minor adjustments to code style, adressed R CMD Check error and notes

.Rbuildignore

@@ -16,3 +16,4 @@
 ^cran-comments\.md$
 ^README\.md$
 ^NEWS\.md$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -53,7 +53,6 @@ BugReports: https://github.com/the-Hull/TREX/issues
 Encoding: UTF-8
 Depends: R (>= 3.5.0)
 Imports: 
-    chron,
     zoo,
     solaR,
     stats,
@@ -67,14 +66,12 @@ Imports:
     tibble,
     dplyr,
     sensitivity,
-    randtoolbox,
-    boot,
     doSNOW,
     msm,
     parallel,
     magrittr,
     tools
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.1
 Suggests: 
     shiny,
     plotly,

R/is.trex.R

@@ -280,13 +280,9 @@ is.trex <-
 
     #p
     if (length(unique(timestamp)) == length(unique(left(timestamp,16)))) {
-      #  output.data <-
-      #  zoo::zoo(data$value, order.by = base::as.POSIXct(format(chron::as.chron(timestamp), "%Y-%m-%d %H:%M"),tz="UTC"))
       output.data <-
         zoo::zoo(data$value, order.by = base::as.POSIXct(paste0(left(timestamp,16),":00"),tz="UTC"))
      } else{
-       #output.data <-
-       #  zoo::zoo(data$value, order.by = base::as.POSIXct(format(as.character(timestamp), "%Y-%m-%d %H:%M"),tz="UTC"))
        agg <-
         stats::aggregate(output.data, by = base::as.POSIXct(paste0(left(timestamp,16),":00"),tz="UTC"), mean)
       output.data <- zoo::zoo(agg, order.by = base::as.POSIXct(zoo::index(agg),tz="UTC"))

R/package-TREX.R

@@ -7,6 +7,4 @@
 #' generating uniform data output and visualisation. The package is designed to deal with large quantities of data and apply commonly
 #' used data-processing methods. The functions have been validated on data collected from different tree species across the northern hemisphere
 #' (Peters et al. 2018 <doi: 10.1111/nph.15241>).
-#' @docType package
-#' @name TREX
-NULL
+"_PACKAGE"

R/tdm_damp.R

@@ -248,7 +248,7 @@ tdm_damp <- function(input,
         ),
         control = list(maxiter = 500)
       ), silent = TRUE)
-      if (class(report) != "try-error") {
+      if (!inherits(report, "try-error")) {
         model_nls <-
           stats::nls(
             k.doy ~ ((a + b * run) / (1 + c * run + d * (run ^ 2))),
@@ -274,7 +274,7 @@ tdm_damp <- function(input,
               ),
               control = list(maxiter = 500)
             ), silent = TRUE)
-          if (class(report) == "try-error") {
+          if (inherits(report, "try-error")) {
             next
           } else{
             model_nls <-
@@ -653,7 +653,7 @@ tdm_damp <- function(input,
       ),
       control = list(maxiter = 500)
     ), silent = TRUE)
-    if (class(report) != "try-error") {
+    if (!inherits(report, "try-error")) {
       model_nls <-
         stats::nls(
           k.doy ~ ((a + b * run) / (1 + c * run + d * (run ^ 2))),
@@ -679,7 +679,7 @@ tdm_damp <- function(input,
             ),
             control = list(maxiter = 500)
           ), silent = TRUE)
-        if (class(report) == "try-error") {
+        if (inherits(report, "try-error")) {
           next
         } else{
           model_nls <-