version 2.2.2

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rshift
 Type: Package
 Title: Paleoecology Functions for Regime Shift Analysis
-Version: 2.2.1
+Version: 2.2.2
 Authors@R: c(person("Alex H.", "Room",
                     role = c("aut", "cre", "cph"),
                     email = "alex.room@btinternet.com",
@@ -26,14 +26,16 @@ Description: Contains a variety of functions, based around
 Suggests: R.rsp
 VignetteBuilder: R.rsp
 Depends: R (>= 3.5.0)
-Imports: grid, tibble, dplyr, ggplot2, magrittr
+Imports: grid, tibble, dplyr, ggplot2
 License: MIT + file LICENSE
 NeedsCompilation: yes
 SystemRequirements: rustc & cargo if building from source
+URL: https://github.com/alexhroom/rshift
+BugReports: https://github.com/alexhroom/rshift/issues
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.2.3
-Packaged: 2023-08-14 17:36:35 UTC; alexhroom
+Packaged: 2023-08-30 10:19:29 UTC; alexhroom
 Author: Alex H. Room [aut, cre, cph] (<https://orcid.org/0000-0002-5314-2331>),
   Felipe Franco-Gaviria [ctb, fnd]
     (<https://orcid.org/0000-0003-4799-1457>),
@@ -42,4 +44,4 @@ Author: Alex H. Room [aut, cre, cph] (<https://orcid.org/0000-0002-5314-2331>),
     for details)
 Maintainer: Alex H. Room <alex.room@btinternet.com>
 Repository: CRAN
-Date/Publication: 2023-08-14 17:50:03 UTC
+Date/Publication: 2023-08-30 11:00:02 UTC

MD5

@@ -1,12 +1,12 @@
-b90a1ae66293babacef20fae0057557d *DESCRIPTION
+eeec7bc37873672e41a636856d200fa2 *DESCRIPTION
 df7d9cd96e743cdd985e8c727837fdf5 *LICENSE
 58cfb950588ff039b7bb86a70a235000 *LICENSE.note
-d13fee9352d1e00feb481f2e21a0ab9b *NAMESPACE
-e09a7172f1b498a0da698de76328cb46 *R/Hellinger_trans.R
-c4e48f145c68172472d4fa6183b30c85 *R/Lanzante.R
-133444377d472e69515bad9649501502 *R/RSI_graph.R
+9dad121018268ed1b027459dc7e5487a *NAMESPACE
+f59aee1f94dcf89bc8c12b2d6c4ff3e3 *R/Hellinger_trans.R
+eb27c6b1fa046b979dd897204e2f6f65 *R/Lanzante.R
+7020f0650ce9c4c6acfa6bf8ab2b2a33 *R/RSI_graph.R
 2dc6590065002e3bd3444b69337b219f *R/Rodionov.R
-1b45e2187b57eee0a82131160ee5d68d *R/absolute_to_percentage.R
+675e958da4e6a53fcc1af58320ed5118 *R/absolute_to_percentage.R
 9ed50886ced6406c37686b653ed6fc3f *R/extendr-wrappers.R
 66679f1dd7f9a3573b6ccffae3d2c18e *R/lake_RSI.R
 ecd833a1a570fc42fcf9d5b20b64e6e0 *R/lake_data.R
@@ -17,8 +17,8 @@ cb47ea68431f5dcfac57048c92937eb0 *configure
 6a7e3276257e33d8dde031a6f1a59afb *data/lake_data.rda
 ca4f3bd6bcfbf429c370d179f45cfc8a *inst/AUTHORS
 fca5e95b47c836d5436fa4b20ca4ca49 *inst/CITATION
-dce3d4e0903a092592ce7daf32c86a71 *inst/doc/STARSmanual.ltx
-4e26cd6dfa1b14a33838772aef750411 *inst/doc/STARSmanual.pdf
+ea7073b5cdd538c754278b25660fff60 *inst/doc/STARSmanual.ltx
+10464d4cd7bac56cca23e30ea4a2558f *inst/doc/STARSmanual.pdf
 93846e9c326301daf7ba01a83d4f1b11 *man/Hellinger_trans.Rd
 e6fa2c42258f181728e1d14954dde761 *man/Lanzante.Rd
 9f6c50ce5fb118038d6d9548c4da3860 *man/RSI_graph.Rd
@@ -28,14 +28,14 @@ df3fc9b0cffee5e4a91f85c0113b4c9d *man/lake_RSI.Rd
 0fb1a9bc6c4996dd92da6a1187c0f89e *man/lake_data.Rd
 e68062d831de3b28748354107a305519 *man/rolling_autoc.Rd
 0495b94fa546a21eb2d338c98d8c3957 *man/rust_rodionov.Rd
-908b7cb68be1c4831b5c5a28ff2e1bed *src/Makevars
-58071ea003ee61404fc60a4c1b1d902f *src/Makevars.win
+f9b4d71515d099f022db176b5b636e2a *src/Makevars
+c0d6b9f9604ac277e8851d4d1ed72d62 *src/Makevars.win
 956a59f45ec296041fbbce2e46bb4105 *src/entrypoint.c
-3e7f4fed13e7fb8b5d2832e414f4d054 *src/rust/Cargo.toml
+9e3cb1bb6a2ff314e1e7ce0bb7ebea28 *src/rust/Cargo.toml
 d4c7febd30951f7fbd584476dbb2dd70 *src/rust/cargo_vendor_config.toml
 0e5139792fee79cb1cd93d115cd5cbe6 *src/rust/src/lib.rs
 667d4e574e3a8e6604b454ef3546faf0 *src/rust/vendor.sh
 5eb3ad1ac90541c210d22ff9cbef3136 *src/rust/vendor.tar.xz
 5422880bb8056e9761b2ae6d74bc83d5 *vignettes/RSI_graph.png
-dce3d4e0903a092592ce7daf32c86a71 *vignettes/STARSmanual.ltx
+ea7073b5cdd538c754278b25660fff60 *vignettes/STARSmanual.ltx
 30c4e8965319f7a6651d9d8d6f848658 *vignettes/bibliography.bib

NAMESPACE

@@ -10,9 +10,8 @@ import(dplyr)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,geom_col)
 importFrom(ggplot2,ggplot)
-importFrom(magrittr,"%>%")
 importFrom(stats,acf)
 importFrom(stats,pnorm)
 importFrom(stats,qt)
-importFrom(tibble,as.tibble)
+importFrom(tibble,as_tibble)
 useDynLib(rshift, .registration = TRUE)

R/Hellinger_trans.R

@@ -7,16 +7,13 @@
 #' @param site The column containing the site of each sample.
 #' @return The `data` dataframe with an added 'hellinger_trans_vals' column.
 #' @import dplyr
-#' @importFrom magrittr %>%
 #' @export
 Hellinger_trans <- function(data, col, site){
 
 
   #creates an empty table with the original table's columns, plus the hellinger values
   #i'm aware this is incredibly hacky, but i couldn't find a better way
-  results <- data %>%
-    cbind(hellinger_trans_vals = c(1:nrow(data))) %>%
-    filter(col == "bad programming")
+  results <- filter(cbind(data, hellinger_trans_vals = c(1:nrow(data))), col == "hack")
   #finds values for each site
   unique_sites <- unique(data[[site]])
   for(s in unique_sites){

R/Lanzante.R

@@ -12,9 +12,8 @@
 #' Lanzante(lake_data, "DCA1", "Age")
 #' Lanzante(lake_data, "DCA1", "Age", p=0.10, merge=TRUE)
 #' @import dplyr
-#' @importFrom magrittr %>%
 #' @importFrom stats pnorm
-#' @importFrom tibble as.tibble
+#' @importFrom tibble as_tibble
 #' @export 
 Lanzante <- function(data, col, time, p =0.05, merge = FALSE){
 
@@ -65,21 +64,18 @@ Lanzante <- function(data, col, time, p =0.05, merge = FALSE){
   #creates vectors for shift years and their corresponding p-values
     if(pnorm(z) <= p){
       p_vals <- c(p_vals, pnorm(z))
-      shift_at <- slice(db, n_1) %>%
-        select(all_of(time))
+      shift_at <- select(slice(db, n_1), all_of(time))
       shift_years <- c(shift_years, as.numeric(shift_at))
-      db <- db %>%
-        slice(-c(n_1))
+      db <- slice(db, -c(n_1))
     } else {
       break
     }
   }
 
   #creates results table
-  results <- as.tibble(cbind(shift_years, p_vals))
+  results <- as_tibble(cbind(shift_years, p_vals))
 
-  timename <- data %>%
-    select(all_of(time))
+  timename <- select(data, all_of(time))
   timename <- colnames(timename)
 
   names(results)[1] <- timename

R/RSI_graph.R

@@ -13,9 +13,6 @@
 #'
 #' @export
 RSI_graph <- function(data, col, time, rsi){
-
-
-  #while Rodionov() requires quotes, this doesn't work if you put quotes around col or time
   p1 <- ggplot(data) + geom_col(aes(x = .data[[time]], y = .data[[col]]))
   p2 <- ggplot(data) + geom_col(aes(x = .data[[time]], y = .data[[rsi]]))
   grid::pushViewport(grid::viewport(layout = grid::grid.layout(2, 1)))

R/absolute_to_percentage.R

@@ -5,15 +5,12 @@
 #' @param site The column containing the site of each sample.
 #' @return The `data` dataframe with an added 'percentage' column.
 #' @import dplyr
-#' @importFrom magrittr %>%
 #' @export 
 absolute_to_percentage <- function(data, col, site){
 
-  #creates an empty table with the original table's columns, plus the hellinger values
+  #creates an empty table with the original table's columns, plus the percentage values
   #i'm aware this is incredibly hacky, but i couldn't find a better way
-  results <- data %>%
-    cbind(percentage = c(1:nrow(data))) %>%
-    filter(col == "bad programming")
+  results <- filter(cbind(data, hellinger_trans_vals = c(1:nrow(data))), col == "hack")
   #finds values for each site
   unique_sites <- unique(data[[site]])
   for(s in unique_sites){

inst/doc/STARSmanual.ltx

@@ -7,7 +7,7 @@
 \usepackage{graphicx}
 \usepackage{caption}
 
-\title{\texttt{rshift} STARS manual - regime shift analysis for paleoecological data\\v2.2.1}
+\title{\texttt{rshift} STARS manual - regime shift analysis for paleoecological data\\v2.2.2}
 
 \author{A. H. Room, F. Franco-Gaviria, D. H. Urrego}
 

src/Makevars

@@ -2,17 +2,23 @@ LIBDIR = rust/target/release
 STATLIB = $(LIBDIR)/librshift.a
 PKG_CFLAGS = -pthread
 PKG_LIBS = -L$(LIBDIR) -lrshift -lresolv -pthread
+CARGOTMP=$(PWD)/.cargo
+export CARGO_HOME=$(CARGOTMP)
 
 #all: clean
 
 $(SHLIB): $(STATLIB)
 
 $(STATLIB):
 	$(TAR) --extract --xz -f ./rust/vendor.tar.xz -C . && \
-	mkdir -p ./.cargo && \
-	cp ./rust/cargo_vendor_config.toml ./.cargo/config.toml; \
+	mkdir -p $(CARGO_HOME) && \
+	cp ./rust/cargo_vendor_config.toml $(CARGO_HOME)/config.toml; \
+	# To comply with CRAN policy the versions of cargo and rustc
+	# need to be inlcuded in the installation log
+	echo `cargo --version` && echo `rustc --version`
 	PATH="${PATH}:${HOME}/.cargo/bin" cargo build -j 2 --release --offline --manifest-path=rust/Cargo.toml
 	rm -Rf $(LIBDIR)/build || true
+	rm -Rf $(CARGO_HOME) || true
 
 clean:
 	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS) rust/target

src/Makevars.win

@@ -10,9 +10,13 @@ $(SHLIB): $(STATLIB)
 $(STATLIB):
 	$(TAR) --extract --xz -f ./rust/vendor.tar.xz -C . && \
 	mkdir -p ./.cargo && \
-	cp ./rust/cargo_vendor_config.toml ./.cargo/config.toml; \
+	cp ./rust/cargo_vendor_config.toml ./.cargo/config.toml;
+	# To comply with CRAN policy the versions of cargo and rustc
+	# need to be inlcuded in the installation log
+	echo `cargo --version` && echo `rustc --version`
 	PATH="$(USERPROFILE)\.cargo\bin:$(PATH)" cargo build --target=$(TARGET) -j 2 --offline --release --manifest-path=rust/Cargo.toml
 	rm -Rf $(LIBDIR)/build || true
+	rm -Rf ./.cargo || true
 
 C_clean:
 	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS)

src/rust/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = 'rshift'
-version = '2.2.1'
+version = '2.2.2'
 edition = '2021'
 
 [lib]

vignettes/STARSmanual.ltx

@@ -7,7 +7,7 @@
 \usepackage{graphicx}
 \usepackage{caption}
 
-\title{\texttt{rshift} STARS manual - regime shift analysis for paleoecological data\\v2.2.1}
+\title{\texttt{rshift} STARS manual - regime shift analysis for paleoecological data\\v2.2.2}
 
 \author{A. H. Room, F. Franco-Gaviria, D. H. Urrego}