at inst/scripts/spectra-trait_neon_leafN_canopy_plsr_example.R:160:1
 6.   └─ggplot2:::deprecate_soft0("3.4.0", "qplot()")

[[2]]
<warning/lifecycle_warning_deprecated>
Warning:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
---
Backtrace:
    ▆
 1. ├─base::source("~/Library/CloudStorage/OneDrive-NASA/Data/Github/spectratrait/inst/scripts/spectra-trait_neon_leafN_canopy_plsr_example.R")
 2. │ ├─base::withVisible(eval(ei, envir))
 3. │ └─base::eval(ei, envir)
 4. │   └─base::eval(ei, envir)
 5. └─ggplot2::geom_abline(...) at inst/scripts/spectra-trait_neon_leafN_canopy_plsr_example.R:289:1
 6.   └─ggplot2::layer(...)
 7.     └─ggplot2:::deprecate_soft0(...)

[[3]]
<warning/lifecycle_warning_deprecated>
Warning:
The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
---
Backtrace:
    ▆
 1. ├─base::source("~/Library/CloudStorage/OneDrive-NASA/Data/Github/spectratrait/inst/scripts/spectra-trait_neon_leafN_canopy_plsr_example.R")
 2. │ ├─base::withVisible(eval(ei, envir))
 3. │ └─base::eval(ei, envir)
 4. │   └─base::eval(ei, envir)
 5. ├─ggplot2::theme(...) at inst/scripts/spectra-trait_neon_leafN_canopy_plsr_example.R:289:1
 6. │ └─ggplot2:::find_args(..., complete = NULL, validate = NULL)
 7. │   └─base::mget(args, envir = env)
 8. └─ggplot2::element_rect(linetype = "solid", fill = NA, size = 1.5)
 9.   └─ggplot2:::deprecate_soft0("3.4.0", "element_rect(size)", "element_rect(linewidth)")