Update function descriptions and examples

R/df_rmtrend_x3p.R

@@ -1,22 +1,18 @@
 #' Removing missing values and the quadratic trend from inner polygon
 #'
 #' Obtained x3p object after removing missing values and the quadratic trend from the inner polygon.
-#' @param insidepoly_df data frame of inside polygon
+#' @param insidepoly_df data frame of inside polygon obtained from \code{wire::x3p_insidepoly_df}
 #' @return x3p object of residuals after removing trend
 #' @import dplyr
 #' @importFrom x3ptools df_to_x3p
 #' @importFrom stats lm predict
 #' @export
 #' @examples
 #' x3p <- x3p_subsamples[[1]]
-#' mask_col <- "#FF0000"
-#' concavity <- 1.5
-#'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = "#FF0000", concavity = 1.5, b = 1)
 #'
 #' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
 #' x3p_inner_nomiss_res
-#'
 #' if (interactive()) {
 #'   x3p_image_autosize(x3p_inner_nomiss_res)
 #' }

R/vec_align_sigs_list.R

@@ -15,14 +15,11 @@
 #' @export
 #' @examples
 #' x3p <- x3p_subsamples[[1]]
-#' mask_col <- "#FF0000"
-#' concavity <- 1.5
-#'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = "#FF0000", concavity = 1.5, b = 1)
 #' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
 #' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, ifsave = FALSE, dir_name = NULL, ifplot = TRUE)
-#'
 #' 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),
 #' ifplot = TRUE)
 #'

R/x3p_MLE_angle_vec.R

@@ -15,16 +15,12 @@
 #' @export
 #' @examples
 #' x3p <- x3p_subsamples[[1]]
-#' mask_col <- "#FF0000"
-#' concavity <- 1.5
-#'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = "#FF0000", concavity = 1.5, b = 1)
 #' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
 #' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, ifsave = FALSE, dir_name = NULL, ifplot = TRUE)
 #'
 #' x3p_MLE_angle_vec(x3p_inner_impute, min_score_cut = 0.1, ifplot = TRUE)
 #'
-#'
 x3p_MLE_angle_vec <- function(x3p, ntheta = 720, min_score_cut = 0.1,
                                      ifplot = FALSE,
                                      loess_span = 0.2) {

R/x3p_impute.R

@@ -18,15 +18,11 @@
 #' @export
 #' @examples
 #' x3p <- x3p_subsamples[[1]]
-#' mask_col <- "#FF0000"
-#' concavity <- 1.5
-#'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = "#FF0000", concavity = 1.5, b = 1)
 #' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
 #'
 #' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, ifsave = FALSE, dir_name = NULL, ifplot = TRUE)
 #' x3p_inner_impute
-#'
 #' if (interactive()) {
 #'   x3p_image_autosize(x3p_inner_impute)
 #' }

R/x3p_insidepoly_df.R

@@ -6,6 +6,14 @@
 #' @param concavity strictly positive value used in \code{concaveman::concaveman}
 #' @param b positive integer value, block size, used in \code{x3ptools::x3p_average}
 #' @return data frame of inside polygon
+#' \itemize{
+#'  \item{x}{x value from input x3p object}
+#'  \item{y}{y value from input x3p object}
+#'  \item{value}{height value from input x3p object}
+#'  \item{mask}{mask value from input x3p object}
+#'  \item{n_neighbor_val_miss}{number of missing immediate neighbor, self included}
+#'  \item{sd_not_miss}{standard deviation for immediate neighbor}
+#' }
 #' @import dplyr
 #' @importFrom x3ptools x3p_extract x3p_average x3p_to_df
 #' @importFrom tidyr pivot_longer
@@ -15,10 +23,8 @@
 #' @export
 #' @examples
 #' x3p <- x3p_subsamples[[1]]
-#' mask_col <- "#FF0000"
-#' concavity <- 1.5
 #'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = "#FF0000", concavity = 1.5, b = 1)
 #' str(insidepoly_df)
 #'
 x3p_insidepoly_df <- function(x3p, mask_col = "#FF0000", concavity = 1.5, b = 10) {

R/x3p_quantile_angle_vec.R

@@ -14,16 +14,12 @@
 #' @export
 #' @examples
 #' x3p <- x3p_subsamples[[1]]
-#' mask_col <- "#FF0000"
-#' concavity <- 1.5
-#'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = "#FF0000", concavity = 1.5, b = 1)
 #' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
 #' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, ifsave = FALSE, dir_name = NULL, ifplot = TRUE)
 #'
 #' x3p_quantile_angle_vec(x3p_inner_impute, min_score_cut = 0.1, ifplot = TRUE)
 #'
-#'
 x3p_quantile_angle_vec <- function(x3p, ntheta = 720, min_score_cut = 0.1,
                                           ifplot = FALSE) {
   theta <-

R/x3p_raw_sig_vec.R

@@ -11,15 +11,12 @@
 #' @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, b = 1)
+#' x3p <- x3p_subsamples[[2]]
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = "#FF0000", concavity = 1.5, b = 1)
 #' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
 #' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, ifsave = FALSE, dir_name = NULL, ifplot = TRUE)
-#'
 #' x3p_bin_rotate <- x3p_vertical(x3p_inner_impute, min_score_cut = 0.1)
+#'
 #' x3p_raw_sig_vec(x3p_bin_rotate, ifplot = TRUE) %>%
 #' str()
 #'

R/x3p_shift_sig_vec.R

@@ -14,15 +14,13 @@
 #' @importFrom tidyr nest unnest
 #' @export
 #' @examples
-#' x3p <- x3p_subsamples[[1]]
-#' mask_col <- "#FF0000"
-#' concavity <- 1.5
+#' x3p <- x3p_subsamples[[2]]
 #'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = "#FF0000", concavity = 1.5, b = 1)
 #' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
 #' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, ifsave = FALSE, dir_name = NULL, ifplot = TRUE)
-#'
 #' x3p_bin_rotate <- x3p_vertical(x3p_inner_impute, min_score_cut = 0.1)
+#'
 #' if (interactive()) {
 #'   x3p_shift_sig_vec(x3p_bin_rotate, ifplot = TRUE) %>%
 #'   str()

R/x3p_surface_polygon.R

@@ -22,6 +22,7 @@
 #'   x3p <- x3p %>% x3p_surface_polygon(sample=1)
 #'   x3p_image(x3p, size = dim(x3p$surface.matrix), zoom=.6)
 #' }
+#'
 x3p_surface_polygon <- function(x3p, colour = "red", sample = 10, center = NULL, concavity = 1.5) {
   stopifnot("x3p" %in% class(x3p), is.numeric(concavity), concavity > 0)
 

R/x3p_vertical.R

@@ -14,16 +14,13 @@
 #' @export
 #' @examples
 #' x3p <- x3p_subsamples[[1]]
-#' mask_col <- "#FF0000"
-#' concavity <- 1.5
 #'
-#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = mask_col, concavity = concavity, b = 1)
+#' insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = "#FF0000", concavity = 1.5, b = 1)
 #' x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
 #' x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, ifsave = FALSE, dir_name = NULL, ifplot = TRUE)
 #'
 #' x3p_bin_rotate <- x3p_vertical(x3p_inner_impute, min_score_cut = 0.1, ifplot = TRUE)
 #' x3p_bin_rotate
-#'
 #' if (interactive()) {
 #'   x3p_image_autosize(x3p_bin_rotate)
 #' }