Description Usage Arguments Details Value Warnings References See Also Examples

`apc`

calculates the Aerobic Plate Count (*APC*) point estimate
and confidence interval of colony forming units (CFU). Adjusts for
too-numerous-to-count (TNTC) plates using the maximum likelihood method of
Haas et al. (2014).

1 2 |

`count` |
A vector of CFU counts in each scorable (countable) plate. |

`amount_scor` |
A vector of inoculum amounts (in ml) in each scorable
plate. See |

`amount_tntc` |
A vector of inoculum amounts (in ml) in each TNTC plate. |

`tntc_limit` |
A vector (or scalar) of the limit above which the plate counts are considered too-numerous-to-count (often 100, 250, or 300). Each plate can potentially have a different value. Default is 250. |

`conf_level` |
A scalar value between zero and one for the confidence level. Typically 0.95 (i.e., a 95 percent confidence interval). |

As an example, assume we start with four plates and 1 ml of
undiluted inoculum. For the first two plates we use a 100-fold dilution;
for the other two plates we use a 1,000-fold dilution. The first two plates
were TNTC with limits of 300 and 250. The other plates had CFU counts of
28 and 20. We now have
`count = c(28, 20)`

,
`amount_scor = 1 * c(.001, .001)`

,
`amount_tntc = 1 * c(.01, .01)`

, and
`tntc_limit = c(300, 250)`

.

Currently, confidence intervals can only be calculated using the likelihood ratio (LR) approach described in Haas et al. (2014).

A list containing:

**APC**: The aerobic plate count point estimate in CFU/ml.**conf_level**: The confidence level used.**LB**: The lower bound of the confidence interval.**UB**: The upper bound of the confidence interval.

The likelihood ratio confidence interval assumptions depend on asymptotic theory. Therefore, the confidence interval results will be better with larger experiments.

`apc()`

will fail in certain cases where the TNTC results are
extremely unlikely to occur when taking the scorable (countable) plates
into consideration. In other words, if the countable plates suggest a low
concentration of microbes, then TNTC plates at higher dilution levels are
probably due to experimental error. Mathematically, the probability is so
small that the likelihood function is essentially zero.

Bacteriological Analytical Manual, 8th Edition, Chapter 3, https://www.fda.gov/food/foodscienceresearch/laboratorymethods/ucm063346.htm

Haas CN, Heller B (1988). "Averaging of TNTC counts."
*Applied and Environmental Microbiology*, 54(8), 2069-2072.
https://aem.asm.org/content/54/8/2069

Haas CN, Rose JB, Gerba CP (2014). "Quantitative microbial risk
assessment, Second Ed." *John Wiley & Sons, Inc.*,
ISBN 978-1-118-14529-6.

`mpn`

for Most Probable Number

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | ```
#------- "Quantitative Microbial Risk Assessment (Haas et al., 2014) --------
# Table 6.1 (Sample A)
my_count <- c(1, 2, 1, 0, 0, 1, 1, 3, 6, 8, 4)
my_amount_scor <- c(1, 1, 1, 1, 1, 2.5, 2.5, 2.5, 2.5, 5, 5)
apc(my_count, my_amount_scor) #1.08
# Table 6.1 (Sample B)
my_count <- c(1, 0, 5, 1, 0, 5, 0, 1, 5, 1, 8)
my_amount_scor <- c(1, 1, 1, 1, 1, 2.5, 2.5, 2.5, 2.5, 5, 5)
apc(my_count, my_amount_scor) #1.08
# Table 6.2
my_count <- c(12, 8, 15, 40, 58)
my_amount_scor <- c(1, 1, 1, 10, 10)
my_amount_tntc <- c(10, 100, 100, 100)
my_tntc_limit <- 100
apc(my_count, my_amount_scor, my_amount_tntc, my_tntc_limit) #~7 (6.03, 7.96)
#----------- "Averaging of TNTC Counts" (Haas & Heller, 1988) ---------------
# Note:
# Results are slightly different due mostly to differences in how the TNTC
# portion of the likelihood function is formulated (i.e., incomplete gamma
# function vs. infinite Poisson sum--see Haas et al. (2014) for details of
# this mathematical relationship).
my_count <- c(10, 12, 23, 48, 63)
my_amount_scor <- c(1, 1, 1, 5, 5)
my_amount_tntc <- c(5, 10, 10)
my_tntc_limit <- 80
apc(my_count, my_amount_scor, my_amount_tntc, my_tntc_limit)
#Haas & Heller: APC = 13.28 CFU/ml
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.