Package: gcplyr 1.10.0

gcplyr: Wrangle and Analyze Growth Curve Data

Easy wrangling and model-free analysis of microbial growth curve data, as commonly output by plate readers. Tools for reshaping common plate reader outputs into 'tidy' formats and merging them with design information, making data easy to work with using 'gcplyr' and other packages. Also streamlines common growth curve processing steps, like smoothing and calculating derivatives, and facilitates model-free characterization and analysis of growth data. See methods at <https://mikeblazanin.github.io/gcplyr/>.

Authors:Mike Blazanin [aut, cre]

gcplyr_1.10.0.tar.gz
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gcplyr.pdf |gcplyr.html✨
gcplyr/json (API)
NEWS

# Install 'gcplyr' in R:
install.packages('gcplyr', repos = c('https://mikeblazanin.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mikeblazanin/gcplyr/issues

Datasets:
  • 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_widedata - Example noisy growth curve data in wide format
  • example_widedata_noiseless - Example growth curve data in wide format

On CRAN:

dplyrggplot2tidyverse

8.20 score 30 stars 76 scripts 385 downloads 49 exports 21 dependencies

Last updated 4 months agofrom:498b415359. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-winOKNov 06 2024
R-4.5-linuxOKNov 06 2024
R-4.4-winOKNov 06 2024
R-4.4-macOKNov 06 2024
R-4.3-winOKNov 06 2024
R-4.3-macOKNov 06 2024

Exports:aucblock_tidydesigncalc_derivcentroidcentroid_bothcentroid_xcentroid_ydoubling_timeextr_valfind_local_extremafind_threshold_crossesfirst_abovefirst_belowfirst_maximafirst_minimafirst_peakfrom_excelgc_smooth.splineimport_blockdesignsimport_blockmeasureslag_timemake_designmake_designpatternmake_examplemake_tidydesignmakemethod_train_smooth_datamax_gcmdpmerge_dfsmin_gcmoving_averagemoving_medianpaste_blockspredict_interpolationprint_dfread_blocksread_tidysread_widesseparate_tidysmooth_datasolve_linearto_exceltrain_smooth_datatrans_block_to_widetrans_wide_to_tidyuninterleavewhich_max_gcwhich_min_gcwrite_blocks

Dependencies:clicpp11dplyrfansigenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselectutf8vctrswithr

Analyzing data

Mike Blazanin

Rendered fromgc06_analyze.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-07-09
Started: 2023-11-03

Best practices and other tips

Mike Blazanin

Rendered fromgc08_conclusion.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-07-09
Started: 2023-11-03

Dealing with noise

Mike Blazanin

Rendered fromgc07_noise.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-03-10
Started: 2023-11-03

Importing and reshaping data

Mike Blazanin

Rendered fromgc02_import_reshape.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-03-09
Started: 2024-01-29

Incorporating experimental designs

Mike Blazanin

Rendered fromgc03_incorporate_designs.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-03-10
Started: 2023-11-03

Introduction to using gcplyr

Mike Blazanin

Rendered fromgc01_gcplyr.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-03-10
Started: 2023-11-03

Pre-processing and plotting data

Mike Blazanin

Rendered fromgc04_preprocess_plot.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-03-10
Started: 2023-11-03

Processing data

Mike Blazanin

Rendered fromgc05_process.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-03-09
Started: 2023-11-03

Using make_design to generate experimental designs

Mike Blazanin

Rendered fromgc10_using_make_design.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-03-09
Started: 2024-03-08

Working with multiple plates

Mike Blazanin

Rendered fromgc09_multiple_plates.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-07-09
Started: 2023-11-03

Readme and manuals

Help Manual

Help pageTopics
Calculate area under the curveauc
Turn tidydesign into block formatblock_tidydesign
Calculate derivatives of vector of datacalc_deriv
Calculate centroidcentroid CentroidFunctions centroid_both centroid_x centroid_y
Calculate doubling time equivalent of per-capita growth ratedoubling_time
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_design_tidy
Example noisy growth curve data in wide formatexample_widedata
Example growth curve data in wide formatexample_widedata_noiseless
Extract parts of an objectextr_val
Find local extrema of a numeric vectorExtremaFunctions find_local_extrema first_maxima first_minima
Find the first local maxima of a numeric vectorfirst_peak
A function that converts base-26 Excel-style letters to numbersfrom_excel
Fit a Smoothing Splinegc_smooth.spline
Import blockdesignsimport_blockdesigns
Import blockmeasuresimport_blockmeasures
Calculate lag timelag_time
Make design data.frame(s)make_design
Make design patternmake_designpattern mdp
Create R objects or files as seen in vignette examplesmake_example
Make tidy design data.framesmake_tidydesign
Create method argument for train of growth curve smoothersmakemethod_train_smooth_data
Collapse a list of dataframes, or merge two dataframes togethermerge_dfs
Maxima and Minimamax_gc MinMaxGC min_gc
Moving window smoothingMovingWindowFunctions moving_average moving_median
Paste a list of blocks into a single blockpaste_blocks
Predict data by linear interpolation from existing datapredict_interpolation
Nicely print the contents of a data.frameprint_df
Read blocksread_blocks
Read tidy-shaped filesread_tidys
Read widesread_wides
Separate a column into multiple columnsseparate_tidy
Smooth datasmooth_data
Return missing information about a linesolve_linear
Find point(s) when a numeric vector crosses some thresholdfind_threshold_crosses first_above first_below ThresholdFunctions
A function that converts numbers into base-26 Excel-style lettersto_excel
Test efficacy of different smoothing parameterstrain_smooth_data
Transform blocks to widestrans_block_to_wide
Pivot widemeasures longertrans_wide_to_tidy
Uninterleave listuninterleave
Where is the Min() or Max() or first TRUE or FALSE?WhichMinMaxGC which_max_gc which_min_gc
Write block designs to csvwrite_blocks