Add examples and fix errors from .data

R/df_rmtrend_x3p.R

@@ -6,14 +6,27 @@
 #' @import dplyr
 #' @importFrom x3ptools df_to_x3p
 #' @importFrom stats lm predict
-#' @importFrom rlang .data
 #' @export
-
+#' @examples
+#' x3p <- x3p_subsamples[[1]]
+#' mask_col <- "#FF0000"
+#' concavity <- 1.5
+#'
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#'
+#' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
+#' x3p_inner_nomiss_res
+#'
+#' if (interactive()) {
+#'   x3p_image_autosize(x3p_inner_nomiss_res)
+#' }
+#'
 df_rmtrend_x3p <- function(insidepoly_df) {
   n_neighbor_val_miss <-
     value <-
     x <-
     y <-
+    . <-
     NULL
 
   x3p_inner_nomiss_df <- insidepoly_df %>%
@@ -22,11 +35,11 @@ df_rmtrend_x3p <- function(insidepoly_df) {
   ### Remove trend
   x3p_inner_nomiss_lm <- lm(value ~ x + y + I(x^2) + I(y^2) + x:y, data = x3p_inner_nomiss_df)
   x3p_inner_nomiss_res_df <- x3p_inner_nomiss_df %>%
-    mutate(value = value - predict(x3p_inner_nomiss_lm, select(.data, x, y)))
+    mutate(value = value - predict(x3p_inner_nomiss_lm, select(., x, y)))
 
   ### Convert df to x3p
   x3p_inner_nomiss_res <- x3p_inner_nomiss_res_df %>%
-    left_join(insidepoly_df[, c("x", "y")], .data) %>%
+    left_join(insidepoly_df[, c("x", "y")], ., by = join_by(x, y)) %>%
     df_to_x3p()
 
   return(x3p_inner_nomiss_res)

R/vec_align_sigs_list.R

@@ -13,7 +13,19 @@
 #' @importFrom ggplot2 ggplot aes geom_line labs xlab ggtitle
 #' @importFrom bulletxtrctr sig_align
 #' @export
-
+#' @examples
+#' x3p <- x3p_subsamples[[1]]
+#' mask_col <- "#FF0000"
+#' concavity <- 1.5
+#'
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
+#' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, x3p, mask_col = mask_col,
+#' concavity = concavity, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
+#'
+#' x3p_bin_rotate <- x3p_vertical(x3p_inner_impute, min_score_cut = 0.1)
+#' vec_align_sigs_list(x3p_raw_sig_vec(x3p_bin_rotate), x3p_shift_sig_vec(x3p_bin_rotate))
+#'
 vec_align_sigs_list <- function(
     sig1,
     sig2,

R/x3p_MLE_angle_vec.R

@@ -12,25 +12,37 @@
 #' @importFrom raster raster
 #' @importFrom imager as.cimg hough_line nfline
 #' @importFrom stats loess predict
-#' @importFrom rlang .data
 #' @export
-
-x3p_MLE_angle_vec <- function(x3p, ntheta = 720, min_score_cut = 2,
+#' @examples
+#' x3p <- x3p_subsamples[[1]]
+#' mask_col <- "#FF0000"
+#' concavity <- 1.5
+#'
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
+#' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, x3p, mask_col = mask_col,
+#' concavity = concavity, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
+#'
+#' x3p_MLE_angle_vec(x3p_inner_impute, min_score_cut = 0.1)
+#'
+#'
+x3p_MLE_angle_vec <- function(x3p, ntheta = 720, min_score_cut = 0.1,
                                      ifplot = FALSE,
                                      loess_span = 0.2) {
   theta <-
     score <-
     theta_mod <-
     theta_mod_shift <-
     rho <-
+    . <-
     NULL
 
   ### Change to contrast color
   x3p_shift <- x3p$surface.matrix
   NA_val <- -(x3p$surface.matrix %>%
     c() %>%
     summary() %>%
-    .data[c("Min.", "Max.")] %>%
+    .[c("Min.", "Max.")] %>%
     abs() %>%
     max() %>%
     ceiling())

R/x3p_image_autosize.R

@@ -10,7 +10,12 @@
 #' @importFrom rgl rglwidget
 #' @importFrom htmltools tagList
 #' @export
-
+#' @examples
+#' x3p <- x3p_subsamples[[1]]
+#' if (interactive()) {
+#'   x3p_image_autosize(x3p)
+#' }
+#'
 x3p_image_autosize <- function(x3p, ifhtml = FALSE, zoom = 0.6, ...) {
   x3p_image(x3p, size = dim(x3p$surface.matrix), zoom = zoom, ...)
 

R/x3p_impute.R

@@ -2,6 +2,7 @@
 #'
 #' Obtained x3p object after imputing the inner polygon.
 #' @param x3p x3p object
+#' @param x3p_mask x3p object for mask
 #' @param mask_col colour for the polygon
 #' @param concavity strictly positive value used in \code{concaveman::concaveman}
 #' @param ifsave whether the imputation procedure gif is going to be saved
@@ -17,15 +18,30 @@
 #' @importFrom magick image_read image_join image_animate image_write
 #' @importFrom stringr str_detect
 #' @importFrom wires x3p_surface_polygon
-#' @importFrom rlang .data
 #' @export
-
-x3p_impute <- function(x3p, mask_col = "#FF0000", concavity = 1.5,
-                                 ifsave = FALSE, dir_name = NULL, ifplot = FALSE) {
+#' @examples
+#' x3p <- x3p_subsamples[[1]]
+#' mask_col <- "#FF0000"
+#' concavity <- 1.5
+#'
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
+#'
+#' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, x3p, mask_col = mask_col,
+#' concavity = concavity, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
+#' x3p_inner_impute
+#'
+#' if (interactive()) {
+#'   x3p_image_autosize(x3p_inner_impute)
+#' }
+#'
+x3p_impute <- function(x3p, x3p_mask, mask_col = "#FF0000",
+                       concavity = 1.5, ifsave = FALSE, dir_name = NULL, ifplot = FALSE) {
   layer <-
     x <-
     y <-
     value <-
+    . <-
     NULL
 
   if (ifsave) {
@@ -139,21 +155,21 @@ x3p_impute <- function(x3p, mask_col = "#FF0000", concavity = 1.5,
       path = dir_name,
       full.names = TRUE
     ) %>%
-      .data[str_detect(.data, pattern = ".png")] %>%
+      .[str_detect(., pattern = ".png")] %>%
       file.remove() %>%
       invisible()
   }
 
-  x3p_inner_focal_impute <- x3p %>%
+  x3p_inner_focal_impute <- x3p_mask %>%
     x3p_delete_mask()
   x3p_inner_focal_impute$surface.matrix <- x3p_inner_nomiss_res_focal_raster %>%
     as.matrix() %>%
     t()
 
-  x3p <- x3p %>%
+  x3p_mask <- x3p_mask %>%
     x3p_surface_polygon(colour = mask_col, concavity = concavity)
   ### Extract inner part as x3p based on mask
-  x3p_inner <- x3p_extract(x3p, mask_vals = mask_col) %>%
+  x3p_inner <- x3p_extract(x3p_mask, mask_vals = mask_col) %>%
     x3p_average(m = 3, na.rm = TRUE)
   x3p_inner_focal_impute <- x3p_add_mask(x3p_inner_focal_impute, x3p_inner$mask)
 

R/x3p_insidepoly_df.R

@@ -11,16 +11,23 @@
 #' @importFrom stats sd
 #' @importFrom raster raster adjacent ncell
 #' @importFrom wires x3p_surface_polygon
-#' @importFrom rlang .data
 #' @export
-
+#' @examples
+#' x3p <- x3p_subsamples[[1]]
+#' mask_col <- "#FF0000"
+#' concavity <- 1.5
+#'
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' str(insidepoly_df)
+#'
 x3p_insidepoly_df <- function(x3p, mask_col = "#FF0000", concavity = 1.5) {
   to <-
     from <-
     neighbor_val <-
     x <-
     y <-
     n_neighbor_val_miss <-
+    . <-
     NULL
 
   x3p <- x3p %>%
@@ -89,10 +96,11 @@ x3p_insidepoly_df <- function(x3p, mask_col = "#FF0000", concavity = 1.5) {
           y = x3p_inner_df$y,
           x = as.character(x),
           y = as.character(y)
-        )
+        ),
+      by = join_by(x, y)
     ) %>%
     full_join(
-      .data,
+      x = .,
       x3p_inner_df_wide_sd_not_miss %>%
         pivot_longer(
           cols = everything(),
@@ -103,7 +111,8 @@ x3p_insidepoly_df <- function(x3p, mask_col = "#FF0000", concavity = 1.5) {
           y = x3p_inner_df$y,
           x = as.character(x),
           y = as.character(y)
-        )
+        ),
+      by = join_by(x, y)
     ) %>%
     mutate(
       x = as.numeric(x),

R/x3p_quantile_angle_vec.R

@@ -11,16 +11,28 @@
 #' @importFrom raster raster
 #' @importFrom imager as.cimg hough_line nfline
 #' @importFrom stats quantile median
-#' @importFrom rlang .data
 #' @export
-
-x3p_quantile_angle_vec <- function(x3p, ntheta = 720, min_score_cut = 2,
+#' @examples
+#' x3p <- x3p_subsamples[[1]]
+#' mask_col <- "#FF0000"
+#' concavity <- 1.5
+#'
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
+#' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, x3p, mask_col = mask_col,
+#' concavity = concavity, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
+#'
+#' x3p_quantile_angle_vec(x3p_inner_impute, min_score_cut = 0.1)
+#'
+#'
+x3p_quantile_angle_vec <- function(x3p, ntheta = 720, min_score_cut = 0.1,
                                           ifplot = FALSE) {
   theta <-
     theta_mod <-
     theta_mod_shift <-
     score <-
     rho <-
+    . <-
     NULL
 
   ### Change to contrast color
@@ -29,7 +41,7 @@ x3p_quantile_angle_vec <- function(x3p, ntheta = 720, min_score_cut = 2,
     -(x3p$surface.matrix %>%
       c() %>%
       summary() %>%
-      .data[c("Min.", "Max.")] %>%
+      .[c("Min.", "Max.")] %>%
       abs() %>%
       max() %>%
       ceiling())

R/x3p_raw_sig_vec.R

@@ -10,7 +10,20 @@
 #' @importFrom ggplot2 ggplot aes geom_line
 #' @importFrom stats na.omit median
 #' @export
-
+#' @examples
+#' x3p <- x3p_subsamples[[1]]
+#' mask_col <- "#FF0000"
+#' concavity <- 1.5
+#'
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
+#' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, x3p, mask_col = mask_col,
+#' concavity = concavity, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
+#'
+#' x3p_bin_rotate <- x3p_vertical(x3p_inner_impute, min_score_cut = 0.1)
+#' x3p_raw_sig_vec(x3p_bin_rotate) %>%
+#' str()
+#'
 x3p_raw_sig_vec <- function(x3p, method = "median", ifplot = FALSE) {
   x <-
     value <-
@@ -36,5 +49,5 @@ x3p_raw_sig_vec <- function(x3p, method = "median", ifplot = FALSE) {
       print()
   }
 
-  return(sig)
+  return(sig$value_summary)
 }

R/x3p_shift_sig_vec.R

@@ -13,7 +13,20 @@
 #' @importFrom purrr map_dbl map set_names
 #' @importFrom tidyr nest unnest
 #' @export
-
+#' @examples
+#' x3p <- x3p_subsamples[[1]]
+#' mask_col <- "#FF0000"
+#' concavity <- 1.5
+#'
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
+#' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, x3p, mask_col = mask_col,
+#' concavity = concavity, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
+#'
+#' x3p_bin_rotate <- x3p_vertical(x3p_inner_impute, min_score_cut = 0.1)
+#' x3p_shift_sig_vec(x3p_bin_rotate) %>%
+#' str()
+#'
 x3p_shift_sig_vec <- function(x3p, method = "median", ifplot = FALSE, delta = -5:5) {
   y <-
     value_nobs <-
@@ -38,7 +51,7 @@ x3p_shift_sig_vec <- function(x3p, method = "median", ifplot = FALSE, delta = -5
     arrange(value_nobs)
 
   ### Sort unique y values
-  y_sort <- inner_join(x3p_df, x3p_df_nobs) %>%
+  y_sort <- inner_join(x3p_df, x3p_df_nobs, by = join_by(y)) %>%
     ### Filter to have at least 2 observations for approx later
     filter(value_nobs >= 2) %>%
     distinct(y) %>%
@@ -119,7 +132,7 @@ x3p_shift_sig_vec <- function(x3p, method = "median", ifplot = FALSE, delta = -5
   )
 
   ### Shift x values
-  x3p_shift_delta_df <- inner_join(x3p_df, x_shift_delta_value_df, by = "y") %>%
+  x3p_shift_delta_df <- inner_join(x3p_df, x_shift_delta_value_df, by = join_by(y)) %>%
     mutate(x_shift_delta = x + x_shift_delta_value)
 
   if (ifplot) {
@@ -188,5 +201,5 @@ x3p_shift_sig_vec <- function(x3p, method = "median", ifplot = FALSE, delta = -5
       print()
   }
 
-  sig
+  return(sig$value_summary)
 }

R/x3p_vertical.R

@@ -12,10 +12,26 @@
 #' @import dplyr
 #' @importFrom x3ptools x3p_bin_stripes x3p_extract x3p_rotate
 #' @export
-
+#' @examples
+#' x3p <- x3p_subsamples[[1]]
+#' mask_col <- "#FF0000"
+#' concavity <- 1.5
+#'
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity)
+#' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
+#' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, x3p, mask_col = mask_col,
+#' concavity = concavity, ifsave = FALSE, dir_name = NULL, ifplot = FALSE)
+#'
+#' x3p_bin_rotate <- x3p_vertical(x3p_inner_impute, min_score_cut = 0.1)
+#' x3p_bin_rotate
+#'
+#' if (interactive()) {
+#'   x3p_image_autosize(x3p_bin_rotate)
+#' }
+#'
 x3p_vertical <- function(x3p_inner_impute, freqs = c(0, 0.3, 0.7, 1),
                                method = "MLE",
-                               ntheta = 720, min_score_cut = 2,
+                               ntheta = 720, min_score_cut = 0.1,
                                ifplot = FALSE,
                                loess_span = 0.2) {
   x3p_bin <- x3p_inner_impute %>%