remove automatic conversion of 'waneyedge' to logical vector, from fd…

…_report, sw_combine and sw_sum
ropensci · Nov 12, 2023 · 5c1077c · 5c1077c
1 parent c1d6df8
commit 5c1077c
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diff --git a/.Rproj.user/429CC01A/pcs/files-pane.pper b/.Rproj.user/429CC01A/pcs/files-pane.pper
@@ -5,5 +5,5 @@
             "ascending": false
         }
     ],
-    "path": "C:/Users/hanecakr/Documents/R_github/fellingdateR/tests/testthat"
+    "path": "C:/Users/hanecakr/Documents/R_github/fellingdateR"
 }
diff --git a/.Rproj.user/429CC01A/pcs/source-pane.pper b/.Rproj.user/429CC01A/pcs/source-pane.pper
@@ -1,4 +1,4 @@
 {
-    "activeTab": 21,
+    "activeTab": 22,
     "activeTabSourceWindow0": 0
 }
diff --git a/.Rproj.user/429CC01A/pcs/windowlayoutstate.pper b/.Rproj.user/429CC01A/pcs/windowlayoutstate.pper
@@ -1,12 +1,12 @@
 {
     "left": {
-        "splitterpos": 349,
+        "splitterpos": 216,
         "topwindowstate": "NORMAL",
         "panelheight": 830,
         "windowheight": 868
     },
     "right": {
-        "splitterpos": 307,
+        "splitterpos": 306,
         "topwindowstate": "NORMAL",
         "panelheight": 830,
         "windowheight": 868

diff --git a/.Rproj.user/429CC01A/pcs/workbench-pane.pper b/.Rproj.user/429CC01A/pcs/workbench-pane.pper
@@ -1,5 +1,5 @@
 {
     "TabSet1": 4,
-    "TabSet2": 1,
+    "TabSet2": 0,
     "TabZoom": {}
 }
diff --git a/R/fd_report.R b/R/fd_report.R
@@ -122,15 +122,8 @@ fd_report <- function(x,
         }
         waneyedge <- df[[waneyedge]] # check is.logical
         if (!is.logical(waneyedge)) {
-                warning(
-                        "--> 'waneyedge' should be a logical vector (TRUE/FALSE),
-indicating the presence of waney edge.\n",
-"--> Converted to TRUE/FALSE based on presence of string 'wK'."
-                )
-                waneyedge <-
-                        ifelse(grepl("wk", waneyedge, ignore.case = TRUE),
-                               TRUE,
-                               FALSE)
+                stop("--> 'waneyedge' should be a logical vector (TRUE/FALSE),
+indicating the presence of waney edge.\n")
         }
         if (is.na(credMass) || credMass <= 0 || credMass >= 1)
                 stop("--> credMass must be between 0 and 1")
@@ -148,7 +141,7 @@ indicating the presence of waney edge.\n",
                 if (length(sw_OK) < length(sw_data)) {
                         stop(
                                 sprintf(
-                                        "'%s' is not a supported sapwood model, or file doesn't exist\n",
+                                        "'%s' is not a supported sapwood model, or file does not exist\n",
                                         sw_data[-sw_OK]
                                 )
                         )

diff --git a/R/sw_combine.R b/R/sw_combine.R
@@ -88,17 +88,9 @@ Some values are possibly missing or the values are not numeric"
 
         cambium <- x[, waneyedge]
         if (!is.logical(cambium)) {
-                warning(
-                        "--> Column 'waneyedge' should be logical (TRUE/FALSE), indicating
-the presence of waney edge.\n",
-"--> Converted to TRUE/FALSE based on presence of string 'wK'."
-                )
-                x[, waneyedge] <-
-                        ifelse(grepl("wk", x[, waneyedge], ignore.case = TRUE),
-                               TRUE,
-                               FALSE)
+                stop("--> 'waneyedge' should be logical vector (TRUE/FALSE), indicating
+the presence of waney edge.\n")
         }
-        cambium <- x[, waneyedge]
 
         timeAxis <- seq(min(endDate) - 3, max(endDate) + 100, by = 1)
 

diff --git a/R/sw_interval.R b/R/sw_interval.R
@@ -73,7 +73,7 @@ sw_interval <- function(n_sapwood = NA,
               file.exists(sw_data))) {
                 stop(
                         sprintf(
-                                "'%s' is not a supported sapwood model, or file doesn't exist\n",
+                                "'%s' is not a supported sapwood model, or file does not exist\n",
                                 sw_data
                         )
                 )

diff --git a/R/sw_sum.R b/R/sw_sum.R
@@ -56,32 +56,8 @@ sw_sum <- function (x,
 
         cambium <- df[[waneyedge]]
         if (!is.logical(cambium)) {
-                which_wk <- which(grepl("wk", cambium, ignore.case = TRUE))
-                converted_T <- cambium[which_wk]
-                converted_F <- cambium[-which_wk]
-                cambium <-
-                        ifelse(grepl("wk", cambium, ignore.case = TRUE),
-                               TRUE,
-                               FALSE)
-                warning(
-                        paste0(
-                                "Column 'waneyedge' in data.frame should be:\n",
-                                "a logical vector (TRUE/FALSE), indicating the presence of waney edge.\n"
-                        )
-                )
-                warning(
-                        sprintf(
-                                "'%s' --> Converted to TRUE based on presence of string 'wK'.\n",
-                                converted_T
-                        )
-                )
-                warning(
-                        sprintf(
-                                "'%s' --> Converted to FALSE based on absence of string 'wK'.\n",
-                                converted_F
-                        )
-                )
-
+                stop("--> 'waneyedge' should be logical vector (TRUE/FALSE), indicating
+the presence of waney edge.\n")
         }
 
         swr <- df[[n_sapwood]]

diff --git a/README.Rmd b/README.Rmd
@@ -264,6 +264,9 @@ This function also works with ring-width data in CHRONO and HALF-CHRONO format.
 
 Furthermore, the `read_fh()` function is case insensitive.
 
+
+In the example below, an .fh file with dated tree-ring series from a medieval ship DOEL1 is read with `read_fh()`. The ring width measurement, in different formats, are converted to a `data.frame`. 
+
 ```{r}
 Doel1 <- system.file("extdata", "DOEL1.fh", package = "fellingdateR")
 
@@ -273,9 +276,40 @@ head(Doel1_trs, 15)
 
 ```
 
-When `header = TRUE`, the `get_header()` function is triggered and HEADER fields in the .fh file are returned as a `data.frame`.
+When `header = TRUE`, the `get_header()` function is triggered and HEADER fields in the .fh file are returned as a `data.frame`, instead of the ring width measurements.
 
 ```{r}
 read_fh(Doel1, verbose = FALSE, header = TRUE)
 
 ```
+
+The `data.frame` with the HEADER fields can then be used as input for the sw_functions:
+
+```{r}
+Doel1_header <- read_fh(Doel1, verbose = FALSE, header = TRUE)
+
+Doel1_header |> 
+   # first convert column 'waneyedge' to a logical vector (in the original .fh file header fields the presence of waney edge is indicated by "WK" - a character string - in the corresponding HEADER field)
+   dplyr::mutate(waneyedge = dplyr::if_else(grepl("wk", waneyedge, ignore.case = TRUE),
+                               TRUE, FALSE)
+   ) |> 
+   sw_combine(plot = TRUE)
+   
+```
+
+The attempt to combine the dated tree-ring series from DOEL1 into a single felling-date range fails. These tree-ring series cannot represent a single event.
+
+However, leaving out the tree-ring series of the keelplank (series "K1_091") of this medieval ship shows that the hull planking and some frame elements could share a common felling date:
+
+```{r}
+Doel1_header |> 
+   dplyr::mutate(waneyedge = dplyr::if_else(grepl("wk", waneyedge, ignore.case = TRUE),
+                               TRUE, FALSE)
+   ) |> 
+   dplyr::filter(series != "K1_091") |> 
+   sw_combine(plot = TRUE)
+```
+
+For more details see: Haneca K. & Daly A. (2014). Tree-Rings, Timbers and Trees: a dendrochronological survey of the 14th-century cog, Doel 1. _International Journal of Nautical Archaeology_ 43, 87–102. https://doi.org/10.1111/1095-9270.12037
+
+