This function reads a Heidelberg format file (.fh) containing
ring width data and returns the HEADER fields as attributes of the
data.frame´with the measurement data.
The Heidelberg file format is described in detail here: https://www.treeringsociety.org/resources/SOM/Brewer_Murphy_SupplementaryMaterial.pdf
Arguments
- fname
A
charactervector specifying the name of the .fh file to read.- BC_correction
A
logical. IfTRUEthe correction moves BC-dates one year forward.- verbose
A
logical. IfFALSE, messages are suppressed during the reading process.- header
A
logical. IfTRUEthe HEADER fields are returned as adata.frame; ifFALSE, the measurement data is returned.
Value
If header is TRUE, a data.frame is returned with HEADER fields as
attributes. If header is FALSE, a data.frame of class rwl with
ring-width measurements in columns is returned, with (calendar) years as
row names.`
Details
This function reads .fh file with ring width data in either block
(decadal format) or column format (e.g., with comment flags) as used by
TSAP program. The function is also capable of reading chronologies or
half-chronos in decadal format. The read_fh function is case-insensitive.
Information found in the HEADER fields is listed as attributes of the
data.frame´with the measurement data. .
The header fields harvested from the .fh file include:
"Project", "FirstMeasurementDate", "Location", "Town", "Street", "Client", "Longitude", "Latitude", "DateOfSampling", "FirstMeasurementDate", "SapWoodRings", "Comment", "MissingRingsAfter", "InvalidRingsAfter", "MissingringsBefore", "DeltaMissingringsBefore", "ChronoMemberKeycodes", "PersId"
References
This function is an extension of read.fh() from the dplR
package (https://github.com/opendendro/dplR), developed and maintained
by Prof. dr. Andy Bunn (Bunn 2008, Bunn 2010, Bunn et al. 2022) on
https://opendendro.org/.
Author
The original read.fh() function is part of the dplR package
(https://github.com/opendendro/dplR) and was developed by Christian Zang,
with new features and patches contributed by Mikko Korpela and Ronald
Visser. This read_fh() function expands the functionalities of the
original dplR::read.fh().
Examples
Doel1 <- system.file("extdata", "DOEL1.fh", package = "fellingdater")
Doel1_trs <- read_fh(Doel1, verbose = FALSE)
head(Doel1_trs, 10)
#> K1_091 S38-BB GD3-1BB GR1mBB GQ1mBB K1_095 GG1-1BB S13mSB S13A-BB S6-SB
#> 1150 NA NA NA NA 3.80 NA NA NA NA NA
#> 1151 NA NA NA NA 4.15 NA NA NA NA NA
#> 1152 NA NA NA NA 4.63 NA NA NA NA NA
#> 1153 NA NA NA NA 4.31 NA NA NA NA NA
#> 1154 NA NA NA NA 3.97 NA NA NA NA NA
#> 1155 NA NA NA NA 4.10 NA NA NA NA NA
#> 1156 NA NA NA NA 2.02 NA NA NA NA NA
#> 1157 NA NA NA NA 3.24 NA NA NA NA NA
#> 1158 2.50 NA NA NA 3.75 NA NA NA NA NA
#> 1159 2.73 NA NA NA 3.07 NA NA NA NA NA
Doel1_header <- read_fh(Doel1, verbose = FALSE, header = TRUE)
Doel1_header
#> series data_type chrono_members species first last length n_sapwood
#> 1 K1_091 Single <NA> QUSP 1158 1292 135 15
#> 2 S38-BB Single <NA> QUSP 1193 1306 114 0
#> 3 GD3-1BB Single <NA> QUSP 1222 1310 89 5
#> 4 GR1mBB Quadro K1_001,K1_004x,GR1-3BB QUSP 1220 1310 91 3
#> 5 GQ1mBB Quadro GQ1-2BB,K1_007,K1_009 QUSP 1150 1314 165 7
#> 6 K1_095 Single <NA> QUSP 1207 1320 114 21
#> 7 GG1-1BB Single <NA> QUSP 1240 1322 83 13
#> 8 S13mSB Quadro S1-3SB,K1_076 QUSP 1164 1322 159 20
#> 9 S13A-BB Single <NA> QUSP 1232 1324 93 19
#> 10 S6-SB Single <NA> QUSP 1221 1324 104 14
#> n_sapwood_chr unmeasured_rings invalid_rings status waneyedge bark pith
#> 1 <NA> NA NA Dated <NA> <NA> -
#> 2 <NA> NA NA Dated <NA> <NA> -
#> 3 <NA> NA NA Dated <NA> <NA> -
#> 4 <NA> NA NA Dated --- - -
#> 5 <NA> NA NA Dated --- - -
#> 6 <NA> NA NA Dated <NA> - -
#> 7 <NA> NA NA Dated <NA> <NA> <NA>
#> 8 <NA> NA NA Dated --- <NA> -
#> 9 <NA> NA 1 Dated WKE <NA> <NA>
#> 10 <NA> NA 1 Dated WKE <NA> <NA>
#> pith_offset pith_offset_delta comments
#> 1 NA NA keelplank
#> 2 NA NA HW/SW boundary | K1_281 | framing timber
#> 3 NA NA K1_370 | hull plank
#> 4 NA NA hull plank
#> 5 NA NA hull plank
#> 6 NA NA inner stem
#> 7 NA NA hull plank
#> 8 NA NA average of S1-3SB,K1_076 | framing timber
#> 9 NA NA framing timber
#> 10 NA NA framing timber
#> project location town zip street
#> 1 Ship timbers DOEL 1 Doel_Deurganckdok <NA> <NA> <NA>
#> 2 Ship timbers DOEL 1 Doel_Deurganckdok <NA> <NA> <NA>
#> 3 Ship timbers DOEL 1 Doel_Deurganckdok <NA> <NA> <NA>
#> 4 Ship timbers DOEL 1 Doel_Deurganckdok Doel <NA> Deurganckdok
#> 5 Ship timbers DOEL 1 Doel_Deurganckdok Doel <NA> Deurganckdok
#> 6 Ship timbers DOEL 1 Doel_Deurganckdok Doel <NA> Deurganckdok
#> 7 <NA> KOGGE ANTWERPEN GG1-1BB <NA> <NA> <NA>
#> 8 Ship timbers DOEL 1 Doel_Deurganckdok <NA> <NA> <NA>
#> 9 Ship timbers DOEL 1 Doel_Deurganckdok <NA> <NA> <NA>
#> 10 <NA> KOGGE ANTWERPEN S6-SB <NA> <NA> <NA>
#> sampling_date measuring_date personal_id client_id longitude latitude
#> 1 <NA> <NA> KH <NA> 4.269711 51.298236
#> 2 <NA> <NA> KH <NA> 4.269711 51.298236
#> 3 <NA> <NA> KH <NA> 4.269711 51.298236
#> 4 <NA> <NA> KH <NA> 4.269711 51.298236
#> 5 <NA> <NA> KH <NA> 4.269711 51.298236
#> 6 <NA> <NA> KH <NA> 4.269711 51.298236
#> 7 <NA> <NA> <NA> <NA> 4.269711 51.298236
#> 8 <NA> <NA> KH <NA> 4.269711 51.298236
#> 9 <NA> <NA> <NA> <NA> 4.269711 51.298236
#> 10 <NA> <NA> <NA> <NA> 4.269711 51.298236