get_growth_fit_for_plot computes a vector of
the fit of the growth data, for comparison against the
OD data.R/estimate_growth_rate.R
get_growth_fit_for_plot.RdGrowth fit for plotting
get_growth_fit_for_plot computes a vector of
the fit of the growth data, for comparison against the
OD data.
get_growth_fit_for_plot( OD_data, t_col = "time", growth_fit, blank_tf = T, verbose = T )
| OD_data | Dataframe of OD data. Expects a column for the time (t_col), and will interpret all other columns as OD data for different samples (identified by their column name). |
|---|---|
| t_col | Name of the time column (defaults to 'time'). |
| growth_fit | Output of estimate_growth_rate for the OD_data; requires columns name, carrying_cap, growth_rate, N0, t_min, t_stat |
| blank_tf | Boolean. Should a blank value be subtracted? |
| verbose | Boolean. Should warnings be returned? |
Simulated log growth matching the input fits.
Other growth rate functions:
.logist(),
estimate_growth_rate()
growth_fit <- estimate_growth_rate(growth_example, t_start = 1, t_col = 'Time_h') get_growth_fit_for_plot(growth_example, t_col = 'Time_h', growth_fit)#> ID time OD #> 1 Donor_OD 0.0000000 0.007447194 #> 2 Donor_OD 0.3243243 0.007447194 #> 3 Donor_OD 0.6486486 0.007447194 #> 4 Donor_OD 0.9729730 0.007447194 #> 5 Donor_OD 1.2972973 0.089975804 #> 6 Donor_OD 1.6216216 0.099680837 #> 7 Donor_OD 1.9459459 0.109964026 #> 8 Donor_OD 2.2702703 0.120737926 #> 9 Donor_OD 2.5945946 0.131893726 #> 10 Donor_OD 2.9189189 0.143304912 #> 11 Donor_OD 3.2432432 0.154832612 #> 12 Donor_OD 3.5675676 0.166332174 #> 13 Donor_OD 3.8918919 0.177660352 #> 14 Donor_OD 4.2162162 0.188682335 #> 15 Donor_OD 4.5405405 0.199277920 #> 16 Donor_OD 4.8648649 0.209346238 #> 17 Donor_OD 5.1891892 0.218808714 #> 18 Donor_OD 5.5135135 0.227610180 #> 19 Donor_OD 5.8378378 0.235718299 #> 20 Donor_OD 6.1621622 0.243121652 #> 21 Donor_OD 6.4864865 0.249826886 #> 22 Donor_OD 6.8108108 0.255855360 #> 23 Donor_OD 7.1351351 0.261239669 #> 24 Donor_OD 7.4594595 0.266020328 #> 25 Donor_OD 7.7837838 0.270242804 #> 26 Donor_OD 8.1081081 0.273955026 #> 27 Donor_OD 8.4324324 0.277205379 #> 28 Donor_OD 8.7567568 0.280041188 #> 29 Donor_OD 9.0810811 0.282507629 #> 30 Donor_OD 9.4054054 0.284647006 #> 31 Donor_OD 9.7297297 0.286498334 #> 32 Donor_OD 10.0540540 0.288097138 #> 33 Donor_OD 10.3783784 0.289475440 #> 34 Donor_OD 10.7027027 0.290661851 #> 35 Donor_OD 11.0270270 0.291681756 #> 36 Donor_OD 11.3513513 0.292557540 #> 37 Donor_OD 11.6756757 0.293308845 #> 38 Donor_OD 12.0000000 0.293952831 #> 39 Recipient_OD 0.0000000 0.007447194 #> 40 Recipient_OD 0.3243243 0.007447194 #> 41 Recipient_OD 0.6486486 0.007447194 #> 42 Recipient_OD 0.9729730 0.007447194 #> 43 Recipient_OD 1.2972973 0.045261797 #> 44 Recipient_OD 1.6216216 0.063389175 #> 45 Recipient_OD 1.9459459 0.084765392 #> 46 Recipient_OD 2.2702703 0.106621052 #> 47 Recipient_OD 2.5945946 0.125938110 #> 48 Recipient_OD 2.9189189 0.140933361 #> 49 Recipient_OD 3.2432432 0.151443115 #> 50 Recipient_OD 3.5675676 0.158292669 #> 51 Recipient_OD 3.8918919 0.162547663 #> 52 Recipient_OD 4.2162162 0.165112601 #> 53 Recipient_OD 4.5405405 0.166630824 #> 54 Recipient_OD 4.8648649 0.167519800 #> 55 Recipient_OD 5.1891892 0.168037030 #> 56 Recipient_OD 5.5135135 0.168336855 #> 57 Recipient_OD 5.8378378 0.168510284 #> 58 Recipient_OD 6.1621622 0.168610475 #> 59 Recipient_OD 6.4864865 0.168668316 #> 60 Recipient_OD 6.8108108 0.168701693 #> 61 Recipient_OD 7.1351351 0.168720949 #> 62 Recipient_OD 7.4594595 0.168732057 #> 63 Recipient_OD 7.7837838 0.168738463 #> 64 Recipient_OD 8.1081081 0.168742159 #> 65 Recipient_OD 8.4324324 0.168744290 #> 66 Recipient_OD 8.7567568 0.168745519 #> 67 Recipient_OD 9.0810811 0.168746228 #> 68 Recipient_OD 9.4054054 0.168746637 #> 69 Recipient_OD 9.7297297 0.168746873 #> 70 Recipient_OD 10.0540540 0.168747009 #> 71 Recipient_OD 10.3783784 0.168747087 #> 72 Recipient_OD 10.7027027 0.168747132 #> 73 Recipient_OD 11.0270270 0.168747158 #> 74 Recipient_OD 11.3513513 0.168747173 #> 75 Recipient_OD 11.6756757 0.168747182 #> 76 Recipient_OD 12.0000000 0.168747187