Package 'centrifugeR'

Title: Non-Trivial Balance of Centrifuge Rotors
Description: Find the numbers of test tubes that can be balanced in centrifuge rotors and show various ways to load them. Refer to Pham (2020) <doi:10.31224/osf.io/4xs38> for more information on package functionality.
Authors: Duy Nghia Pham [aut, cre]
Maintainer: Duy Nghia Pham <[email protected]>
License: GPL-3
Version: 0.1.8
Built: 2025-02-12 03:10:12 UTC
Source: https://github.com/phamdn/centrifuger

Help Index

centrifugeR: Non-Trivial Balance of Centrifuge Rotors

Description

Find the numbers of test tubes that can be balanced in centrifuge rotors and show various ways to load them. Refer to Pham (2020) doi:10.31224/osf.io/4xs38 for more information on package functionality.

Guidelines

centrifugeR helps obtain the perfect centrifuge balance. Call rotor to know how many tubes can be loaded into the rotor and see different ways to place these tubes. Alternatively, call launch to run the Shiny app. Also, call rotorVerify to verify the balance of pre-existing tube configurations. Call rotorSpeed for RPM/RCF conversion.

Copyright

centrifugeR: Non-Trivial Balance of Centrifuge Rotors. Copyright (C) 2020-2022 Duy Nghia Pham

centrifugeR is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

centrifugeR is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with centrifugeR. If not, see https://www.gnu.org/licenses/.

Author(s)

Duy Nghia Pham [email protected]

Run the Shiny App

Description

Run the Shiny App

Usage

launch()

Convert Hole Positions to Coordinates

Description

p2c returns the coordinates of rotor holes. This is not meant to be called directly.

Usage

p2c(x, y)

Arguments

x

an integer or a vector, the hole position(s).
y

an integer, the number of rotor holes.

Value

p2c returns a vector of coordinates.

Draw a Rotor

Description

pie2 was modified after pie. This is not meant to be called directly.

Usage

pie2(
  x,
  labels = names(x),
  edges = 200,
  radius = 0.8,
  clockwise = FALSE,
  init.angle = if (clockwise) 90 else 0,
  density = NULL,
  angle = 45,
  col = NULL,
  border = NULL,
  lty = NULL,
  main = NULL,
  panel = NULL,
  ...
)

Arguments

x

See pie for more details.
labels

See pie for more details.
edges

See pie for more details.
radius

See pie for more details.
clockwise

See pie for more details.
init.angle

See pie for more details.
density

See pie for more details.
angle

See pie for more details.
col

See pie for more details.
border

See pie for more details.
lty

See pie for more details.
main

See pie for more details.
panel

a letter for labeling panel.
...

See pie for more details.

Value

pie2 returns a figure.

Balance Tubes Using Higher-Order Symmetrical Configurations

Description

rotor returns the numbers of tubes that can and cannot be loaded in a centrifuge rotor and optionally shows various ways to balance a certain number of tubes.

Usage

rotor(n, k = NULL, seed = 1, elapse = 1)

Arguments

n

an integer, the number of rotor holes.
k

an integer, the number of tubes (optional).
seed

an integer, the seed for random number generation. Setting a seed ensures the reproducibility of the result. See set.seed for more details.
elapse

an integer, the constrained time in seconds for random sampling.

Details

The number of rotor holes n ranges from 4 to 48.

Value

rotor returns a list with two components:

check

a list with three components:

n

the number of rotor holes.

valid

a vector containing the numbers of tubes that can be loaded.

invalid

a vector containing the numbers of tubes that cannot be loaded.
load

a list with three components:

k

the number of tubes.

decompose

a data frame showing different ways to decompose k.

hole

a data frame showing hole positions to load tubes.

visual

a list of rotor images showing hole positions to load tubes.

References

Sivek G. On vanishing sums of distinct roots of unity. Integers. 2010;10(3):365-8.

Peil O, Hauryliuk V. A new spin on spinning your samples: balancing rotors in a non-trivial manner. arXiv preprint arXiv:1004.3671. 2010 Apr 21.

See Also

rotorVerify for verifying the balance of pre-existing tube configurations.

Examples

rotor(30, 7)

Check Centrifuge Rotors

Description

rotorCheck returns the numbers of tubes that can and cannot be loaded in a single operation.

Usage

rotorCheck(n, k = NULL)

Arguments

n

an integer, the number of rotor buckets.
k

an integer, the number of tubes.

Details

The number of rotor buckets n ranges from 4 to 48.

If k is specified, rotorCheck will check whether the input number of tubes can be loaded or not.

Value

rotorCheck returns a list with two components:

valid

a vector containing the numbers of tubes that can be loaded.
invalid

a vector containing the numbers of tubes that cannot be loaded.

References

Sivek G. On vanishing sums of distinct roots of unity. Integers. 2010;10(3):365-8.

See Also

rotorEqual for balancing tubes of equal mass and rotorUnequal for balancing tubes of unequal mass.

Balance Tubes of Equal Mass

Description

rotorEqual returns the positions of rotor buckets that must be loaded or empty to balance tubes of equal mass.

Usage

rotorEqual(n, k, seed = 2019)

Arguments

n

an integer, the number of rotor buckets.
k

an integer, the number of tubes.
seed

an integer, the seed for random number generation. Setting a seed ensures the reproducibility of the result. See set.seed for more details.

Details

The number of rotor buckets n ranges from 4 to 48. The number of tubes k must be greater than 0 and smaller than the number of rotor buckets n.

Value

rotorEqual returns a list with two components:

loaded

a vector containing the positions of rotor buckets that must be loaded.
empty

a vector containing the positions of rotor buckets that must be empty.

rotorEqual also plots a schematic diagram of the centrifuge rotor.

References

Sivek G. On vanishing sums of distinct roots of unity. Integers. 2010;10(3):365-8.

Peil O, Hauryliuk V. A new spin on spinning your samples: balancing rotors in a non-trivial manner. arXiv preprint arXiv:1004.3671. 2010 Apr 21.

See Also

rotorCheck for checking centrifuge rotors and rotorUnequal for balancing tubes of unequal mass.

Calculate RPM/RCF

Description

rotorSpeed converts rotational speed to relative centrifuge force and vice versa.

Usage

rotorSpeed(radius, value, type)

Arguments

radius

a numeric, the centrifugal radius in millimeters.
value

a numeric, the rotational speed in revolutions per minute or the relative centrifuge force in × g.
type

the type of the above-mentioned value, "rpm" for rotational speed or "rcf" for relative centrifuge force.

Value

rotorSpeed returns a numeric that is the rotational speed in revolutions per minute or the relative centrifuge force in × g.

References

Rickwood D, editor. Centrifugation: a practical approach. London: Information Retrieval Ltd; 1978. 224 p.

Examples

rotorSpeed(100, 12000, "rpm")
rotorSpeed(100, 6000, "rcf")

Balance Tubes of Unequal Mass

Description

rotorUnequal returns the required masses and the positions of tubes of unequal initial mass.

Usage

rotorUnequal(n, mass = NULL, seed = 2019)

Arguments

n

an integer, the number of rotor buckets.
mass

a numeric vector with optional names attribute, the masses (and optional names) of tubes.
seed

an integer, the seed for random number generation. Setting a seed ensures the reproducibility of the result. See set.seed for more details.

Details

The number of rotor buckets n ranges from 4 to 48. The number of tubes (i.e. length(mass)) should not be greater than the number of rotor buckets n.

If mass is not specified, the names and the masses of tubes must then be taken from the keyboard. In case mass has no names attribute, tubes will be named automatically (i.e. S1, S2, S3, etc.).

Value

rotorUnequal returns a data frame with three columns:

initial

a vector containing the initial masses of tubes.
required

a vector containing the required masses of tubes.
position

a vector containing the bucket positions of tubes.

rotorUnequal also plots a schematic diagram of the centrifuge rotor.

References

Sivek G. On vanishing sums of distinct roots of unity. Integers. 2010;10(3):365-8.

Peil O, Hauryliuk V. A new spin on spinning your samples: balancing rotors in a non-trivial manner. arXiv preprint arXiv:1004.3671. 2010 Apr 21.

See Also

rotorCheck for checking centrifuge rotors and rotorEqual for balancing tubes of equal mass.

Examples

# Call the function then input the names and the masses of tubes
rotorUnequal(30)
liver
10.05
gill
9.68
muscle
9.88

# Prepare the masses of tubes then call the function
samples <- round(rnorm(19, mean = 10, sd = 0.5), 2)
rotorUnequal(30, samples)

# Prepare the masses and the names of tubes then call the function
small.samples <- c(10.05, 9.68, 9.88)
names(small.samples) <- c("liver", "gill", "muscle")
rotorUnequal(30, small.samples)

Verify Centrifuge Balance

Description

rotorVerify checks whether the rotor is balanced given the positions of tubes of equal mass.

Usage

rotorVerify(n, pos)

Arguments

n

an integer, the number of rotor buckets.
pos

an integer vector, the positions of tubes.

Details

The number of rotor buckets n ranges from 4 to 48. The positions of tubes pos ranges from 1 to n.

Value

rotorVerify returns 1 if the rotor is balanced and 0 if the rotor is unbalanced.

References

Johnsson M. Balancing a centrifuge. R-bloggers. 2016. Available from: https://www.r-bloggers.com/2016/06/balancing-a-centrifuge/.

See Also

rotorCheck for checking centrifuge rotors.

Examples

rotorVerify(30, c(10, 20, 30))
rotorVerify(30, c(1, 11, 21, 4, 28))