Number of Cells at Time t

Description

This function gives the number of cells or absorbance (N) at time t when the parameters to the logistic equation are K, N0, and r.

Usage

NAtT(k, n0, r, t)

Arguments

Value

The number of cells, or N, at time t

Summarize Growth Curves

Description

This function finds the parameters that describe the input data's growth. It does so by fitting the logistic curve to your growth curve measurements.

Usage

SummarizeGrowth(data_t, data_n, t_trim = 0, bg_correct = "min", blank = NA)

Arguments

Details

The logistic curve equation is

N_t = \frac{N_0 K} {N_0 + (K-N_0)e^{-rt}}

where N_t is the number of cells (or the absorbance reading) at time t, N_0 is the initial cell count (or absorbance reading), K is the carrying capacity, and r is the growth rate.

The fitness proxies returned are the parameters of the logistic equation and the area under the curve (a measure that integrates the effects of N_0, K, and r). See gcfit for more documentation on these.

Value

An object of type gcfit containing the "fitness" proxies, as well as the input data and the fitted model.

See Also

See the accompanying Vignette for an example of how to use and interpret SummarizeGrowth. https://CRAN.R-project.org/package=growthcurver/vignettes/Growthcurver-vignette.html.

See also gcfit.

Examples

# We can check that the parameters that are found are the same
# as we use to generate fake experimental data. To do so, let's first
# generate the "experimental" data using the logistic equation,
# e.g., absorbance readings from a single well in a plate reader over time.

k_in <- 0.5   # the initial carrying capacity
n0_in <- 1e-5 # the initial absorbance reading
r_in <- 1.2   # the initial growth rate
N <- 50       # the number of "measurements" collected during the growth
              # curve experiment

data_t <- 0:N * 24 / N   # the times the measurements were made (in hours)
data_n <- NAtT(k = k_in, n0 = n0_in, r = r_in, t = data_t) # the measurements

# Now summarize the "experimental" growth data that we just generated
gc <- SummarizeGrowth(data_t, data_n)

# Get the possible metrics for fitness proxies
gc$vals$r           # growth rate is a common choice for fitness
gc$vals$t_gen       # doubling time, or generation time, is also common
gc$vals$k
gc$vals$n0
gc$vals$auc_l
gc$vals$auc_e
gc$vals$t_mid

# Compare the data with the fit visually by plotting it
plot(gc)

Summarize Growth Curves

Description

This function finds the parameters that describe the input data's growth for a plate of growth curves. It does so by fitting the logistic curve to your growth curve measurements.

Usage

SummarizeGrowthByPlate(
  plate,
  t_trim = 0,
  bg_correct = "min",
  plot_fit = FALSE,
  plot_file = "growthcurver.pdf"
)

Arguments

Details

The logistic curve equation is

N_t = \frac{N_0 K} {N_0 + (K-N_0)e^{-rt}}

where N_t is the number of cells (or the absorbance reading) at time t, N_0 is the initial cell count (or absorbance reading), K is the carrying capacity, and r is the growth rate.

The fitness proxies returned are the parameters of the logistic equation and the area under the curve (a measure that integrates the effects of N_0, K, and r). See gcfit for more documentation on these.

This method expects that your data adhere to a particular format.

• The data are provided in a data.frame

• One column in the data.frame is named "time" and contains the time measurements (e.g., hours).

• Each remaining column contains the readings from a single well in a plate reader. The name of the column will be used to identify the sample in the output data.

• There are no missing values or non-numeric data in the data.frame.

Value

A data.table containing the summary metrics and residual error from the fit of the logistic curve to the data. The names of the input columns are used to identify each well (or sample).

See Also

See the accompanying Vignette for an example of how to use and interpret SummarizeGrowthByPlate. https://CRAN.R-project.org/package=growthcurver/vignettes/Growthcurver-vignette.html

Examples

#Get the summary metrics for the entire plate of sample data provided
#with the Growthcurver package

#First, load the example data provided with Growthcurver. Note that there is
#a column named "time" -- this is necessary for Growthcurver to know which
#column contains the time measurements. In this dataset, the repeated
#measurements from a single well in a plate are given in a column of data.

myPlate <- growthdata
names(myPlate)

#Next, do the analysis for all the columns.
summary_plate <- SummarizeGrowthByPlate(plate = myPlate)

#The output is a data frame that contains the information on the best
#fit for each column of data.
head(summary_plate)      # Use head to display just the first few rows

Creates an object of class gcfit.

Description

This is a constructor function for the "gcfit" class. This class is most often obtained as the return value when calling SummarizeGrowth.

Usage

gcfit(gc_vals, log_mod, data_t, data_n)

Arguments

Value

An object of class gcfit, which is a list of three objects, that combines the parameters (vals = gc_vals, model = log_mod, data = list(data_t, data_n))

Creates an object of type gcvals.

Description

Constructor function for the "gcvals" class. This object is most often obtained when calling SummarizeGrowth (it is the first parameter in the gcvals object).

Usage

gcvals(
  k,
  k_se,
  k_p,
  n0,
  n0_se,
  n0_p,
  r,
  r_se,
  r_p,
  sigma,
  df,
  t_mid,
  dt,
  auc_l,
  auc_e,
  note
)

Arguments

Value

An object of class gcvals.

Simulated growth curve data

Description

A dataset containing absorbance measurements over time of microbes growing in a plate reader for 1 day. The growth curves for a whole plate are included.

Usage

growthdata

Format

A data frame with 145 observations and 97 variables:

time

time, in hours

A1

absorbance readings of well A1

A2

absorbance readings of well A2

A3

absorbance readings of well A3

A4

absorbance readings of well A4

A5

absorbance readings of well A5

A6

absorbance readings of well A6

A7

absorbance readings of well A7

A8

absorbance readings of well A8

A9

absorbance readings of well A9

A10

absorbance readings of well A10

A11

absorbance readings of well A11

A12

absorbance readings of well A12

B1

absorbance readings of well B1

B2

absorbance readings of well B2

B3

absorbance readings of well B3

B4

absorbance readings of well B4

B5

absorbance readings of well B5

B6

absorbance readings of well B6

B7

absorbance readings of well B7

B8

absorbance readings of well B8

B9

absorbance readings of well B9

B10

absorbance readings of well B10

B11

absorbance readings of well B11

B12

absorbance readings of well B12

C1

absorbance readings of well C1

C2

absorbance readings of well C2

C3

absorbance readings of well C3

C4

absorbance readings of well C4

C5

absorbance readings of well C5

C6

absorbance readings of well C6

C7

absorbance readings of well C7

C8

absorbance readings of well C8

C9

absorbance readings of well C9

C10

absorbance readings of well C10

C11

absorbance readings of well C11

C12

absorbance readings of well C12

D1

absorbance readings of well D1

D2

absorbance readings of well D2

D3

absorbance readings of well D3

D4

absorbance readings of well D4

D5

absorbance readings of well D5

D6

absorbance readings of well D6

D7

absorbance readings of well D7

D8

absorbance readings of well D8

D9

absorbance readings of well D9

D10

absorbance readings of well D10

D11

absorbance readings of well D11

D12

absorbance readings of well D12

E1

absorbance readings of well E1

E2

absorbance readings of well E2

E3

absorbance readings of well E3

E4

absorbance readings of well E4

E5

absorbance readings of well E5

E6

absorbance readings of well E6

E7

absorbance readings of well E7

E8

absorbance readings of well E8

E9

absorbance readings of well E9

E10

absorbance readings of well E10

E11

absorbance readings of well E11

E12

absorbance readings of well E12

F1

absorbance readings of well F1

F2

absorbance readings of well F2

F3

absorbance readings of well F3

F4

absorbance readings of well F4

F5

absorbance readings of well F5

F6

absorbance readings of well F6

F7

absorbance readings of well F7

F8

absorbance readings of well F8

F9

absorbance readings of well F9

F10

absorbance readings of well F10

F11

absorbance readings of well F11

F12

absorbance readings of well F12

G1

absorbance readings of well G1

G2

absorbance readings of well G2

G3

absorbance readings of well G3

G4

absorbance readings of well G4

G5

absorbance readings of well G5

G6

absorbance readings of well G6

G7

absorbance readings of well G7

G8

absorbance readings of well G8

G9

absorbance readings of well G9

G10

absorbance readings of well G10

G11

absorbance readings of well G11

G12

absorbance readings of well G12

H1

absorbance readings of well H1

H2

absorbance readings of well H2

H3

absorbance readings of well H3

H4

absorbance readings of well H4

H5

absorbance readings of well H5

H6

absorbance readings of well H6

H7

absorbance readings of well H7

H8

absorbance readings of well H8

H9

absorbance readings of well H9

H10

absorbance readings of well H10

H11

absorbance readings of well H11

H12

absorbance readings of well H12