Function reference • gcplyr

Reading files

Functions for reading files into R

read_blocks(): Read blockmeasures

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 caret::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

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