,
Hauke Sonnenberg [ctb] ,
Christoph Sprenger [ctb] ,
GeoSalz [fnd],
Kompetenzzentrum Wasser Berlin gGmbH (KWB) [cph]| Title: | R Package for Documenting Workflow Used in Project "geosalz" |
|---|---|
| Description: | R Package for Documenting Workflow Used in Project "geosalz". |
| Authors: | Michael Rustler [aut, cre] ,
Hauke Sonnenberg [ctb] ,
Christoph Sprenger [ctb] ,
GeoSalz [fnd],
Kompetenzzentrum Wasser Berlin gGmbH (KWB) [cph] |
| Maintainer: | Michael Rustler <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.7.0 |
| Built: | 2024-10-26 05:12:47 UTC |
| Source: | https://github.com/KWB-R/kwb.geosalz |
add_para_metadata
add_para_metadata(df, lookup_para_path, parameters_path)add_para_metadata(df, lookup_para_path, parameters_path)
df |
df |
lookup_para_path |
lookup_para_path |
parameters_path |
parameters_path |
return "df" with added parameter metadata
add_site_metadata
add_site_metadata(df, site_path)add_site_metadata(df, site_path)
df |
df |
site_path |
site_path |
data frame with added site metadata
Check if all strings are not empty
all_defined(x)all_defined(x)
x |
vector of character |
TRUE or FALSE
Helper function: cat_green_bold_0
cat_green_bold_0(...)cat_green_bold_0(...)
... |
text passed to crayon::green() |
formatted text output
Helper function: cat_red_bold_0
cat_red_bold_0(...)cat_red_bold_0(...)
... |
text passed to crayon::red |
formatted text output
Helper function: column_pattern_gather_ignore
column_pattern_gather_ignore( fields = c("Datum", "KN", "[iI]nterne Nr.", "Name der", "Ort", "Probe", "Prü", "Untersuchung", "Labor", "Jahr", "Galer", "Detail", "Meß", "Zeit", "Bezei", "Monat") )column_pattern_gather_ignore( fields = c("Datum", "KN", "[iI]nterne Nr.", "Name der", "Ort", "Probe", "Prü", "Untersuchung", "Labor", "Jahr", "Galer", "Detail", "Meß", "Zeit", "Bezei", "Monat") )
fields |
column names to be ignored for gathering (default: c( "Datum", "KN", "[iI]nterne Nr.", "Name der", "Ort", "Probe", "Pr\u00FC", "Untersuchung", "Labor", "Jahr", "Galer", "Detail", "Me\u00DF", "Zeit", "Bezei", "Monat") |
vector with ignored columns for gathering
Helper function: column_pattern_gather_ignore_clean
column_pattern_gather_ignore_clean( fields = c("LabSampleCode", "Date", "Time", "Waterbody", "ExSiteCode", "Site") )column_pattern_gather_ignore_clean( fields = c("LabSampleCode", "Date", "Time", "Waterbody", "ExSiteCode", "Site") )
fields |
column names to be ignored for gathering (default: c("LabSampleCode", "Date", "Time", "Waterbody", "ExSiteCode", Site") |
vector with ignored columns for gathering
Convert PhreeqC input to "wide" format
convert_phreeqc_input_to_wide(phreeqc_input)convert_phreeqc_input_to_wide(phreeqc_input)
phreeqc_input |
PhreeqC input as retrieved by |
PhreeqC input in "wide" format
Convert to SF
convert_to_sf( df, crs_source = 25833, crs_target = 4326, col_coord_x = "Rechtswert_UTM_33_N", col_cood_y = "Hochwert_UTM_33_N" )convert_to_sf( df, crs_source = 25833, crs_target = 4326, col_coord_x = "Rechtswert_UTM_33_N", col_cood_y = "Hochwert_UTM_33_N" )
df |
data frame or tibble with spatial data |
crs_source |
origingal CRS (default: 25833) |
crs_target |
target CRS (default: 4326) |
col_coord_x |
column name of latitude (default: "Rechtswert_UTM_33_N") |
col_cood_y |
column name of longitude (default: "Hochwert_UTM_33_N") |
data frame or tibble converted to sf
gwl_master <- jsonlite::fromJSON("https://kwb-r.github.io/wasserportal/stations_gwl_master.json") convert_to_sf(gwl_master)gwl_master <- jsonlite::fromJSON("https://kwb-r.github.io/wasserportal/stations_gwl_master.json") convert_to_sf(gwl_master)
Convert xls to xlsx
convert_xls_as_xlsx( input_dir, export_dir = tempdir(), office_folder = safe_office_folder(), dbg = TRUE )convert_xls_as_xlsx( input_dir, export_dir = tempdir(), office_folder = safe_office_folder(), dbg = TRUE )
input_dir |
input directory containing .xls files |
export_dir |
export directory (default: tempdir()) |
office_folder |
office folder path (default: |
dbg |
debug (default: TRUE) |
Helper function: convert_xls_to_xlsx
convert_xls_to_xlsx(exe, xls, xlsx, i, n_files, dbg = TRUE)convert_xls_to_xlsx(exe, xls, xlsx, i, n_files, dbg = TRUE)
exe |
exe |
xls |
xls |
xlsx |
xlsx |
i |
i |
n_files |
n_files |
dbg |
debug (default: TRUE) |
Helper function: copy_lookup_para_file
copy_lookup_para_file( from_dir, to_dir, overwrite = FALSE, recursive = TRUE, file_pattern = "^lookup_para\\.csv$" )copy_lookup_para_file( from_dir, to_dir, overwrite = FALSE, recursive = TRUE, file_pattern = "^lookup_para\\.csv$" )
from_dir |
input directory with xlsx files |
to_dir |
target directory where to copy the xlsx files |
overwrite |
should existing files be overwritten (TRUE) otherwise (FALSE) ? (default: FALSE) |
recursive |
if TRUE recursively find all xlsx files in the directory specified in parameter "from_dir" (default: TRUE) |
file_pattern |
pattern for identifying lookup_para file (default: "^lookup_para\.csv$") |
Helper function: copy_xlsx_files
copy_xlsx_files( from_dir, to_dir, overwrite = FALSE, recursive = TRUE, file_pattern = "[xX][lL][sS][xX]" )copy_xlsx_files( from_dir, to_dir, overwrite = FALSE, recursive = TRUE, file_pattern = "[xX][lL][sS][xX]" )
from_dir |
input directory with xlsx files |
to_dir |
target directory where to copy the xlsx files |
overwrite |
should existing files be overwritten (TRUE) otherwise (FALSE) ? (default: FALSE) |
recursive |
if TRUE recursively find all xlsx files in the directory specified in parameter "from_dir" (default: TRUE) |
file_pattern |
pattern for identifying xlsx fles (default: "[xX][lL][sS][xX]") |
Create EMSHOFF91 Import Data Frame
create_emshoff91_import( ods_dir, files_to_ignore = c("cl25", "clliste", "rupelauf", "salzlast") )create_emshoff91_import( ods_dir, files_to_ignore = c("cl25", "clliste", "rupelauf", "salzlast") )
ods_dir |
directory to ".ods" files created manually by importing original ".wq1" files into LibreOffice 7.0 on Ubuntu with encoding (Western Europe (DOS/OS2-437/US)) and exporting to ".ods" format |
files_to_ignore |
tidied names of files to ignore due to complex data input structure not yet covered by importer (default: c("cl25", "clliste", "gwnguete", "rupelauf", "salzlast")) |
data frame with columns "ods_paths" (full paths to ".ods" files), "ods_files" (their "basenames") and "ods_names_clean" (tidied names used as identifier)
## Not run: ods_dir <- "<replace-with-path-to-files>/emshoff91/converted_ods" emshoff91_import <- create_emshoff91_import(ods_dir) ## End(Not run)## Not run: ods_dir <- "<replace-with-path-to-files>/emshoff91/converted_ods" emshoff91_import <- create_emshoff91_import(ods_dir) ## End(Not run)
Measurement Chains: Create an SFTP Connection
create_sftp_connection()create_sftp_connection()
sftp connection
Helper function: delete_registry
delete_registry(office_folder = safe_office_folder(), dbg = TRUE)delete_registry(office_folder = safe_office_folder(), dbg = TRUE)
office_folder |
office folder path (default: |
dbg |
debug (default: TRUE) |
Measurement Chains: download data
download_measurementchains_data( sftp_paths, target_directory = temp_dir(), sftp_connection = create_sftp_connection(), run_parallel = TRUE, debug = FALSE )download_measurementchains_data( sftp_paths, target_directory = temp_dir(), sftp_connection = create_sftp_connection(), run_parallel = TRUE, debug = FALSE )
sftp_paths |
character vector with paths to files to be downloaded. As
retrieved by |
target_directory |
target directory |
sftp_connection |
an SFTP connnection as retrieved by
|
run_parallel |
default: TRUE |
debug |
show debug messages (default: FALSE) |
tibble with columns file_id, sftp_path and local_path of csv files
## Not run: mc_files <- kwb.geosalz::get_measurementchains_files() target_directory <- tempdir() local_paths <- kwb.geosalz::download_measurementchains_data( sftp_paths = mc_files$sftp_path, target_directory) ## End(Not run)## Not run: mc_files <- kwb.geosalz::get_measurementchains_files() target_directory <- tempdir() local_paths <- kwb.geosalz::download_measurementchains_data( sftp_paths = mc_files$sftp_path, target_directory) ## End(Not run)
Emshoff 91: list to data frame
emshoff91_list_to_df(emshoff91_list)emshoff91_list_to_df(emshoff91_list)
emshoff91_list |
list as retrieved by |
tibble
Emshoff 91: remap values from imported tibble
emshoff91_remap_values( emshoff91_df, remap_list = list(fi_mi = "fi_mi_m_nn", ku_sto = "kupp_st", lf = "el_lf", progr = "beprob_progr", strat = "stratigr", uv254 = "uv_ext"), delete_cols = TRUE )emshoff91_remap_values( emshoff91_df, remap_list = list(fi_mi = "fi_mi_m_nn", ku_sto = "kupp_st", lf = "el_lf", progr = "beprob_progr", strat = "stratigr", uv254 = "uv_ext"), delete_cols = TRUE )
emshoff91_df |
tibble as retrieved by |
remap_list |
list with values to be remapped. Names of the list are columns values contained in list values should be mapped to (default: list(fi_mi = "fi_mi_m_nn", ku_sto = "kupp_st", lf = "el_lf", progr = "beprob_progr", strat = "stratigr", uv254 = "uv_ext")) |
delete_cols |
should unneeded columns be deleted, i.e. the ones where data where mapped from (default: TRUE) |
data frame with remapped values and deleted columns were this values were copied from (default: TRUE)
Helper function: gather_and_join_1
gather_and_join_1(tmp_data, columns_keep, metadata, dbg = FALSE)gather_and_join_1(tmp_data, columns_keep, metadata, dbg = FALSE)
tmp_data |
tmp_data |
columns_keep |
columns_keep |
metadata |
metadata |
dbg |
dbg (default: FALSE) |
gathered and joined data frame
Helper function: gather_and_join_2
gather_and_join_2(tmp_content, columns_keep, header)gather_and_join_2(tmp_content, columns_keep, header)
tmp_content |
tmp_content |
columns_keep |
columns_keep |
header |
header |
gathered and joined data frame
Helper function: get_excelcnv_exe
get_excelcnv_exe(office_folder = safe_office_folder())get_excelcnv_exe(office_folder = safe_office_folder())
office_folder |
office folder path (default: |
path containing 'excelcnv.exe'
get_foerdermengen
get_foerdermengen( xlsx_path, sheet_name = "WW Q Rhow ", sheet_range = "A4:S127" )get_foerdermengen( xlsx_path, sheet_name = "WW Q Rhow ", sheet_range = "A4:S127" )
xlsx_path |
path to xlsx file with pumping rates |
sheet_name |
sheet_name (default: "WW Q Rhow ") |
sheet_range |
sheet_range (default: "A4:S127") |
data frame with annual pumping rates per waterworks
Get Abtraction of Friedrichshagen Well Galleries
get_foerdermengen_gal_fri(path)get_foerdermengen_gal_fri(path)
path |
path to "2018-04-27 Rohwasser Bericht - Galeriefördermengen.xlsx" |
tidy data frame with abstraction rates for waterworks Friedrichshagen
Get Measurement Chain Data on KWB Cloud
get_measurement_chain_data_on_cloud(dbg = TRUE)get_measurement_chain_data_on_cloud(dbg = TRUE)
dbg |
logical indicating whether or not to show debug messages |
data frame with the content of "mc_data.zip" in the GeoSalz project
folder on the Nextcloud server. The SFTP paths to the files from which the
data in "mc_data.zip" originate are returned in attribute "sftp_paths".
If either of the files "mc_data.zip" or "mc_files.csv" does not exist,
NULL is returned.
Measurement Chains: Get Tidied Files Metadata
get_measurementchains_files( sftp_connection = create_sftp_connection(), debug = FALSE )get_measurementchains_files( sftp_connection = create_sftp_connection(), debug = FALSE )
sftp_connection |
an SFTP connnection as retrieved by
|
debug |
show debug messages (default: FALSE) |
tibble with information on available files and tidied meta-information based on file naming
## Not run: mc_files <- kwb.geosalz::get_measurementchains_files() str(mc_files) ## End(Not run)## Not run: mc_files <- kwb.geosalz::get_measurementchains_files() str(mc_files) ## End(Not run)
Measurement Chains: Get Metadata
get_measurementchains_metadata(file = extdata_file("metadata_messketten.csv"))get_measurementchains_metadata(file = extdata_file("metadata_messketten.csv"))
file |
path to measurement chains metadata file. Default: kwb.geosalz:::extdata_file("metadata_messketten.csv") |
tibble with measurement chains metadata
mc_metadata <- kwb.geosalz::get_measurementchains_metadata() str(mc_metadata) mc_metadatamc_metadata <- kwb.geosalz::get_measurementchains_metadata() str(mc_metadata) mc_metadata
Measurement Chains: get statistics for data
get_measurmentchains_data_stats(mc_data)get_measurmentchains_data_stats(mc_data)
mc_data |
tibble with measurement chains data as retrieved by
|
tibble with colunns datetime min/max, q10 (10 median, q90 (90
Helper function: get_meta_sheet_or_stop
get_meta_sheet_or_stop(sheets, pattern, file)get_meta_sheet_or_stop(sheets, pattern, file)
sheets |
sheets |
pattern |
pattern |
file |
file |
meta sheet name
Get Information on Pandoc
get_pandoc_info()get_pandoc_info()
data frame with columns pandoc_directory,
pandoc_version if Pandoc is installed, otherwise a message is
printed that pandoc is not installed.
get_parameters_meta
get_parameters_meta(xlsx_path, sheet_name = "nur Parameterliste")get_parameters_meta(xlsx_path, sheet_name = "nur Parameterliste")
xlsx_path |
path to EXCEL spreadsheet with parameter metadata |
sheet_name |
name of sheet containing metadata table (default: "nur Parameterliste") |
imported parameter metadata with cleaned columns names
Get PhreeqC data
get_phreeqc_data(lab_bwb)get_phreeqc_data(lab_bwb)
lab_bwb |
imported BWB lab data as retrieved by |
tibble with columns solution, par_name_phreeqc (which are not empty or NA) and numeric_value
Helper function: get_site_id
get_site_id(string, pattern = "^[0-9]{1,4}")get_site_id(string, pattern = "^[0-9]{1,4}")
string |
vector with character strings |
pattern |
pattern used for identifying site_id (default: "^[0-9]1,4") |
extracted site_id's from input string
import_labor
import_labor(files, export_dir, func = read_bwb_header2)import_labor(files, export_dir, func = read_bwb_header2)
files |
vector with full paths of xlsx input files |
export_dir |
export directory |
func |
function to be used (default: |
list with length equal to number of input files
Order Measurement Chain Data
order_measurement_chain_data(data)order_measurement_chain_data(data)
data |
data frame as retrieved by
|
data, ordered by "parameter", "sensor_id", "datum_uhrzeit"
Plot measurementchain and well operation in combined plot
plot_measurementchain_and_well_operation( mc_dat, well_op_data_meta, brunnen_nr = 9, para = "Leitfaehigkeit", y_label = "elektr. Leitfähigkeit (µS/cm)", date_min = as.Date("2023-05-10"), date_max = Sys.Date() )plot_measurementchain_and_well_operation( mc_dat, well_op_data_meta, brunnen_nr = 9, para = "Leitfaehigkeit", y_label = "elektr. Leitfähigkeit (µS/cm)", date_min = as.Date("2023-05-10"), date_max = Sys.Date() )
mc_dat |
mc_dat |
well_op_data_meta |
well_op_data_meta |
brunnen_nr |
well id (default: 9) |
para |
parameter (either: "Leitfaehigkeit" or "Temperatur") |
y_label |
y label (default: "elektr. Leitfaehigkeit (µS/cm)") |
date_min |
minimum date for plotting (default: as.Date("2023-05-10")) |
date_max |
maximum date for plotting (default: Sys.Date()) |
combined plot
Measurement Chains: plott
plot_measurementchains(mc_data, para = "Leitfaehigkeit")plot_measurementchains(mc_data, para = "Leitfaehigkeit")
mc_data |
as retrieved by |
para |
parameter to plot "Leitfaehigkeit" or "Temperatur" (default: Leitfaehigkeit") |
plot of selected measurement chain parameter
Prepare PhreeqC input
prepare_phreeqc_input(lab_bwb_phreeqc, title = "")prepare_phreeqc_input(lab_bwb_phreeqc, title = "")
lab_bwb_phreeqc |
selected BWB lab data as retrieved by |
title |
user defined title (default: "") |
data frame with input structure for kwb.phreeqc
Helper function: print_datatype_info_if
print_datatype_info_if(dbg, tbl_datatypes, columns_keep)print_datatype_info_if(dbg, tbl_datatypes, columns_keep)
dbg |
dbg |
tbl_datatypes |
tbl_datatypes |
columns_keep |
columns_keep |
wrapper around read_bwb_header2 and
read_bwb_header1_meta
read_bwb_data( files, meta_pattern = "META", keep_pattern = column_pattern_gather_ignore(), site_id_pattern = "^[0-9]{1,4}", dbg = TRUE )read_bwb_data( files, meta_pattern = "META", keep_pattern = column_pattern_gather_ignore(), site_id_pattern = "^[0-9]{1,4}", dbg = TRUE )
files |
file path(s) to EXCEL spreadsheet |
meta_pattern |
(default: "META") |
keep_pattern |
(default: |
site_id_pattern |
(default: "^[0-9]1,4") |
dbg |
debug (default: TRUE) |
data.table with imported xls(x) files
Import: read_bwb_header1_meta
read_bwb_header1_meta( file, meta_pattern = "META", keep_pattern = column_pattern_gather_ignore(), dbg = FALSE )read_bwb_header1_meta( file, meta_pattern = "META", keep_pattern = column_pattern_gather_ignore(), dbg = FALSE )
file |
path(s) to EXCEL spreadsheet |
meta_pattern |
meta_pattern default("META") |
keep_pattern |
keep_pattern (default: |
dbg |
debug (default: FALSE) |
data.table with imported xls(x) files
Import: read_bwb_header2
read_bwb_header2( file, skip = 2, keep_pattern = column_pattern_gather_ignore(), site_id_pattern = "^[0-9]{1,4}", dbg = TRUE )read_bwb_header2( file, skip = 2, keep_pattern = column_pattern_gather_ignore(), site_id_pattern = "^[0-9]{1,4}", dbg = TRUE )
file |
file path(s) to EXCEL spreadsheet |
skip |
number of rows to skip in each sheet (default: 2) |
keep_pattern |
(default: column_pattern_gather_ignore()) |
site_id_pattern |
(default: "^[0-9]1,4") |
dbg |
debug (default: TRUE) |
data.table with imported xls(x) files
Import: read_bwb_header4
read_bwb_header4( file, skip = 4, keep_pattern = column_pattern_gather_ignore(), site_id_pattern = "^[0-9]{1,4}", dbg = TRUE )read_bwb_header4( file, skip = 4, keep_pattern = column_pattern_gather_ignore(), site_id_pattern = "^[0-9]{1,4}", dbg = TRUE )
file |
file path(s) to EXCEL spreadsheet |
skip |
number of rows to skip in each sheet (default: 4) |
keep_pattern |
(default: column_pattern_gather_ignore()) |
site_id_pattern |
(default: "^[0-9]1,4") |
dbg |
debug (default: TRUE) |
data.table with imported xls(x) files
Reads a Single EMSHOFF 91 ODS File into Tibble
read_emshoff91_ods(emshoff91_import_selected)read_emshoff91_ods(emshoff91_import_selected)
emshoff91_import_selected |
a row as retrieved by |
imports ods file into tibble
Read Isotopes
read_isotopes(path)read_isotopes(path)
path |
path to Isotopes delim (field separator ";") |
imported isotopes data
Read Lab BWB
read_lab_bwb(path, sheet = "Analysen")read_lab_bwb(path, sheet = "Analysen")
path |
path to file with lab BWB data |
sheet |
name of sheet containing analysis data. Default: "Analysen" |
cleaned data frame with master data and lab values for all samples but only for selected parameters (columns A-BA and HB-HC)
Read Master Data
read_master_data(path)read_master_data(path)
path |
path to file with master data (currently in file: lab BWB data) |
imported master data contained in sheet "Stammdaten"
Measurement Chains: read csv data from multiple files
read_measurementchains_data( csv_files, datetime_installation = as_gmt_plus_one("2022-09-27 11:00:00"), run_parallel = TRUE, debug = FALSE )read_measurementchains_data( csv_files, datetime_installation = as_gmt_plus_one("2022-09-27 11:00:00"), run_parallel = TRUE, debug = FALSE )
csv_files |
vector of paths as retrieved by
|
datetime_installation |
datetime of first logger installation in well K10. Used to filter out older measurement data! Default: kwb.geosalz:::as_gmt_plus_one("2022-09-27 11:00:00") |
run_parallel |
default: TRUE |
debug |
show debug messages (default: FALSE) |
data frame with imported data from csv files
## Not run: mc_files <- kwb.geosalz::get_measurementchains_files() target_directory <- tempdir() csv_files <- kwb.geosalz::download_measurementchains_data( sftp_paths = mc_files$sftp_path, target_directory ) mc_data <- kwb.geosalz::read_measurementchains_data(csv_files) ## End(Not run)## Not run: mc_files <- kwb.geosalz::get_measurementchains_files() target_directory <- tempdir() csv_files <- kwb.geosalz::download_measurementchains_data( sftp_paths = mc_files$sftp_path, target_directory ) mc_data <- kwb.geosalz::read_measurementchains_data(csv_files) ## End(Not run)
Reads Multiple EMSHOFF 91 ODS Files into List
read_multiple_emshoff91_ods(emshoff91_import)read_multiple_emshoff91_ods(emshoff91_import)
emshoff91_import |
a tibble as retrieved by |
imports mulitple ods files into a list of tibbles
## Not run: ods_dir <- "<replace-with-path-to-files>/emshoff91/emshoff91/converted_ods" ods_dir <- "C:/users/mrustl/Downloads/emshoff91/emshoff91/converted_ods" emshoff91_import <- create_emshoff91_import(ods_dir) read_multiple_emshoff91_ods(emshoff91_import) ## End(Not run)## Not run: ods_dir <- "<replace-with-path-to-files>/emshoff91/emshoff91/converted_ods" ods_dir <- "C:/users/mrustl/Downloads/emshoff91/emshoff91/converted_ods" emshoff91_import <- create_emshoff91_import(ods_dir) read_multiple_emshoff91_ods(emshoff91_import) ## End(Not run)
Replace n.a. (not available) and n.b. (not determined) from lab data with NA
replace_nanb_with_na(string)replace_nanb_with_na(string)
string |
string |
string with NA instead of "n.a." or "n.b." (including 0-10 spaces between "n" and "a"/"b"
string <- c("19.2", "n.b.", "n. b.", "n. b.", "n.a.", "n. a.", "n. a.") replace_nanb_with_na(string)string <- c("19.2", "n.b.", "n. b.", "n. b.", "n.a.", "n. a.", "n. a.") replace_nanb_with_na(string)
Helper function: safe_office_folder
safe_office_folder(office_path = "C:/Program Files (x86)/Microsoft Office")safe_office_folder(office_path = "C:/Program Files (x86)/Microsoft Office")
office_path |
office folder path (default: "C:/Program Files (x86)/Microsoft Office") |
path of office folder (if existing)
Helper function: stop if duplicated sample ids are found
stop_if_duplicated_samples_found(df, col_sampleid, path, sheet = "")stop_if_duplicated_samples_found(df, col_sampleid, path, sheet = "")
df |
data frame with samples in wide format |
col_sampleid |
column name of sample id |
path |
path to file from which |
sheet |
optional in case EXCEL is used (default: "") |
error in case duplicated samples were found
Helper function: stop_on_missing_or_inform_on_extra_sheets
stop_on_missing_or_inform_on_extra_sheets(has_site_id, file, sheets)stop_on_missing_or_inform_on_extra_sheets(has_site_id, file, sheets)
has_site_id |
has_site_id |
file |
file |
sheets |
sheets |
Helper function: to_full_metadata2
to_full_metadata_2(header, file, sheet)to_full_metadata_2(header, file, sheet)
header |
header |
file |
file |
sheet |
sheet |
data frame with metadata for header2 (EXCEL) files
Helper function: to_full_metadata_4
to_full_metadata_4(header, file, sheet)to_full_metadata_4(header, file, sheet)
header |
header |
file |
file |
sheet |
sheet |
data frame with metadata for header4 (EXCEL) files
Measurement Chains: write csv data
write_measurementchains_data( mc_data, target_directory, to_zip = FALSE, debug = FALSE )write_measurementchains_data( mc_data, target_directory, to_zip = FALSE, debug = FALSE )
mc_data |
measurement chains data as retrieved by
|
target_directory |
target directory |
to_zip |
should data be zipped? (default: FALSE), if TRUE only a temporary csv file is created which will be subsequently zipped and deleted |
debug |
print debug messages (default: FALSE) |
writes csv data to path