Adding first draft of paper.md for JOSS

.Rproj.user/429CC01A/pcs/files-pane.pper

@@ -5,5 +5,5 @@
             "ascending": false
         }
     ],
-    "path": "C:/Users/hanecakr/Documents/R_github/fellingdateR"
+    "path": "C:/Users/hanecakr/Documents/R_github/fellingdateR/inst/paper"
 }

.Rproj.user/429CC01A/pcs/windowlayoutstate.pper

@@ -1,14 +1,14 @@
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.Rproj.user/429CC01A/rmd-outputs

@@ -1,7 +1,3 @@
-C:/Users/hanecakr/AppData/Local/Temp/Rtmpyi37iu/preview-a0c20363b9.html
-C:/Users/hanecakr/AppData/Local/Temp/Rtmpyi37iu/preview-234824286f5b.html
-C:/Users/hanecakr/AppData/Local/Temp/Rtmpkvmuwl/preview-2ec83a8f2a35.html
-C:/Users/hanecakr/AppData/Local/Temp/Rtmpkvmuwl/preview-4d3452916d08.html
 
 
 

DESCRIPTION

@@ -1,7 +1,6 @@
 Package: fellingdateR
-Title: `fellingdateR` is an R package that aims to facilitate the organisation, 
-  analysis and interpretation of tree-ring data from wooden heritage objects 
-  and structures
+Title: Estimate, report and combine felling dates from historical tree-ring 
+    series
 Version: 0.0.0.9003
 Authors@R: c(
     person("Kristof", "Haneca", , "[email protected]",role = c("aut", "cre"),
@@ -12,8 +11,12 @@ Authors@R: c(
         comment = c(ORCID = "0000-0001-6966-1729"))    
     )
 Description: `fellingdateR` is an R package that aims to facilitate the 
-  organization, analysis and interpretation of tree-ring data from wooden 
-  cultural heritage objects and structures.
+  analysis and interpretation of tree-ring data from wooden 
+  cultural heritage objects and structures. The package aims to facilitate and
+  standardize the reporting, interpretation and combination of felling date
+  estimates.
+URL: https://github.com/hanecakr/fellingdateR
+BugReports: https://github.com/hanecakr/fellingdateR/issues
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

R/cor_table.R

@@ -78,6 +78,14 @@
 #'   - t_St: Student's t-value
 #'   - t_BP: t-values according to the Baillie & Pilcher (1973) algorithm
 #'   - t_Ho: t-values according to the Hollstein (1980) algorithm
+#' @examples
+#' # example code
+#'
+#' Doel1 <- system.file("extdata", "DOEL1.fh", package = "fellingdateR")
+#' Doel1_trs <- read_fh(Doel1, verbose = FALSE)
+#' # crossdating ring-width series from Doel 1 against each other:
+#'
+#' cor_results <- cor_table(Doel1_trs, output = "table", min_overlap = 80)
 #'
 cor_table <-
      function(x,

R/get_header.R

@@ -9,6 +9,10 @@
 #'   `rwl`.
 #'
 #' @return A `data.frame` with 29 header fields.
+#' @examples
+#' Doel1 <- system.file("extdata", "DOEL1.fh", package = "fellingdateR")
+#' Doel1_trs <- read_fh(Doel1, verbose = FALSE)
+#' get_header(Doel1_trs)
 #'
 #' @export
 

R/movAv.R

@@ -23,6 +23,10 @@
 #'
 #' @return A `numeric` vector of the same length of `x` with the computed
 #'   running mean values.
+#' @examples
+#' num_vec <- rnorm(100)
+#' movAv(num_vec, w = 20)
+#'
 #' @export
 
 movAv <- function(x,

R/sw_combine_plot.R

@@ -8,6 +8,10 @@
 
 #' @return A ggplot-style graph.
 #' @export
+#' @examples
+#' fellingdateR:::dummy2
+#' combo <- sw_combine(fellingdateR:::dummy2)
+#' sw_combine_plot(combo)
 #'
 #'
 sw_combine_plot <- function(x) {

R/sw_interval.R

@@ -28,6 +28,23 @@
 #'   * If `TRUE`, a ggplot-style graph is returned of the individual
 #'   sapwood model and estimate of the felling date range.
 #'   * If `FALSE`, a list with the numeric output of the modelling process is returned.
+#' @examples
+#' # 10 sapwood rings observed and the Wazny 1990 sapwood model:
+#' sw_interval(n_sapwood = 10,
+#'             last = 1234,
+#'             hdi = TRUE,
+#'             credMass = .95,
+#'             sw_data = "Wazny_1990",
+#'             densfun = "lognormal",
+#'             plot = FALSE)
+#'  # same example as above, but with numerical output (hdi = FALSE):
+#' sw_interval(n_sapwood = 10,
+#'             last = 1234,
+#'             hdi = FALSE,
+#'             credMass = .95,
+#'             sw_data = "Wazny_1990",
+#'             densfun = "lognormal",
+#'             plot = FALSE)
 #'
 #' @export
 #'

R/sw_interval_plot.R

@@ -6,6 +6,16 @@
 #' @param x Output of [sw_interval()].
 #'
 #' @return  A ggplot-style graph.
+#' @examples
+#' tmp <- sw_interval(n_sapwood = 10,
+#'             last = 1000,
+#'             hdi = FALSE,
+#'             credMass = .95,
+#'             sw_data = "Hollstein_1980",
+#'             densfun = "lognormal",
+#'             plot = FALSE)
+#' sw_interval_plot(tmp)
+#'
 #' @export
 #'
 sw_interval_plot <- function(x) {

R/sw_model.R

@@ -27,6 +27,10 @@
 #'   process is returned.
 #'
 #' @export
+#' @examples
+#' sw_model("Sohar_2012_ELL_c")
+#'
+#' sw_model("Hollstein_1980")
 #'
 sw_model <-
         function(sw_data = "Hollstein_1980",

R/sw_sum_plot.r

@@ -7,7 +7,9 @@
 #' @param x The output of `sw_sum()`.
 #' @param bar_col The fill color for the bars.
 #' @param spline_col The line color of the fitted smoothing spline.
-#' @param dot_col The color of the dots that represent exact felling dates.
+#' @param dot_col The color of the shapes that represent exact felling dates.
+#' @param dot_size A size argument for the shapes that represent exact felling dates.
+#' @param dot_shape Number corresponding to the point symbol available in R for the shapes that represent exact felling dates.
 #'
 #' @return A ggplot style graph.
 #' @export
@@ -21,7 +23,9 @@
 sw_sum_plot <- function(x,
                         bar_col = "steelblue",
                         spline_col = "red3",
-                        dot_col = "steelblue4") {
+                        dot_col = "steelblue4",
+                        dot_size = 2,
+                        dot_shape = 21) {
 
         # to avoid notes in CMD check
         spline <- SPD_wk <- year <- y <- SPD <- SPD_movAv <- NULL
@@ -75,8 +79,10 @@ p <-
                            na.rm = T) +
         { if (nrow(fd) > 0) ggplot2::geom_point(data = fd,
                             ggplot2::aes(x = year, y = SPD + y * p_max/20),
-                            size = 2,
-                            colour = dot_col,
+                            size = dot_size,
+                            fill = dot_col,
+                            color = dot_col,
+                            shape = dot_shape,
                             na.rm = T) } +
         ggplot2::scale_x_continuous(
                 limits = c(plyr::round_any(plot_range[1], 10, floor),