Import, Process, Analyse, and Calculate Rates from Respirometry Data
Function for calc_rate with replicate number in summary
Automatically calculate rolling window
Omit NA, NaN, Inf and -Inf from a vector or dataframe columns
Plot convert_rate.ft objects
Plot convert_rate objects
Plot inspect.ft objects
Plot inspect objects
Plot oxy_crit objects
Plot output of test_lin
Print adjust_rate.ft objects
Print adjust_rate objects
Print auto_rate.int objects
Print auto_rate objects
Print calc_rate.bg objects
Print calc_rate.ft objects
Print calc_rate.int objects
Print calc_rate objects
Print convert_DO objects
Print convert_rate.ft objects
Print convert_rate objects
Print inspect.ft objects
Print inspect objects
Print oxy_crit objects
Prints the density object for summary.auto_rate S3 Basically copied fr...
Perform regular rolling regression
Perform rolling regression based on time units.
Select columns
Select rate results based on a range of criteria
Randomly generate data for internal testing of auto_rate()'s linear ...
Normal rolling regression
Checks if an oxygen concentration/pressure unit or metabolic rate unit...
Returns an error message if an oxygen concentration/pressure unit or m...
Average calc_rate.ft object rates
Average calc_rate.int object rates
Average calc_rate object rates
Average convert_DO object values
Average convert_rate.ft object rates
Average convert_rate object rates
Average inspect.ft object rates
Average inspect object rates
Average oxy_crit object rates
Validate adjust_rate or auto_rate or oxy_crit method input
Get midpoint between two values or within a vector For getting midpoin...
Summarise inspect.ft objects
Summarise inspect objects
Summarise oxy_crit objects
Adjust rates in flowthrough respirometry to account for background res...
Adjust rates to account for background respiration or oxygen flux.
Convert between multipliers of the same unit, e.g. mg to kg
Convert between multipliers of the same AREA unit, e.g. mm2 to km2
Run auto_rate on multiple replicates in intermittent-flow respirometry...
Automatically determine most linear, highest, lowest and rolling oxyge...
Identify decimal character For European formatted files with commas as...
Pipe graphics direct from tidyverse-related package
Import respirometry system raw data files (DEPRECATED)
Explore and visualise flowthrough respirometry data and check for erro...
Explore and visualise respirometry data and check for common errors
Kernel density function
Perform a linear regression on a data frame
Average adjust_rate.ft rates
Average adjust_rate object rates
Average auto_rate.int object rates
Average auto_rate object rates
Average calc_rate.bg object rates
Function for auto_rate with replicate number in summary plus limit to ...
Perform rolling regression and rank from ABSOLUTE highest to lowest
Obtain rate values at non-overlapping intervals of a dataset
Linear detection method
Perform rolling regression and rank from ABSOLUTE lowest to highest
Perform rolling regression and rank from NUMERICAL maximum to minimum ...
Perform rolling regression and rank from NUMERICAL minimum to maximum ...
Perform rolling regression of fixed width and do not reorder results
Perform broken-stick regressions
Calculate background oxygen uptake or input rates
Calculate rate of change in oxygen from flowthrough respirometry data
Extract rates from multiple replicates in intermittent-flow respiromet...
Calculate rate of change in oxygen over time
Validates acceptable classes of inputs Set single or multiple inputs t...
Convert between units of dissolved oxygen
Convert between units of absolute, mass-specific, or area-specific met...
Print results of convert_MR
Convert a unitless oxygen rate value from flowthrough respirometry to ...
Convert a unitless oxygen rate value to absolute, mass-specific or are...
Convert values of temperature, volume, mass, area, and atmospheric pre...
Extract row, time and DO indices from a subset dataframe
Extracts time and volume units from flowrate unit already parsed by un...
Parse date-time data to numeric time for use in respR functions
Generate a DO ~ PO2 data table from a DO timeseries
Plot convert_rate.ft summary tables
Plot convert_rate and auto_rate summary tables
Calculate critical oxygen values, such as PCrit
Plot adjust_rate.ft objects
Plot adjust_rate objects
Plot auto_rate.int objects
Plot auto_rate objects
Plot calc_rate.bg objects
Plot calc_rate.ft objects
Plot calc_rate.int objects
Plot calc_rate objects
Plot convert_DO objects
Subsample a data frame object
Subset a data.frame, inspect, or inspect.ft object
Summarise adjust_rate.ft objects
Summarise adjust_rate objects
Summarise auto_rate.int objects
Summarise auto_rate objects
Summarise calc_rate.bg objects
Summarise calc_rate.ft objects
Summarise calc_rate.int objects
Summarise calc_rate objects
Summarise convert_DO objects
Summarise convert_rate.ft objects
Summarise convert_rate objects
Perform auto_rate() iteratively and extract performance metrics
Subset data by time and perform a linear regression.
Perform time-width rolling regression
Print examples of unit inputs
Search for and classify units
Search for and classify oxygen units as used in concentration or rates
Cleans units from units.val to remove the suffix (.o2, .flow, etc)
Check unit string against allowed values. See util_fns.R file for rege...
Validation function for auto_rate
Provides a structural, reproducible workflow for the processing and analysis of respirometry data. It contains analytical functions and utilities for working with oxygen time-series to determine respiration or oxygen production rates, and to make it easier to report and share analyses. See Harianto et al. 2019 <doi:10.1111/2041-210X.13162>.
Useful links