Package 'cascade' reference manual

Title:	Contextualizing untargeted Annotation with Semi-quantitative Charged Aerosol Detection for pertinent characterization of natural Extracts
Description:	This package provides the infrastructure to perform Automated Composition Assessment of Natural Extracts.
Authors:	Adriano Rutz [aut, cre]
Maintainer:	Adriano Rutz <[email protected]>
License:	GPL (>= 3)
Version:	0.0.0.9000
Built:	2024-11-22 11:23:21 UTC
Source:	https://github.com/adafede/cascade

Add chromato line

Description

Add chromato line

Usage

add_chromato_line(
  plot,
  chromato,
  shift = 0,
  normalize_time,
  name,
  color,
  polarity = "pos"
)
add_chromato_line(
  plot,
  chromato,
  shift = 0,
  normalize_time,
  name,
  color,
  polarity = "pos"
)

Arguments

`plot`	Plot
`chromato`	Chromato
`shift`	Shift
`normalize_time`	Normalize time
`name`	Name
`color`	Color
`polarity`	Polarity

Value

A plot with added chromato line

Examples

NULL
NULL

Baseline chromatogram

Description

Baseline chromatogram

Usage

baseline_chromatogram(df)
baseline_chromatogram(df)

Arguments

df

Dataframe

Value

A dataframe with baselined chromatogram

Examples

NULL
NULL

Change intensity name

Description

Change intensity name

Usage

change_intensity_name(df, name)
change_intensity_name(df, name)

Arguments

`df`	Dataframe
`name`	Name

Value

A dataframe with changed intensity name

Examples

NULL
NULL

Check chromatograms

Description

Check chromatograms

Usage

check_chromatograms(
  chromatograms = c("bpi_pos", "cad_pos", "pda_pos"),
  normalize_time = FALSE,
  shift_cad = 0,
  shift_pda = 0,
  type = "improved"
)
check_chromatograms(
  chromatograms = c("bpi_pos", "cad_pos", "pda_pos"),
  normalize_time = FALSE,
  shift_cad = 0,
  shift_pda = 0,
  type = "improved"
)

Arguments

`chromatograms`	Chromatograms
`normalize_time`	Normalized time
`shift_cad`	Shift CAD
`shift_pda`	Shift PDA
`type`	Type

Value

A plot

Examples

NULL
NULL

Check chromatograms alignment

Description

Check chromatograms alignment

Usage

check_chromatograms_alignment(
  file_negative = NULL,
  file_positive = NULL,
  time_min = 0.5,
  time_max = 32.5,
  cad_shift = 0.05,
  pda_shift = 0.1,
  fourier_components = 0.01,
  frequency = 1,
  resample = 1,
  chromatograms = c("bpi_pos", "cad_pos", "pda_pos"),
  type = "baselined",
  normalize_intensity = TRUE,
  normalize_time = FALSE,
  show_example = FALSE
)
check_chromatograms_alignment(
  file_negative = NULL,
  file_positive = NULL,
  time_min = 0.5,
  time_max = 32.5,
  cad_shift = 0.05,
  pda_shift = 0.1,
  fourier_components = 0.01,
  frequency = 1,
  resample = 1,
  chromatograms = c("bpi_pos", "cad_pos", "pda_pos"),
  type = "baselined",
  normalize_intensity = TRUE,
  normalize_time = FALSE,
  show_example = FALSE
)

Arguments

`file_negative`	Negative file path
`file_positive`	Positive file path
`time_min`	Minimum time
`time_max`	Maximum time
`cad_shift`	CAD shift
`pda_shift`	PDA shift
`fourier_components`	Fourier components
`frequency`	Frequency
`resample`	Resample
`chromatograms`	Chromatograms to plot
`type`	Type. "baselined" or "improved"
`normalize_intensity`	Normalize intensity? Default to TRUE
`normalize_time`	Normalize time? Default to FALSE
`show_example`	Show example? Default to FALSE

Value

A plot with (non-)aligned chromatograms

Examples

## Not run: 
check_chromatograms_alignment(show_example = TRUE)

## End(Not run)
## Not run: 
check_chromatograms_alignment(show_example = TRUE)

## End(Not run)

Check export dir

Description

Check export dir

Usage

check_export_dir(dir)
check_export_dir(dir)

Arguments

dir

Dir

Value

A log of checked dir

Examples

NULL
NULL

Check chromatograms alignment

Description

Check chromatograms alignment

Usage

check_peaks_integration(
  file = NULL,
  features = NULL,
  detector = "cad",
  chromatogram = "baselined",
  min_area = 0.005,
  min_intensity = 10000,
  shift = 0.05,
  show_example = FALSE,
  fourier_components = 0.01,
  time_min = 0.5,
  time_max = 32.5,
  frequency = 1,
  resample = 1
)
check_peaks_integration(
  file = NULL,
  features = NULL,
  detector = "cad",
  chromatogram = "baselined",
  min_area = 0.005,
  min_intensity = 10000,
  shift = 0.05,
  show_example = FALSE,
  fourier_components = 0.01,
  time_min = 0.5,
  time_max = 32.5,
  frequency = 1,
  resample = 1
)

Arguments

`file`	File path
`features`	Features path
`detector`	Detector
`chromatogram`	Chromatogram
`min_area`	Minimum area
`min_intensity`	Minimum intensity
`shift`	shift
`show_example`	Show example? Default to FALSE
`fourier_components`	Fourier components
`time_min`	Time min
`time_max`	Time max
`frequency`	Frequency
`resample`	Resample

Value

A plot with (non-)aligned chromatograms

Examples

## Not run: 
check_peaks_integration(show_example = TRUE)

## End(Not run)
## Not run: 
check_peaks_integration(show_example = TRUE)

## End(Not run)

Compare peaks

Description

Compare peaks

Usage

compare_peaks(x, list_ms_peaks, peaks_prelist)
compare_peaks(x, list_ms_peaks, peaks_prelist)

Arguments

`x`	X
`list_ms_peaks`	list_ms_peaks
`peaks_prelist`	peaks_prelist

Value

A comparison score

Examples

NULL
NULL

Deriv

Description

Deriv

Usage

deriv(x, y)
deriv(x, y)

Arguments

`x`	X
`y`	Y

Value

The derivative

Examples

NULL
NULL

Extract chromatogram

Description

Extract chromatogram

Usage

extract_chromatogram(list, type)
extract_chromatogram(list, type)

Arguments

`list`	List
`type`	Type

Value

An extracted chromatogram

Examples

NULL
NULL

Extract MS peak

Description

Extract MS peak

Usage

extract_ms_peak(x)
extract_ms_peak(x)

Arguments

x

Value

A peak

Examples

NULL
NULL

Extract MS progress

Description

Extract MS progress

Usage

extract_ms_progress(xs, ms_data, peaks_prelist)
extract_ms_progress(xs, ms_data, peaks_prelist)

Arguments

`xs`	XS
`ms_data`	MS Data
`peaks_prelist`	Peaks prelist

Value

A list of extracted MS peaks

Examples

NULL
NULL

Filter FFT

Description

Filter FFT

Usage

filter_fft(x, components)
filter_fft(x, components)

Arguments

`x`	X
`components`	Components

Value

The fourier filtered x

Examples

NULL
NULL

Temp GT function

Description

Temp GT function

Usage

format_gt(table, title = "", subtitle = "")
format_gt(table, title = "", subtitle = "")

Arguments

`table`	Table
`title`	Title
`subtitle`	Subtitle

Value

A formatted GT table

Examples

NULL
NULL

Generate IDs

Description

Generate IDs

Usage

generate_ids(
  taxa = c("Swertia", "Kopsia", "Ginkgo"),
  comparison = c("Swertia", "Kopsia"),
  no_stereo = TRUE,
  filter_ms_conditions = TRUE,
  start = "0",
  end = "9999",
  limit = "1000000"
)
generate_ids(
  taxa = c("Swertia", "Kopsia", "Ginkgo"),
  comparison = c("Swertia", "Kopsia"),
  no_stereo = TRUE,
  filter_ms_conditions = TRUE,
  start = "0",
  end = "9999",
  limit = "1000000"
)

Arguments

`taxa`	Taxa
`comparison`	Comparison
`no_stereo`	No stereo
`filter_ms_conditions`	Filter MS conditions
`start`	Start
`end`	End
`limit`	Limit

Value

IDs

Examples

## Not run: 
generate_ids()

## End(Not run)
## Not run: 
generate_ids()

## End(Not run)

Generate pseudochromatograms

Description

Generate pseudochromatograms

Usage

generate_pseudochromatograms(
  annotations = NULL,
  features_informed = NULL,
  features_not_informed = NULL,
  file = NULL,
  detector = "cad",
  show_example = FALSE,
  min_confidence = 0.4,
  min_similarity_prefilter = 0.6,
  min_similarity_filter = 0.8,
  mode = "pos",
  organism = "Swertia chirayita",
  fourier_components = 0.01,
  frequency = 1,
  resample = 1,
  shift = 0.05,
  time_min = 0.5,
  time_max = 32.5
)
generate_pseudochromatograms(
  annotations = NULL,
  features_informed = NULL,
  features_not_informed = NULL,
  file = NULL,
  detector = "cad",
  show_example = FALSE,
  min_confidence = 0.4,
  min_similarity_prefilter = 0.6,
  min_similarity_filter = 0.8,
  mode = "pos",
  organism = "Swertia chirayita",
  fourier_components = 0.01,
  frequency = 1,
  resample = 1,
  shift = 0.05,
  time_min = 0.5,
  time_max = 32.5
)

Arguments

`annotations`	Annotations
`features_informed`	Features informed
`features_not_informed`	Features not informed
`file`	File
`detector`	Detector
`show_example`	Show example? Default to FALSE
`min_confidence`	Min confidence
`min_similarity_prefilter`	Min similarity pre filter
`min_similarity_filter`	Min similarity filter
`mode`	Mode
`organism`	Organism
`fourier_components`	Fourier components
`frequency`	Frequency
`resample`	Resample
`shift`	Shift
`time_min`	Time min
`time_max`	Time max

Value

A list of plots

Examples

## Not run: 
generate_pseudochromatograms(show_example = TRUE)

## End(Not run)
## Not run: 
generate_pseudochromatograms(show_example = TRUE)

## End(Not run)

Generate IDs

Description

Generate IDs

Usage

generate_tables(
  annotations = NULL,
  file_negative = NULL,
  file_positive = NULL,
  min_confidence = 0.4,
  show_example = FALSE,
  export_csv = TRUE,
  export_html = TRUE,
  export_dir = "data/processed",
  export_name = "cascade_table"
)
generate_tables(
  annotations = NULL,
  file_negative = NULL,
  file_positive = NULL,
  min_confidence = 0.4,
  show_example = FALSE,
  export_csv = TRUE,
  export_html = TRUE,
  export_dir = "data/processed",
  export_name = "cascade_table"
)

Arguments

`annotations`	Annotations
`file_negative`	File negative
`file_positive`	File positive
`min_confidence`	Min confidence
`show_example`	Show example? Default to FALSE
`export_csv`	Export CSV
`export_html`	Export HTML
`export_dir`	Export Dir
`export_name`	Export name

Value

Tables

Examples

## Not run: 
generate_tables()

## End(Not run)
## Not run: 
generate_tables()

## End(Not run)

Get peaks

Description

Get peaks

Usage

get_peaks(
  chrom_list,
  lambdas,
  fit = c("egh", "gaussian", "raw"),
  sd.max = 50,
  max.iter = 100,
  time.units = c("min", "s", "ms"),
  estimate_purity = FALSE,
  noise_threshold = 0.001,
  collapse = FALSE,
  ...
)
get_peaks(
  chrom_list,
  lambdas,
  fit = c("egh", "gaussian", "raw"),
  sd.max = 50,
  max.iter = 100,
  time.units = c("min", "s", "ms"),
  estimate_purity = FALSE,
  noise_threshold = 0.001,
  collapse = FALSE,
  ...
)

Arguments

`chrom_list`	Chrom list
`lambdas`	Lambdas
`fit`	Fit
`sd.max`	Sd max
`max.iter`	Max iter
`time.units`	Time units
`estimate_purity`	Estimate purity
`noise_threshold`	Noise Threshold
`collapse`	Collapse
`...`	...

Value

Peaks

Note

This was imported from {chromatographR} package and parallelization was removed as it was causing issues on Windows.

Author(s)

Ethan Bass

Source

https://github.com/ethanbass/chromatographR

Examples

NULL
NULL

Hierarchies grouped progress

Description

Hierarchies grouped progress

Usage

hierarchies_grouped_progress(xs)
hierarchies_grouped_progress(xs)

Arguments

xs

Value

A list of grouped hierarchies

Examples

NULL
NULL

Hierarchies Progress

Description

Hierarchies Progress

Usage

hierarchies_progress(xs)
hierarchies_progress(xs)

Arguments

xs

Value

A list of hierarchies

Examples

NULL
NULL

Histograms progress

Description

Histograms progress

Usage

histograms_progress(xs)
histograms_progress(xs)

Arguments

xs

Value

A list of histograms

Examples

NULL
NULL

Improve signal

Description

Improve signal

Usage

improve_signal(
  df,
  fourier_components = 0.01,
  frequency = 2,
  resample = 1,
  time_min = 0,
  time_max = Inf
)
improve_signal(
  df,
  fourier_components = 0.01,
  frequency = 2,
  resample = 1,
  time_min = 0,
  time_max = Inf
)

Arguments

`df`	Dataframe
`fourier_components`	Fourier components
`frequency`	Frequency
`resample`	Resample
`time_min`	Time min
`time_max`	Time max

Value

A dataframe with improved signal

Examples

NULL
NULL

Improve signals progress

Description

Improve signals progress

Usage

improve_signals_progress(
  xs,
  fourier_components = 0.01,
  frequency = 2,
  resample = 1,
  time_min = 0,
  time_max = Inf
)
improve_signals_progress(
  xs,
  fourier_components = 0.01,
  frequency = 2,
  resample = 1,
  time_min = 0,
  time_max = Inf
)

Arguments

`xs`	XS
`fourier_components`	Fourier components
`frequency`	Frequency
`resample`	Resample
`time_min`	Time min
`time_max`	Time max

Value

A list of data frames with improved signals

Examples

NULL
NULL

Join peaks

Description

Join peaks

Usage

join_peaks(chromatograms, peaks, min_area)
join_peaks(chromatograms, peaks, min_area)

Arguments

`chromatograms`	Chromatograms
`peaks`	Peaks
`min_area`	Min area

Value

A dataframe with joined peaks

Examples

NULL
NULL

Keep best candidates

Description

Keep best candidates

Usage

keep_best_candidates(df)
keep_best_candidates(df)

Arguments

df

Dataframe

Value

A dataframe containing the best candidates only

Examples

NULL
NULL

Load annotations

Description

Load annotations

Usage

load_annotations(file = NULL, show_example = FALSE, mode = "pos")
load_annotations(file = NULL, show_example = FALSE, mode = "pos")

Arguments

`file`	File
`show_example`	Show example? Default to FALSE
`mode`	Mode

Value

A table of annotations

Examples

NULL
NULL

Load chromatograms

Description

Load chromatograms

Usage

load_chromatograms(file = NULL, show_example = FALSE, example_polarity = "pos")
load_chromatograms(file = NULL, show_example = FALSE, example_polarity = "pos")

Arguments

`file`	File
`show_example`	Show example? Default to FALSE
`example_polarity`	Example polarity

Value

A list of chromatograms

Examples

NULL
NULL

Load features

Description

Load features

Usage

load_features(file = NULL, show_example = FALSE)
load_features(file = NULL, show_example = FALSE)

Arguments

`file`	File
`show_example`	Show example? Default to FALSE

Value

A table of features

Examples

NULL
NULL

Load features informed

Description

Load features informed

Usage

load_features_informed(file = NULL, show_example = FALSE)
load_features_informed(file = NULL, show_example = FALSE)

Arguments

`file`	File
`show_example`	Show example? Default to FALSE

Value

A table of informed features

Examples

NULL
NULL

Load features not informed

Description

Load features not informed

Usage

load_features_not_informed(file = NULL, show_example = FALSE)
load_features_not_informed(file = NULL, show_example = FALSE)

Arguments

`file`	File
`show_example`	Show example? Default to FALSE

Value

A table of non informed features

Examples

NULL
NULL

Load MS data

Description

Load MS data

Usage

load_ms_data(file = NULL, show_example = FALSE)
load_ms_data(file = NULL, show_example = FALSE)

Arguments

`file`	File
`show_example`	Show example? Default to FALSE

Value

MS data

Examples

NULL
NULL

Load name

Description

Load name

Usage

load_name(
  file = NULL,
  default = "210619_AR_06_V_03_2_01.mzML",
  show_example = FALSE
)
load_name(
  file = NULL,
  default = "210619_AR_06_V_03_2_01.mzML",
  show_example = FALSE
)

Arguments

`file`	File
`default`	Default
`show_example`	Show example? Default to FALSE

Value

A name

Examples

NULL
NULL

Make chromatographiable

Description

Make chromatographiable

Usage

make_chromatographiable(
  df,
  mass_min = 50,
  mass_max = 1500,
  logp_min = -1,
  logp_max = 6
)
make_chromatographiable(
  df,
  mass_min = 50,
  mass_max = 1500,
  logp_min = -1,
  logp_max = 6
)

Arguments

`df`	Dataframe
`mass_min`	Mass min
`mass_max`	Mass max
`logp_min`	Log P min
`logp_max`	Log P max

Value

A dataframe containing chromatographiable compounds

Examples

NULL
NULL

Make confident

Description

Make confident

Usage

make_confident(df, score)
make_confident(df, score)

Arguments

`df`	Dataframe
`score`	Score

Value

A dataframe containing annotations with scores above the confidence threshold set

Examples

NULL
NULL

Make no stereo

Description

Make no stereo

Usage

make_no_stereo(df)
make_no_stereo(df)

Arguments

df

Dataframe

Value

A dataframe with no stereo structures

Examples

NULL
NULL

Make other

Description

Make other

Usage

make_other(dataframe, value = "peak_area")
make_other(dataframe, value = "peak_area")

Arguments

`dataframe`	Dataframe
`value`	Value

Value

A dataframe with harmonized "other" subcategories

Examples

NULL
NULL

Middle pts

Description

Middle pts

Usage

middle_pts(x)
middle_pts(x)

Arguments

x

Value

Middle pts

Examples

NULL
NULL

Molinfo

Description

Molinfo

Usage

molinfo(x)
molinfo(x)

Arguments

x

Value

A mol image

Examples

NULL
NULL

No other

Description

No other

Usage

no_other(dataframe)
no_other(dataframe)

Arguments

dataframe

Dataframe

Value

A dataframe with no other

Examples

NULL
NULL

Normalize chromato

Description

Normalize chromato

Usage

normalize_chromato(x, df_xy)
normalize_chromato(x, df_xy)

Arguments

`x`	X
`df_xy`	Df X Y

Value

A normalized chromato

Examples

NULL
NULL

Normalize chromatograms list

Description

Normalize chromatograms list

Usage

normalize_chromatograms_list(
  list,
  shift = 0,
  normalize_intensity = TRUE,
  normalize_time = FALSE
)
normalize_chromatograms_list(
  list,
  shift = 0,
  normalize_intensity = TRUE,
  normalize_time = FALSE
)

Arguments

`list`	List
`shift`	Shift
`normalize_intensity`	Normalize time
`normalize_time`	Normalize intensity

Value

A dataframe with normalized chromatograms

Examples

NULL
NULL

P ACN I

Description

P ACN I

Usage

p_acn_i(acn_eluent, q1, q2, q3)
p_acn_i(acn_eluent, q1, q2, q3)

Arguments

`acn_eluent`	ACN eluent
`q1`	Q1
`q2`	Q2
`q3`	Q3

Value

P ACN I

Examples

NULL
NULL

Peaks progress

Description

Peaks progress

Usage

peaks_progress(df_xy)
peaks_progress(df_xy)

Arguments

df_xy

Df X Y

Value

A list of peaks

Examples

NULL
NULL

Plot chromatogram

Description

Plot chromatogram

Usage

plot_chromatogram(df, text)
plot_chromatogram(df, text)

Arguments

`df`	Dataframe
`text`	Text

Value

A plot of a chromatogram

Examples

NULL
NULL

Plot histograms

Description

Plot histograms

Usage

plot_histograms(dataframe, chromatogram, label, y = "values", xlab = TRUE)
plot_histograms(dataframe, chromatogram, label, y = "values", xlab = TRUE)

Arguments

`dataframe`	Dataframe
`chromatogram`	Chromatogram
`label`	Label
`y`	Y
`xlab`	Xlab

Value

A plot of histograms

Examples

NULL
NULL

Plot histograms confident

Description

Plot histograms confident

Usage

plot_histograms_confident(
  dataframe,
  chromatogram,
  level = "max",
  time_min,
  time_max
)
plot_histograms_confident(
  dataframe,
  chromatogram,
  level = "max",
  time_min,
  time_max
)

Arguments

`dataframe`	Dataframe
`chromatogram`	Chromatogram
`level`	Level
`time_min`	Time min
`time_max`	Time max

Value

A plot of confident histograms

Examples

NULL
NULL

Plot histograms litt

Description

Plot histograms litt

Usage

plot_histograms_litt(dataframe, label, y = "values", xlab = TRUE)
plot_histograms_litt(dataframe, label, y = "values", xlab = TRUE)

Arguments

`dataframe`	Dataframe
`label`	Label
`y`	Y
`xlab`	Xlab

Value

A plot of literature histograms

Examples

NULL
NULL

Plot histograms taxo

Description

Plot histograms taxo

Usage

plot_histograms_taxo(
  dataframe,
  chromatogram,
  level = "max",
  mode = "pos",
  time_min,
  time_max
)
plot_histograms_taxo(
  dataframe,
  chromatogram,
  level = "max",
  mode = "pos",
  time_min,
  time_max
)

Arguments

`dataframe`	Dataframe
`chromatogram`	Chromatogram
`level`	Level
`mode`	Mode
`time_min`	Time min
`time_max`	Time max

Value

A plot of taxo histograms

Examples

NULL
NULL

Plot peak detection

Description

Plot peak detection

Usage

plot_peak_detection(df1, df2, fun)
plot_peak_detection(df1, df2, fun)

Arguments

`df1`	DF 1 containing chromatogram
`df2`	DF 2 containing peaks
`fun`	Fun

Value

A plot with (non-)detected peaks

Examples

NULL
NULL

Plot results 1

Description

Plot results 1

Usage

plot_results_1(list, chromatogram, mode = "pos", time_min, time_max)
plot_results_1(list, chromatogram, mode = "pos", time_min, time_max)

Arguments

`list`	List
`chromatogram`	Chromatogram
`mode`	Mode
`time_min`	Time min
`time_max`	Time max

Value

A list of plots

Examples

NULL
NULL

Plot results 2

Description

Plot results 2

Usage

plot_results_2(list)
plot_results_2(list)

Arguments

list

List

Value

A list of plots

Examples

NULL
NULL

Predict response

Description

Predict response

Usage

predict_response(
  acn = 100,
  peak_area,
  p1q1 = 1e-05,
  p1q2 = -6e-04,
  p1q3 = -0.0778,
  p2q1 = 2e-05,
  p2q2 = -0.00022,
  p2q3 = 0.05499,
  p3q1 = -0.00017,
  p3q2 = 0.0209,
  p3q3 = 1.4041
)
predict_response(
  acn = 100,
  peak_area,
  p1q1 = 1e-05,
  p1q2 = -6e-04,
  p1q3 = -0.0778,
  p2q1 = 2e-05,
  p2q2 = -0.00022,
  p2q3 = 0.05499,
  p3q1 = -0.00017,
  p3q2 = 0.0209,
  p3q3 = 1.4041
)

Arguments

`acn`	ACN
`peak_area`	Peak area
`p1q1`	P1Q1
`p1q2`	P1Q2
`p1q3`	P1Q3
`p2q1`	P2Q1
`p2q2`	P2Q2
`p2q3`	P2Q3
`p3q1`	P3Q1
`p3q2`	P3Q2
`p3q3`	P3Q3

Value

The concentration

Examples

NULL
NULL

Prehistograms progress

Description

Prehistograms progress

Usage

prehistograms_progress(xs)
prehistograms_progress(xs)

Arguments

xs

Value

A list of prehistograms

Examples

NULL
NULL

Prepare comparison

Description

Prepare comparison

Usage

prepare_comparison(
  features_informed = NULL,
  features_not_informed = NULL,
  candidates_confident,
  min_similarity_prefilter = 0.6,
  min_similarity_filter = 0.8,
  mode = "pos",
  show_example = FALSE
)
prepare_comparison(
  features_informed = NULL,
  features_not_informed = NULL,
  candidates_confident,
  min_similarity_prefilter = 0.6,
  min_similarity_filter = 0.8,
  mode = "pos",
  show_example = FALSE
)

Arguments

`features_informed`	Features informed
`features_not_informed`	Features not informed
`candidates_confident`	Candidates confident
`min_similarity_prefilter`	Min similarity pre filter
`min_similarity_filter`	Min similarity filter
`mode`	Mode
`show_example`	Show example? Default to FALSE

Value

A list of peaks

Examples

NULL
NULL

Prepare features

Description

Prepare features

Usage

prepare_features(df, min_intensity, name)
prepare_features(df, min_intensity, name)

Arguments

`df`	Df
`min_intensity`	Min intensity
`name`	Name

Value

A dataframe of prepared features

Examples

NULL
NULL

Prepare hierarchy

Description

Prepare hierarchy

Usage

prepare_hierarchy(
  dataframe,
  type = "analysis",
  detector = "ms",
  rescale = FALSE
)
prepare_hierarchy(
  dataframe,
  type = "analysis",
  detector = "ms",
  rescale = FALSE
)

Arguments

`dataframe`	Dataframe
`type`	Type
`detector`	Detector
`rescale`	Rescale

Value

A dataframe with prepared hierarchy

Examples

NULL
NULL

Prepare mz

Description

Prepare mz

Usage

prepare_mz(x)
prepare_mz(x)

Arguments

x

Value

A list of prepared mz's

Examples

NULL
NULL

Prepare peaks

Description

Prepare peaks

Usage

prepare_peaks(x)
prepare_peaks(x)

Arguments

x

Value

Prepared peaks

Examples

NULL
NULL

Prepare plot

Description

Prepare plot

Usage

prepare_plot(dataframe, organism = "species")
prepare_plot(dataframe, organism = "species")

Arguments

`dataframe`	Dataframe
`organism`	Organism

Value

A dataframe prepared for plots

Examples

NULL
NULL

Prepare plot 2

Description

Prepare plot 2

Usage

prepare_plot_2(dataframe)
prepare_plot_2(dataframe)

Arguments

dataframe

Dataframe

Value

A dataframe prepared for plots

Examples

NULL
NULL

Prepare rt

Description

Prepare rt

Usage

prepare_rt(x, shift = 0)
prepare_rt(x, shift = 0)

Arguments

`x`	X
`shift`	Shift

Value

Prepared RTs

Examples

NULL
NULL

Preprocess chromatograms

Description

Preprocess chromatograms

Usage

preprocess_chromatograms(
  detector = "cad",
  fourier_components = 0.01,
  frequency = 2,
  list,
  name,
  resample = 1,
  shift = 0,
  signal_name = "UV.1_CAD_1_0",
  time_min = 0,
  time_max = Inf
)
preprocess_chromatograms(
  detector = "cad",
  fourier_components = 0.01,
  frequency = 2,
  list,
  name,
  resample = 1,
  shift = 0,
  signal_name = "UV.1_CAD_1_0",
  time_min = 0,
  time_max = Inf
)

Arguments

`detector`	Detector
`fourier_components`	Fourier components
`frequency`	Frequency
`list`	List
`name`	Name
`resample`	Resample
`shift`	Shift
`signal_name`	Signal name
`time_min`	Time min
`time_max`	Time max

Value

A list of preprocessed chromatograms

Examples

NULL
NULL

Preprocess peaks

Description

Preprocess peaks

Usage

preprocess_peaks(
  detector = "cad",
  df_features,
  df_long,
  df_xy,
  name,
  shift = 0,
  min_area = 0
)
preprocess_peaks(
  detector = "cad",
  df_features,
  df_long,
  df_xy,
  name,
  shift = 0,
  min_area = 0
)

Arguments

`detector`	Detector
`df_features`	DF features
`df_long`	DF long
`df_xy`	DF X Y
`name`	Name
`shift`	shift
`min_area`	Minimum area

Value

A list of lists and dataframe with preprocessed peaks

Examples

NULL
NULL

Process compare peaks

Description

Process compare peaks

Usage

process_compare_peaks(
  file = NULL,
  features = NULL,
  type = "baselined",
  detector = "cad",
  export_dir = "data/interim/peaks",
  show_example = FALSE,
  fourier_components = 0.01,
  frequency = 1,
  min_area = 0.005,
  min_intensity = 10000,
  resample = 1,
  shift = 0.05,
  time_min = 0.5,
  time_max = 32.5
)
process_compare_peaks(
  file = NULL,
  features = NULL,
  type = "baselined",
  detector = "cad",
  export_dir = "data/interim/peaks",
  show_example = FALSE,
  fourier_components = 0.01,
  frequency = 1,
  min_area = 0.005,
  min_intensity = 10000,
  resample = 1,
  shift = 0.05,
  time_min = 0.5,
  time_max = 32.5
)

Arguments

`file`	File path
`features`	Features path
`type`	Type. "original", "baselined" or "improved"
`detector`	Detector
`export_dir`	Export directory
`show_example`	Show example? Default to FALSE
`fourier_components`	Fourier components
`frequency`	Frequency
`min_area`	Min area
`min_intensity`	Min intensity
`resample`	Resample
`shift`	Shift
`time_min`	Time min
`time_max`	Time max

Value

A plot with (non-)aligned chromatograms

Examples

## Not run: 
check_chromatograms_alignment(show_example = TRUE)

## End(Not run)
## Not run: 
check_chromatograms_alignment(show_example = TRUE)

## End(Not run)

Queries progress

Description

Queries progress

Usage

queries_progress(
  xs,
  start = "0",
  end = "9999",
  limit = "1000000",
  query_part_1,
  query_part_2,
  query_part_3,
  query_part_4
)
queries_progress(
  xs,
  start = "0",
  end = "9999",
  limit = "1000000",
  query_part_1,
  query_part_2,
  query_part_3,
  query_part_4
)

Arguments

`xs`	XS
`start`	Start
`end`	End
`limit`	Limit
`query_part_1`	query_part_1
`query_part_2`	query_part_2
`query_part_3`	query_part_3
`query_part_4`	query_part_4

Value

A list of queries

Examples

NULL
NULL

Save histograms progress

Description

Save histograms progress

Usage

save_histograms_progress(xs)
save_histograms_progress(xs)

Arguments

xs

Value

Saved histograms

Examples

NULL
NULL

Save treemaps progress

Description

Save treemaps progress

Usage

save_treemaps_progress(xs, type = "treemap")
save_treemaps_progress(xs, type = "treemap")

Arguments

`xs`	XS
`type`	Type

Value

Saved treemaps

Examples

NULL
NULL

Second der

Description

Second der

Usage

second_der(x, y)
second_der(x, y)

Arguments

`x`	X
`y`	Y

Value

The second derivative

Examples

NULL
NULL

Signal sharpening

Description

Signal sharpening

Usage

signal_sharpening(
  time,
  intensity,
  k2 = 250,
  k4 = 1250000,
  sigma = 0.05,
  Smoothing_width = 8,
  Baseline_adjust = 0
)
signal_sharpening(
  time,
  intensity,
  k2 = 250,
  k4 = 1250000,
  sigma = 0.05,
  Smoothing_width = 8,
  Baseline_adjust = 0
)

Arguments

`time`	time
`intensity`	intensity
`k2`	K2
`k4`	K4
`sigma`	Sigma
`Smoothing_width`	Smoothing width
`Baseline_adjust`	Baseline adjust

Value

A sharpened signal

Examples

NULL
NULL

Tables progress

Description

Tables progress

Usage

tables_progress(xs, structures_classified)
tables_progress(xs, structures_classified)

Arguments

`xs`	XS
`structures_classified`	structures classified

Value

A list of tables

Examples

NULL
NULL

Taxon name to QID

Description

Taxon name to QID

Usage

taxon_name_to_qid(taxon_name)
taxon_name_to_qid(taxon_name)

Arguments

taxon_name

Taxon name

Value

A QID

Examples

## Not run: 
taxon_name_to_qid(taxon_name = "Gentiana lutea")

## End(Not run)
## Not run: 
taxon_name_to_qid(taxon_name = "Gentiana lutea")

## End(Not run)

Transform MS

Description

Transform MS

Usage

transform_ms(x)
transform_ms(x)

Arguments

x

Value

A list with transformed MS

Examples

NULL
NULL

Treemaps progress

Description

Treemaps progress

Usage

treemaps_progress(xs, type = "treemap", hierarchies)
treemaps_progress(xs, type = "treemap", hierarchies)

Arguments

`xs`	XS
`type`	Type
`hierarchies`	Hierarchies

Value

A list of treemaps

Examples

NULL
NULL

Treemaps progress no title

Description

Treemaps progress no title

Usage

treemaps_progress_no_title(xs, type = "treemap", hierarchies)
treemaps_progress_no_title(xs, type = "treemap", hierarchies)

Arguments

`xs`	XS
`type`	Type
`hierarchies`	Hierarchies

Value

A list of treemaps with no title

Examples

NULL
NULL

Wiki progress

Description

Wiki progress

Usage

wiki_progress(xs)
wiki_progress(xs)

Arguments

xs

Value

A list of results of Wikidata queries

Examples

NULL
NULL

Y as NA

Description

Y as NA

Usage

y_as_na(x, y)
y_as_na(x, y)

Arguments

`x`	x
`y`	y

Value

Y's replaced as NA's in X

Examples

NULL
NULL

Package 'cascade'

Help Index

Add chromato line

Description

Usage

Arguments

Value

Examples

Baseline chromatogram

Description

Usage

Arguments

Value

Examples

Change intensity name

Description

Usage

Arguments

Value

Examples

Check chromatograms

Description

Usage

Arguments

Value

Examples

Check chromatograms alignment

Description

Usage

Arguments

Value

Examples

Check export dir

Description

Usage

Arguments

Value

Examples

Check chromatograms alignment

Description

Usage

Arguments

Value

Examples

Compare peaks

Description

Usage

Arguments

Value

Examples

Deriv

Description

Usage

Arguments

Value

Examples

Extract chromatogram

Description

Usage

Arguments

Value

Examples

Extract MS peak

Description

Usage

Arguments

Value

Examples

Extract MS progress

Description

Usage

Arguments

Value

Examples

Filter FFT

Description

Usage

Arguments

Value

Examples