Merge pull request #212 from januarharianto/master

sync dev
januarharianto · Mar 29, 2024 · 9fbe6ca · 9fbe6ca
2 parents f29b884 + 3f47f34
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -3,7 +3,6 @@
 ^\.Rproj\.user$     # used for temporary files.
 ^README\.Rmd$       # An Rmarkdown file used to generate README.md
 ^cran-comments\.md$ # Comments for CRAN submission
-^NEWS\.md$          # A news file written in Markdown
 ^manuscript$        # Folder that contains the files for the manuscript
 ^docs$              # Folder that stores HTML vignettes
 ^doc$               # Folder that stores HTML vignettes
@@ -13,6 +12,7 @@
 ^data-raw$
 ^.DS_Store$
 ^t5.rda$
+cran-comments.md
 
 # Insurance
 vignettes
@@ -24,3 +24,4 @@ vignettes
 Changelog
 ^CITATION\.cff$
 ^codecov\.yml$
+^CRAN-SUBMISSION$
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -0,0 +1,3 @@
+Version: 2.3.2
+Date: 2023-11-16 15:53:23 UTC
+SHA: 2cdfcb90c240c379300bf0f55abbb8df2b6a2e5d
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: respR
 Type: Package
 Title: Import, Process, Analyse, and Calculate Rates from Respirometry Data
-Date: 2023-06-04
-Version: 2.3.1
+Date: 2023-11-16
+Version: 2.3.2
 Maintainer: Nicholas Carey <nicholascarey@gmail.com>
 Authors@R: c(
     person(given = "Nicholas", 
@@ -37,7 +37,6 @@ Imports:
     magrittr,
     marelac,
     purrr,
-    readxl,
     roll,
     segmented,
     stats,

diff --git a/NAMESPACE b/NAMESPACE
@@ -117,7 +117,6 @@ importFrom(parallel,makeCluster)
 importFrom(parallel,parLapply)
 importFrom(parallel,stopCluster)
 importFrom(purrr,reduce)
-importFrom(readxl,read_excel)
 importFrom(roll,roll_lm)
 importFrom(stats,quantile)
 importFrom(stringr,str_replace)

diff --git a/NEWS.md b/NEWS.md
@@ -1,17 +1,8 @@
 
-<!---
-Each version should:
-List its release date in the above format.
-Group changes to describe their impact on the project, as follows:
-Added:        for new features.
-Changed:      for changes in existing functionality.
-Deprecated:   for once-stable features removed in upcoming releases.
-Removed:      for deprecated features removed in this release.
-Fixed:        for any bug fixes.
-Security:     to invite users to upgrade in case of vulnerabilities. 
-
-All version changes go in here now when you make a commit! 
---->
+## Version 2.3.2 -- 2023-11-15
+
+Minor changes to unit tests and documentation. 
+
 
 ## Version 2.3.1 -- 2023-06-05
 

diff --git a/R/auto_rate_funs.R b/R/auto_rate_funs.R
@@ -2,7 +2,7 @@
 #'
 #' This is an internal function for `auto_rate()`. Used to validate inputs
 #'
-#' @param df data.frame object.
+#' @param x data.frame object.
 #' @param by string.
 #' @param method string.
 #'
@@ -424,26 +424,26 @@ static_roll <- function(df, win) {
 #' @return a data.table object
 #' @keywords internal
 #' @import parallel
-time_roll <- function(dt, width, parallel = FALSE) {
+time_roll <- function(df, width, parallel = FALSE) {
   future_lapply <- plan <- NULL # global variables hack (unfortunate)
-  dt <- data.table::data.table(dt)
-  data.table::setnames(dt, 1:2, c("V1", "V2"))
+  df <- data.table::data.table(df)
+  data.table::setnames(df, 1:2, c("V1", "V2"))
 
   # The cutoff specifies where to stop the rolling regression, based on width
-  time_cutoff <- max(dt[,1]) - width
-  row_cutoff <- max(dt[, which(V1 <= time_cutoff)])
+  time_cutoff <- max(df[,1]) - width
+  row_cutoff <- max(df[, which(V1 <= time_cutoff)])
 
   # if(parallel) {
   #   oplan <- plan()
   #   on.exit(plan(oplan), add = TRUE)
   #   if (os() == 'win') {
   #     plan(multicore)
   #   } else plan(multisession)
-  #   out <- future_lapply(1:row_cutoff, function(x) time_lm(dt,
-  #     dt[[1]][x], dt[[1]][x] + width))
+  #   out <- future_lapply(1:row_cutoff, function(x) time_lm(df,
+  #     df[[1]][x], df[[1]][x] + width))
   # } else {
-  #   out <- lapply(1:row_cutoff, function(x) time_lm(dt,
-  #     dt[[1]][x], dt[[1]][x] + width))
+  #   out <- lapply(1:row_cutoff, function(x) time_lm(df,
+  #     df[[1]][x], df[[1]][x] + width))
   # }
 
   # parallelisation
@@ -453,11 +453,11 @@ time_roll <- function(dt, width, parallel = FALSE) {
       cl <- parallel::makeCluster(no_cores)
     } else cl <- parallel::makeCluster(no_cores, type = "FORK")
     parallel::clusterExport(cl, "time_lm")
-    out <- parallel::parLapply(cl, 1:row_cutoff, function(x) time_lm(dt,
-                                                                     dt[[1]][x], dt[[1]][x] + width))
+    out <- parallel::parLapply(cl, 1:row_cutoff, function(x) time_lm(df,
+                                                                     df[[1]][x], df[[1]][x] + width))
     parallel::stopCluster(cl)  # stop cluster (release cores)
-  } else out <- lapply(1:row_cutoff, function(x) time_lm(dt,
-                                                         dt[[1]][x], dt[[1]][x] + width))
+  } else out <- lapply(1:row_cutoff, function(x) time_lm(df,
+                                                         df[[1]][x], df[[1]][x] + width))
 
   out <- data.table::rbindlist(out)
   return(out)

diff --git a/R/import_file.R b/R/import_file.R
@@ -76,7 +76,6 @@
 #'   directory, as determined by the `path` parameter.
 #'
 #' @importFrom data.table data.table fread
-#' @importFrom readxl read_excel
 #' @importFrom xml2 xml_text
 #' @importFrom xml2 read_html
 #' @importFrom tools file_path_sans_ext

diff --git a/R/inspect.R b/R/inspect.R
@@ -191,6 +191,7 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' ## By default, assumes time is col 1 and oxygen col2:
 #' inspect(sardine.rd)
 #'
@@ -222,6 +223,7 @@
 #' ## allow better y-axis label visibility
 #' inspect(sardine.rd, time = 1, oxygen = 2,
 #'         las = 1, mai = c(0.3, 0.35, 0.35, 0.15))
+#' }
 
 inspect <- function(x, time = NULL, oxygen = NULL,
                     width = 0.1, plot = TRUE, add.data = NULL, ...) {

diff --git a/R/startup.R b/R/startup.R
@@ -19,10 +19,6 @@ Visit this site for help documentation and vignettes:
 
     http://bit.ly/respr_pkg
 
-And follow respR on Twitter for latest news:
-
-    http://twitter.com/respr_pkg
-
 ======================================================================")
 
     packageStartupMessage(start_msg)

diff --git a/README.md b/README.md
@@ -15,7 +15,6 @@
 [![Github watchers](https://img.shields.io/github/watchers/januarharianto/respR?label=Watch&style=social)](https://img.shields.io/github/watchers/januarharianto/respR?style=social)
 [![Github sponsor](https://img.shields.io/static/v1?label=Sponsor&message=%E2%9D%A4&logo=GitHub&style=social)](https://github.com/sponsors/nicholascarey)
 [![Mastodon](https://img.shields.io/badge/dynamic/json?label=Mastodon&query=totalItems&url=https%3A%2F%2Fmas.to%2Fusers%2FrespR%2Ffollowers.json&logo=mastodon&style=social)](https://mas.to/@respR)
-[![Twitter](https://img.shields.io/twitter/follow/respR_pkg.svg?label=Follow&style=social)](https://twitter.com/respR_pkg?ref_src=twsrc%5Etfw)
 
 <!-- badges: end -->
 
@@ -44,6 +43,12 @@ A highlight of the package is the `auto_rate()` function. This uses machine lear
 install.packages("respR")
 ```
 
+You can also install the latest version direct from [**Github**](https://github.com/januarharianto/respr/):
+
+```r
+devtools::install_github("januarharianto/respR")
+```
+
 ## Getting started
 
 Visit the `respR` [**website**](https://januarharianto.github.io/respR/) to get started. The site has a range of vignettes detailing the functionality, plus example workflows, documentation, and more. 
@@ -56,7 +61,7 @@ We are also happy to help directly. If you have problems using the package or ge
 
 The package has also been [**peer reviewed and published**](https://doi.org/10.1111/2041-210X.13162) in *Methods in Ecology and Evolution*. Please cite this publication if you use `respR` in your published work. 
 
-`respR` has been used to examine metabolic rates and photosynthesis in corals, plankton, micro- and macro-algae, fish, crustaceans, echinoderms, cephalopods, bivalves and more, in both lab and field studies. Check the [**respR in use**](https://januarharianto.github.io/respR/articles/citations.html) page to see a list of published studies which have used the package to analyse their data.
+`respR` has been used to examine metabolic rates and photosynthesis in corals, plankton, micro- and macro-algae, fish, crustaceans, echinoderms, cephalopods, bivalves and more, in both lab and field studies. Check the [**respR Citations**](https://januarharianto.github.io/respR/articles/citations.html) page to see a list of published studies which have used the package to analyse their data.
 
  \
  \
@@ -66,11 +71,11 @@ The package has also been [**peer reviewed and published**](https://doi.org/10.1
 
 See [**here**](https://januarharianto.github.io/respR/articles/contact.html) for more ways of providing feedback and getting in touch if you are having issues.
 
-For the latest news and regular updates from the world of respirometry follow `respR` on **<a rel="me" href="https://mas.to/@respR">Mastodon</a>** or [**Twitter**](https://twitter.com/respR_pkg). 
+For the latest news and regular updates from the world of respirometry follow `respR` on **<a rel="me" href="https://mas.to/@respR">Mastodon</a>**. 
 
 ## Support package development
 
-If you would like to help support the package development or just buy us a beer to say thanks see [here](https://januarharianto.github.io/respR/articles/contact.html#support-future-development) 
+If you would like to help support the package development or just buy us a beer to say thanks see [**here**](https://januarharianto.github.io/respR/articles/contact.html#support-future-development) 
 
 ## Developers
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -140,7 +140,7 @@ navbar:
         href: articles/contact.html
       - text: "Release Notes"
         href: articles/release_notes.html
-      - text: "respR in Use"
+      - text: "respR Citations"
         href: articles/citations.html
       - text: "Future Features"
         href: articles/future.html

diff --git a/cran-comments.md b/cran-comments.md
@@ -0,0 +1 @@
+No code changes, so should be no issues. Literally the only change is slight alteration to a value in one unit test. This is done in response to a package author contacting me because a pending update was rejected by CRAN due to this test failing in my package, which is a reverse dependency.
diff --git a/man/inspect.Rd b/man/inspect.Rd
diff --git a/man/time_roll.Rd b/man/time_roll.Rd
diff --git a/man/validate_auto_rate.Rd b/man/validate_auto_rate.Rd
diff --git a/pkgdown/pkgdown_script.R b/pkgdown/pkgdown_script.R
@@ -15,17 +15,20 @@ pkgdown::build_site(lazy = TRUE, devel = TRUE, preview = TRUE)
 # ? not sure what this does
 #pkgdown::preview_site(pkg = ".", path = ".", preview = NA)
 
+# builds top page
 pkgdown::build_home(preview = TRUE)
 
+# build a single article
 pkgdown::build_article("closed")
 
 pkgdown::build_article("flowthrough")
 pkgdown::preview_page('articles/flowthrough.html')
 
+# add a new vignetter
 usethis::use_vignette("intermittent_old", "Intermittent-flow respirometry: Alternative approaches")
 
 
-# sets up GH Actions workflow. Which isn't working.
+# sets up GH Actions workflow. Needs tested.
 #usethis::use_pkgdown_github_pages()
 
 
@@ -35,4 +38,7 @@ usethis::use_vignette("intermittent_old", "Intermittent-flow respirometry: Alter
 ## Sometimes gets stuck on git command.
 ## Stopping and building site then trying again seems to work.
 ## Although last time took MANY attempts
+##
+## BUT - even if it seems to freeze - check GHub and site - it might have successfully
+## triggered the 'pages build and deployment' GH action anyway...
 pkgdown::deploy_to_branch()
diff --git a/tests/testthat/test-oxy_crit.R b/tests/testthat/test-oxy_crit.R
@@ -149,8 +149,8 @@ capture.output({  ## stops printing of outputs on assigning
                  2.6003)
     expect_equal(round(oxy_crit(squid, plot=F)$crit$crit.midpoint, 4),
                  2.5944)
-    expect_equal(round(oxy_crit(squid, method = "segmented", plot=F)$crit, 4),
-                 2.6003)
+    expect_equal(round(oxy_crit(squid, method = "segmented", plot=F)$crit, 2),
+                 2.60)
   })
 
   test_that("oxy_crit - works with oxygen~rate data", {