fix dplyr::filter stats::filter conflicts;

replace %>% with |>
ianjonsen · Oct 17, 2023 · b3baf49 · b3baf49
1 parent e8523b6
commit b3baf49
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Showing 21 changed files with 161 additions and 180 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: aniMotum
 Title: Fit Continuous-Time State-Space and Latent Variable Models for Quality Control of Argos Satellite (and Other) Telemetry Data and for Estimating Changes in Animal Movement
-Version: 1.1-01.9061
+Version: 1.1-01.9075
 Date: 2023-09-18
 Authors@R: 
     c(

diff --git a/NAMESPACE b/NAMESPACE
@@ -32,14 +32,12 @@ importFrom(TMB,MakeADFun)
 importFrom(TMB,newtonOption)
 importFrom(TMB,oneStepPredict)
 importFrom(TMB,sdreport)
-importFrom(dplyr,"%>%")
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,count)
 importFrom(dplyr,distinct)
 importFrom(dplyr,everything)
-importFrom(dplyr,filter)
 importFrom(dplyr,first)
 importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)

diff --git a/R/aniMotum-package.R b/R/aniMotum-package.R
@@ -23,8 +23,8 @@
 ##' 
 ##' @keywords aniMotum
 ##' @importFrom utils data flush.console globalVariables
-##' @importFrom dplyr %>% select mutate slice group_by
-##' @importFrom dplyr distinct arrange filter left_join lag full_join bind_cols
+##' @importFrom dplyr select mutate slice group_by
+##' @importFrom dplyr distinct arrange left_join lag full_join bind_cols
 ##' @importFrom dplyr summarise
 ##' @importFrom tibble as_tibble tibble
 ##' @importFrom sf st_as_sf st_set_crs st_transform st_is_longlat st_crs

diff --git a/R/fmap.R b/R/fmap.R
@@ -37,18 +37,6 @@
 ##' @param rev reverse colour palette (logical)
 ##' @param last_loc colour to render last location of each track (default = NULL)
 ##' @param ... additional arguments passed to [ggspatial::annotation_map_tile]
-##' @importFrom ggplot2 ggplot geom_sf aes aes_string ggtitle xlim ylim unit 
-##' @importFrom ggplot2 element_text theme  scale_fill_gradientn scale_fill_manual 
-##' @importFrom ggplot2 element_blank scale_colour_manual scale_colour_gradientn
-##' @importFrom ggplot2 element_line coord_sf
-##' @importFrom sf st_bbox st_transform st_crop st_as_sf st_as_sfc st_buffer 
-##' @importFrom sf st_crs st_coordinates st_cast st_multipolygon st_polygon st_union
-##' @importFrom sf st_make_valid
-##' @importFrom utils data
-##' @importFrom grDevices extendrange grey
-##' @importFrom dplyr group_by summarise
-##' @importFrom grDevices hcl.colors
-##' @importFrom rnaturalearth ne_countries
 ##' @export
 
 fmap <- function(x,

diff --git a/R/grab.R b/R/grab.R
@@ -28,7 +28,7 @@
 ##' @return a `tibble` with all individual `tibble`'s appended
 ##'
 ##' @importFrom sf st_crs st_coordinates st_transform st_geometry st_as_sf st_set_crs
-##' @importFrom dplyr group_by mutate ungroup "%>%" bind_rows
+##' @importFrom dplyr group_by mutate ungroup bind_rows
 ##' @importFrom tibble as_tibble
 ##'
 ##' @examples
@@ -119,26 +119,26 @@ grab <- function(x, what = "fitted", as_sf = FALSE, normalise = FALSE, group = F
                  }
 
                  out <- lapply(1:length(out_lst), function(i) {
-                   st_as_sf(out_lst[[i]], coords = c("lon", "lat")) %>%
-                     st_set_crs("+proj=longlat +datum=WGS84 +no_defs") %>%
+                   st_as_sf(out_lst[[i]], coords = c("lon", "lat")) |>
+                     st_set_crs("+proj=longlat +datum=WGS84 +no_defs") |>
                      st_transform(prj[[pos]])
                  })
                  out <- bind_rows(out)
 
                } else if (any(test)) {
                  out <- lapply(1:length(out_lst), function(i) {
                    if(nrow(out_lst[[i]]) >= 1){
-                    st_as_sf(out_lst[[i]], coords = c("lon", "lat")) %>%
-                      st_set_crs("+proj=longlat +datum=WGS84 +no_defs") %>%
+                    st_as_sf(out_lst[[i]], coords = c("lon", "lat")) |>
+                      st_set_crs("+proj=longlat +datum=WGS84 +no_defs") |>
                        st_transform(prj[[1]])
                    }
                  })
                  out <- bind_rows(out)
 
                }
              } else if (nrow(x) == 1) {
-               out <- st_as_sf(out_lst[[1]], coords = c("lon", "lat")) %>%
-                 st_set_crs("+proj=longlat +datum=WGS84 +no_defs") %>%
+               out <- st_as_sf(out_lst[[1]], coords = c("lon", "lat")) |>
+                 st_set_crs("+proj=longlat +datum=WGS84 +no_defs") |>
                  st_transform(prj[[1]])
              }
 
@@ -162,12 +162,12 @@ grab <- function(x, what = "fitted", as_sf = FALSE, normalise = FALSE, group = F
                    out <- out[, c("id", "date", "x.se", "y.se", "logit_g", "logit_g.se",
                            "g", "geometry")]
                    if(normalise & !group) {
-                     out <- out %>% 
-                       group_by(id) %>%
-                       mutate(g = (g - min(g))/(max(g) - min(g))) %>%
+                     out <- out |> 
+                       group_by(id) |>
+                       mutate(g = (g - min(g))/(max(g) - min(g))) |>
                        ungroup()
                      } else if(normalise & group) {
-                     out <- out %>% 
+                     out <- out |> 
                        mutate(g = (g - min(g))/(max(g) - min(g)))
                    }
                    out
@@ -178,12 +178,12 @@ grab <- function(x, what = "fitted", as_sf = FALSE, normalise = FALSE, group = F
                  out <- out[, c("id", "date", "x.se", "y.se", "logit_g",
                                 "logit_g.se", "g", "geometry")]
                  if(normalise & !group) {
-                   out <- out %>% 
-                     group_by(id) %>%
-                     mutate(g = (g - min(g))/(max(g) - min(g))) %>%
+                   out <- out |> 
+                     group_by(id) |>
+                     mutate(g = (g - min(g))/(max(g) - min(g))) |>
                      ungroup()
                  } else if(normalise & group) {
-                   out <- out %>% 
+                   out <- out |> 
                      mutate(g = (g - min(g))/(max(g) - min(g)))
                  }
                } else {
@@ -215,12 +215,12 @@ grab <- function(x, what = "fitted", as_sf = FALSE, normalise = FALSE, group = F
                     out <- out[, c("id", "date", "lon", "lat", "x", "y", 
                             "x.se", "y.se", "logit_g", "logit_g.se", "g")]
                     if(normalise & !group) {
-                      out <- out %>% 
-                        group_by(id) %>%
-                        mutate(g = (g - min(g))/(max(g) - min(g))) %>%
+                      out <- out |> 
+                        group_by(id) |>
+                        mutate(g = (g - min(g))/(max(g) - min(g))) |>
                         ungroup()
                     } else if(normalise & group) {
-                      out <- out %>% 
+                      out <- out |> 
                         mutate(g = (g - min(g))/(max(g) - min(g)))
                     }
                     out
@@ -233,12 +233,12 @@ grab <- function(x, what = "fitted", as_sf = FALSE, normalise = FALSE, group = F
                 out <- out[, c("id", "date", "lon", "lat", "x", "y", "x.se", "y.se", "logit_g",
                                "logit_g.se", "g")]
                 if(normalise & !group) {
-                  out <- out %>% 
-                    group_by(id) %>%
-                    mutate(g = (g - min(g))/(max(g) - min(g))) %>%
+                  out <- out |> 
+                    group_by(id) |>
+                    mutate(g = (g - min(g))/(max(g) - min(g))) |>
                     ungroup()
                 } else if(normalise & group) {
-                  out <- out %>% 
+                  out <- out |> 
                     mutate(g = (g - min(g))/(max(g) - min(g)))
                 }
                } else {
@@ -275,12 +275,12 @@ grab <- function(x, what = "fitted", as_sf = FALSE, normalise = FALSE, group = F
            out <- bind_rows(out)
            out <- as_tibble(out)
            if(normalise & !group) {
-             out <- out %>% 
-               group_by(id) %>%
-               mutate(g = (g - min(g))/(max(g) - min(g))) %>%
+             out <- out |> 
+               group_by(id) |>
+               mutate(g = (g - min(g))/(max(g) - min(g))) |>
                ungroup()
            } else if(normalise & group) {
-             out <- out %>% 
+             out <- out |> 
                mutate(g = (g - min(g))/(max(g) - min(g)))
            }
            out

diff --git a/R/map.R b/R/map.R
@@ -149,7 +149,7 @@ map <- function(x,
       conf <- lapply(1:nrow(x), function(j)
         with(x, elps(x[j], y[j], x.se[j], y.se[j], 90)))
       lapply(conf, function(x)
-        st_polygon(list(x))) %>%
+        st_polygon(list(x))) |>
         st_multipolygon()
     })
 

diff --git a/R/map_multi_track_base.R b/R/map_multi_track_base.R
@@ -23,11 +23,10 @@
 ##' @importFrom ggplot2 ggplot geom_sf aes ggtitle xlim ylim unit 
 ##' @importFrom ggplot2 element_text theme scale_fill_gradientn scale_fill_manual 
 ##' @importFrom ggplot2 element_blank scale_colour_manual scale_colour_gradientn
-##' @importFrom ggplot2 element_rect coord_sf 
+##' @importFrom ggplot2 element_rect coord_sf element_line 
 ##' @importFrom rnaturalearth ne_countries
 ##' @importFrom sf st_union st_convex_hull st_intersection st_collection_extract 
 ##' @importFrom sf st_sf st_crs st_make_valid st_geometry
-##' @importFrom dplyr "%>%"
 ##' 
 ##' @keywords internal
 map_multi_track_base <- function(map_type, 
@@ -58,21 +57,21 @@ map_multi_track_base <- function(map_type,
 
   if (by.date) {
     lab_dates <-
-      with(loc_sf, pretty(seq(min(date), max(date), l = 10), n = 5)) %>% as.Date()
+      with(loc_sf, pretty(seq(min(date), max(date), l = 10), n = 5)) |> as.Date()
   }
 
   prj <- st_crs(loc_sf)
 
   ## get worldmap
   if (map_type == "default") {
     if (requireNamespace("rnaturalearthhires", quietly = TRUE)) {
-      wm <- ne_countries(scale = 10, returnclass = "sf") %>%
-        st_transform(crs = prj) %>%
+      wm <- ne_countries(scale = 10, returnclass = "sf") |>
+        st_transform(crs = prj) |>
         st_make_valid()
       if(!silent) cat("using map scale: 10\n")
     } else {
-      wm <- ne_countries(scale = 50, returnclass = "sf") %>%
-        st_transform(crs = prj) %>%
+      wm <- ne_countries(scale = 50, returnclass = "sf") |>
+        st_transform(crs = prj) |>
         st_make_valid()
       if(!silent) cat("using map scale: 50\n")
     }
@@ -81,12 +80,12 @@ map_multi_track_base <- function(map_type,
     if(!is.null(obs_sf)) pts <- obs_sf
     else pts <- loc_sf
 
-    land <- st_buffer(pts, dist = buffer) %>% 
-      st_union() %>% 
-      st_convex_hull() %>% 
-      st_intersection(wm) %>% 
-      st_collection_extract('POLYGON') %>% 
-      st_sf() %>%
+    land <- st_buffer(pts, dist = buffer) |> 
+      st_union() |> 
+      st_convex_hull() |> 
+      st_intersection(wm) |> 
+      st_collection_extract('POLYGON') |> 
+      st_sf() |>
       st_make_valid()
 
     p <- ggplot() + 

diff --git a/R/map_multi_track_mp.R b/R/map_multi_track_mp.R
@@ -21,11 +21,10 @@
 ##' @importFrom ggplot2 ggplot geom_sf aes ggtitle xlim ylim unit 
 ##' @importFrom ggplot2 element_text theme scale_fill_gradientn scale_fill_manual 
 ##' @importFrom ggplot2 element_blank scale_colour_manual scale_colour_gradientn
-##' @importFrom ggplot2 element_rect coord_sf
+##' @importFrom ggplot2 element_rect coord_sf element_line
 ##' @importFrom rnaturalearth ne_countries
 ##' @importFrom sf st_union st_convex_hull st_intersection st_collection_extract 
 ##' @importFrom sf st_sf st_crs st_make_valid
-##' @importFrom dplyr "%>%" filter
 ##' 
 ##' @keywords internal
 map_multi_track_mp <- function(map_type, 
@@ -53,26 +52,26 @@ map_multi_track_mp <- function(map_type,
   ## get worldmap
   if (map_type == "default") {
     if (requireNamespace("rnaturalearthhires", quietly = TRUE)) {
-      wm <- ne_countries(scale = 10, returnclass = "sf") %>%
-        st_transform(crs = prj) %>%
+      wm <- ne_countries(scale = 10, returnclass = "sf") |>
+        st_transform(crs = prj) |>
         st_make_valid()
       if(!silent) cat("using map scale: 10\n")
     } else {
-      wm <- ne_countries(scale = 50, returnclass = "sf") %>%
-        st_transform(crs = prj) %>%
+      wm <- ne_countries(scale = 50, returnclass = "sf") |>
+        st_transform(crs = prj) |>
         st_make_valid()
       if(!silent) cat("using map scale: 50\n")
     }
 
     ## define map region & clip land polygons
     if(!is.null(obs_sf)) pts <- obs_sf
     else pts <- loc_sf
-    land <- st_buffer(pts, dist = buffer) %>% 
-                               st_union() %>% 
-                               st_convex_hull() %>% 
-                               st_intersection(wm) %>% 
-                               st_collection_extract('POLYGON') %>% 
-                               st_sf() %>%
+    land <- st_buffer(pts, dist = buffer) |> 
+                               st_union() |> 
+                               st_convex_hull() |> 
+                               st_intersection(wm) |> 
+                               st_collection_extract('POLYGON') |> 
+                               st_sf() |>
       st_make_valid()
 
     p <- ggplot() + 
@@ -132,14 +131,14 @@ map_multi_track_mp <- function(map_type,
   if (all(aes$est, aes$mp)) {
     p <- p +
       geom_sf(
-        data = loc_sf %>% filter(g > 0.5),
+        data = loc_sf |> dplyr::filter(g > 0.5),
         aes(colour = g),
         size = aes$df$size[1],
         stroke = 0.1,
         shape = aes$df$shape[1]
       ) +
       geom_sf(
-        data = loc_sf %>% filter(g <= 0.5),
+        data = loc_sf |> dplyr::filter(g <= 0.5),
         aes(colour = g),
         size = aes$df$size[1],
         stroke = 0.1,

diff --git a/R/map_single_track_base.R b/R/map_single_track_base.R
@@ -22,11 +22,10 @@
 ##' @importFrom ggplot2 ggplot geom_sf aes ggtitle xlim ylim unit 
 ##' @importFrom ggplot2 element_text theme scale_fill_gradientn scale_fill_manual 
 ##' @importFrom ggplot2 element_blank scale_colour_manual scale_colour_gradientn
-##' @importFrom ggplot2 element_rect coord_sf
+##' @importFrom ggplot2 element_rect coord_sf element_line
 ##' @importFrom rnaturalearth ne_countries
 ##' @importFrom sf st_union st_convex_hull st_intersection st_collection_extract 
 ##' @importFrom sf st_sf st_crs st_make_valid
-##' @importFrom dplyr "%>%"
 ##' 
 ##' @keywords internal
 map_single_track_base <- function(map_type, 
@@ -49,34 +48,34 @@ map_single_track_base <- function(map_type,
 
   if (by.date) {
     lab_dates <-
-      with(loc_sf, pretty(seq(min(date), max(date), l = 10), n = 5)) %>% as.Date()
+      with(loc_sf, pretty(seq(min(date), max(date), l = 10), n = 5)) |> as.Date()
   }
 
   prj <- st_crs(loc_sf)
 
   ## get worldmap
   if (map_type == "default") {
     if (requireNamespace("rnaturalearthhires", quietly = TRUE)) {
-      wm <- ne_countries(scale = 10, returnclass = "sf") %>%
-        st_transform(crs = prj) %>%
+      wm <- ne_countries(scale = 10, returnclass = "sf") |>
+        st_transform(crs = prj) |>
         st_make_valid()
       if(!silent) cat("using map scale: 10\n")
     } else {
-      wm <- ne_countries(scale = 50, returnclass = "sf") %>%
-        st_transform(crs = prj) %>%
+      wm <- ne_countries(scale = 50, returnclass = "sf") |>
+        st_transform(crs = prj) |>
         st_make_valid()
       if(!silent) cat("using map scale 50\n")
     }
 
     ## define map region & clip land polygons
     if(!is.null(obs_sf)) pts <- obs_sf
     else pts <- loc_sf
-    land <- suppressWarnings(st_buffer(pts, dist = buffer) %>% 
-                               st_union() %>% 
-                               st_convex_hull() %>% 
-                               st_intersection(wm) %>% 
-                               st_collection_extract('POLYGON') %>% 
-                               st_sf() %>%
+    land <- suppressWarnings(st_buffer(pts, dist = buffer) |> 
+                               st_union() |> 
+                               st_convex_hull() |> 
+                               st_intersection(wm) |> 
+                               st_collection_extract('POLYGON') |> 
+                               st_sf() |>
       st_make_valid())
 
     p <- ggplot() +