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Reading files

Functions for reading files into R

read_blocks()
Read blocks
read_wides()
Read wides
read_tidys()
Read tidy-shaped files

Importing files

Wrapper functions that read and transform data

import_blockmeasures()
Import blockmeasures
import_blockdesigns()
Import blockdesigns

Creating designs

Functions to facilitate generating designs

make_design()
Make design data.frame(s)
make_designpattern() mdp()
Make design pattern
write_blocks()
Write block designs to csv

Manipulating data in R

Functions that transform, manipulate, or reshape data

trans_block_to_wide()
Transform blocks to wides
trans_wide_to_tidy()
Pivot widemeasures longer
merge_dfs()
Collapse a list of dataframes, or merge two dataframes together
paste_blocks()
Paste a list of blocks into a single block
separate_tidy()
Separate a column into multiple columns

Processing growth curve data

Functions to smooth or calculate derivatives of growth curve data

smooth_data()
Smooth data
moving_average() moving_median()
Moving window smoothing
calc_deriv()
Calculate derivatives of vector of data
gc_smooth.spline()
Fit a Smoothing Spline
train_smooth_data()
Test efficacy of different smoothing parameters
makemethod_train_smooth_data()
Create method argument for train of growth curve smoothers
predict_interpolation()
Predict data by linear interpolation from existing data

Analyzing growth curve data

Functions to analyze growth curve data by summarizing into metrics

find_local_extrema() first_maxima() first_minima()
Find local extrema of a numeric vector
find_threshold_crosses() first_below() first_above()
Find point(s) when a numeric vector crosses some threshold
auc()
Calculate area under the curve
doubling_time()
Calculate doubling time equivalent of per-capita growth rate
lag_time()
Calculate lag time
centroid() centroid_x() centroid_y() centroid_both()
Calculate centroid

Utility functions

Various functions providing simple utilities

uninterleave()
Uninterleave list
to_excel()
A function that converts numbers into base-26 Excel-style letters
from_excel()
A function that converts base-26 Excel-style letters to numbers
solve_linear()
Return missing information about a line
max_gc() min_gc()
Maxima and Minima
which_min_gc() which_max_gc()
Where is the Min() or Max() or first TRUE or FALSE?
extr_val()
Extract parts of an object
print_df()
Nicely print the contents of a data.frame

Example data

Example wide-shaped data.frames of growth curves data

example_widedata
Example noisy growth curve data in wide format
example_widedata_noiseless
Example growth curve data in wide format
example_design_tidy
Design for example growth curve data A tidy-shaped dataset with the experimental design (i.e. plate layout) for the example data included with gcplyr.

Example function

Function to generate files or objects seen in documentation examples

make_example()
Create R objects or files as seen in vignette examples

Legacy functions

These functions have been deprecated

first_peak()
Find the first local maxima of a numeric vector
make_tidydesign()
Make tidy design data.frames
block_tidydesign()
Turn tidydesign into block format