html tweaks for notes for cran submission

SimonDedman · Oct 1, 2024 · a53c0d3 · a53c0d3
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 2023.08.31
-Date: 2023-09-01 16:02:09 UTC
-SHA: ee6217a76f6ace8b250108daca5ed2ddc3cb59a1
+Version: 2024.09.30
+Date: 2024-09-30 12:53:29 UTC
+SHA: f4d8d073d55c1706ca542b9f5ec4593304ff9bbc
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: gbm.auto
 Title: Automated Boosted Regression Tree Modelling and Mapping Suite
-Version: 2024.09.30
+Version: 2024.10.01
 Authors@R: person("Simon", "Dedman", , "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9108-972X"))
 Description: Automates delta log-normal boosted regression tree abundance
     prediction. Loops through parameters provided (LR (learning rate), TC

diff --git a/NEWS.md b/NEWS.md
@@ -1,10 +1,10 @@
 ---
 title: "NEWS.md"
 author: "Simon Dedman"
-date: "2024-09-30"
+date: "2024-10-01"
 output: html_document
 ---
-# v2024.09.30
+# v2024.10.01
 * shapefiles and other rgdal dependencies removed, CRAn push
 
 # v2023.08.31

diff --git a/R/gbm.auto.R b/R/gbm.auto.R
@@ -183,7 +183,7 @@
 #'
 #' I strongly recommend that you download papers 1 to 5 (or just the doctoral thesis) on
 #' <http://www.simondedman.com>, with emphasis on P4 (the guide) and P1 (statistical background).
-#' Elith et al 2008 (<http://refhub.elsevier.com/S0304-3800(15)00207-0/sbref0085>) is also strongly
+#' Elith et al 2008 (<https://besjournals.onlinelibrary.wiley.com/doi/10.1111/j.1365-2656.2008.01390.x>) is also strongly
 #' recommended.
 #' Just because you CAN try every conceivable combination of tc, lr, bf, all, at once doesn't mean
 #' you should. Try a range of lr in shrinking orders of magnitude from 0.1 to 0.000001, find the

diff --git a/README.Rmd b/README.Rmd
@@ -26,7 +26,7 @@ Automatically runs numerous processes from R packages 'gbm' and 'dismo' and scri
 
 Also see each script's Details section in the manual pages, as these frequently contain tips or common bugfixes.
 
-I strongly recommend that you download papers 1 to 5 (or just the doctoral thesis) on <http://www.simondedman.com>, with emphasis on P4 (the guide) and P1 (statistical background). Elith et al 2008 (<https://www.doi.org/10.1111/j.1365-2656.2008.01390.x>) is also strongly recommended. Also it's imperative you read the R help files for each function before you use them. In RStudio: Packages tab, scroll to gbm.auto, click its name, the click the function to see its man (manual) page. Read the whole thing. Function man pages can also be accessed from the console by typing
+I strongly recommend that you download papers 1 to 5 (or just the doctoral thesis) on <http://www.simondedman.com>, with emphasis on P4 (the guide) and P1 (statistical background). Elith et al 2008 (<https://besjournals.onlinelibrary.wiley.com/doi/10.1111/j.1365-2656.2008.01390.x>) is also strongly recommended. Also it's imperative you read the R help files for each function before you use them. In RStudio: Packages tab, scroll to gbm.auto, click its name, the click the function to see its man (manual) page. Read the whole thing. Function man pages can also be accessed from the console by typing
 
 ``` r
 ?function

diff --git a/README.md b/README.md
@@ -24,12 +24,12 @@ frequently contain tips or common bugfixes.
 I strongly recommend that you download papers 1 to 5 (or just the
 doctoral thesis) on <http://www.simondedman.com>, with emphasis on P4
 (the guide) and P1 (statistical background). Elith et al 2008
-(<https://www.doi.org/10.1111/j.1365-2656.2008.01390.x>) is also
-strongly recommended. Also it’s imperative you read the R help files for
-each function before you use them. In RStudio: Packages tab, scroll to
-gbm.auto, click its name, the click the function to see its man (manual)
-page. Read the whole thing. Function man pages can also be accessed from
-the console by typing
+(<https://besjournals.onlinelibrary.wiley.com/doi/10.1111/j.1365-2656.2008.01390.x>)
+is also strongly recommended. Also it’s imperative you read the R help
+files for each function before you use them. In RStudio: Packages tab,
+scroll to gbm.auto, click its name, the click the function to see its
+man (manual) page. Read the whole thing. Function man pages can also be
+accessed from the console by typing
 
 ``` r
 ?function

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,7 +1,7 @@
 ---
 title: "cran-comments"
 author: "Simon Dedman"
-date: "30 September 2024"
+date: "01 October 2024"
 output: html_document
 ---
 

diff --git a/man/gbm.auto.Rd b/man/gbm.auto.Rd