Introduction

The use of resistance drilling for density assessment is becoming more and more used across different disciplines. This R package provides a way to do the density analysis in R by loading the measurements, trimming them automatically or by hand. It is also possible to remove trends from profiles and measure ring widths. Please note that this package was written with a focus on forestry, where density profiles are usually obtained on living standing trees. Other uses are also possible, wherever you are using density profiles.

Let’s load the library to see what it can do:

library(densitr)

Loading resistance drilling density profiles

In the current version of densitr, only files (*.dpa) created by Rinntech Resistograph® devices are supported. It was tested to work on files produced by R650-RC Resistograph®. Other file types are currently not supported, they might be added later on. Contributions and pull requests are always welcome.

Never try to load *.dpa files directly from the Resistograph device into R, always copy them first onto your computer and load them from there. Try at your own risk. This vignette uses some example density profiles recorded using an Rinntech Resistograph® R650-SC, which are included with this package. There is a total of 15 profiles, representing various tree species. Some are drilled bark-to-bark, while others were drilled bark-to-pith because of their dimensions.

Loading a single file is simple:

dp <- dpload(dp.file = system.file("extdata", "00010001.dpa", package = "densitr"))
dp
#> 
#> 
#> Density profile ID:  00010001
#> 
#> Total length:    11521 x 1/100 mm
#> Trimmed: start not trimmed, end not trimmed
#> 
#> Data preview: 
#>  amplitude position       ID
#>          0        1 00010001
#>          0        2 00010001
#>          0        3 00010001
#>          0        4 00010001
#>          0        5 00010001
#>          0        6 00010001
#> ...

The function returns an S3 object with the class of dp, which is essentially a list with two items. In the first, $data, you will find a data frame with all of the actual profile data. Column position of that data frame holds the horizontal position as saved by the device when drilling. Column amplitude holds actual density values as recorded by the device. In the second list of an dpa object, $footer, you will find additional information about the individual density profile, as recorded by the device.

View dp measurement data:

head(dp$data)
#>   amplitude position       ID
#> 1         0        1 00010001
#> 2         0        2 00010001
#> 3         0        3 00010001
#> 4         0        4 00010001
#> 5         0        5 00010001
#> 6         0        6 00010001

View dp additional data:

head(dp$footer)
#>         ID Length yMin yMax    xUnit yUnit      Keycode     Date Time Version
#> 1 00010001 115 mm  100 1500 1/100 mm   rel 00010001.dpa 20191126 1025     200
#>   Project ResistographProfileNumber Revision End_Of_Drilling
#> 1    0001                         1 1355BExt     SWITCH_BACK

We can also plot an individual density profile:

plot(dp)

When plotting density profiles, units for both axis are extracted from $footer, as is the measurement ID.

Loading several files is also easy, just specify the argument dpa.directory with a folder path. This returns a list of density profiles. By default this function works recursively and also looks into all subfolder, set the recursive = FALSE avoid that.

dp.list <- dpload(dp.directory = system.file("extdata", package = "densitr"))
#> found 15 density profiles, loading...
#> loaded 15 density profiles

Inspect the list by displaying the first two items:

head(dp.list, 2)
#> $`00010001`
#> 
#> 
#> Density profile ID:  00010001
#> 
#> Total length:    11521 x 1/100 mm
#> Trimmed: start not trimmed, end not trimmed
#> 
#> Data preview: 
#>  amplitude position       ID
#>          0        1 00010001
#>          0        2 00010001
#>          0        3 00010001
#>          0        4 00010001
#>          0        5 00010001
#>          0        6 00010001
#> ...
#> 
#> $`00010002`
#> 
#> 
#> Density profile ID:  00010002
#> 
#> Total length:    11430 x 1/100 mm
#> Trimmed: start not trimmed, end not trimmed
#> 
#> Data preview: 
#>  amplitude position       ID
#>          0        1 00010002
#>          0        2 00010002
#>          4        3 00010002
#>          7        4 00010002
#>          7        5 00010002
#>          7        6 00010002
#> ...

Trimming

A typical resistance drilling measurement starts with an increase in resistance values in between the measurement start and the immersion of the needle in the wood. Similarly, if the needle exits of the opposite of the wood, there will be a decrease in values due to lack of resistance. Bark-to-bark measurements should be trimmed on both sides, while bark-to-pith only at the beginning.

dpdetect_s(dp.list[[1]])
#> [1] 1949

dpdetect_s(dp.list[[1]], return.plot = TRUE)

dpdetect_e(dp.list[[1]])
#> [1] 10655

dptrim(dp.list[[1]])
#> 
#> 
#> Density profile ID:  00010001
#> 
#> Total length:    8707 x 1/100 mm
#> Trimmed: start trimmed, end trimmed
#> 
#> Data preview: 
#>  amplitude position       ID
#>        429     1949 00010001
#>        429     1950 00010001
#>        430     1951 00010001
#>        432     1952 00010001
#>        433     1953 00010001
#>        434     1954 00010001
#> ...

dptrim(dp.list[[1]], return.plot = TRUE)

dp.trimmed  <- dptriml(dp.list)
#> started trimming 15 files
#> ########################################
#> trimming report: 
#> analysed 15 file(s) 
#> start detection failed in: 0 file(s)
#> end detection failed in: 6 file(s).
#> ########################################
#> end fail(s):
#> 00050045, 00050046, 00050012, 00050013, 00050036, 00050038