scan_crit_time returns the
conjugation rates and critical times corresponding to
a DRT conjugation experiment, assuming different gamma.T values.
For the ASM to return a proper conjugation estimate
the time point of measurement must be smaller than
min(tcrit1, tcrit2, tcrit3).
scan_crit_time( DRT, tol_factor = 10, id_cols = c("ID"), mult_seq = 10^seq(-2, 5, 1), verbose = T )
| DRT | Dataframe. Data corresponding to the first conjugation experiment. Necessary columns: D.0, R.0 are initial pop sizes; psi.D, psi.R, psi.T are growth rates. If gamma.D is not among the columns, the function will attempt to estimate gamma.D from the data given. This requires D.t, R.t, T.t (final population sizes) and t (the time of measurement). If gamma.T is among the columns, the input under TRT will be ignored. |
|---|---|
| tol_factor | Double. The imprecision factor: this factor indicates how close the system is allowed to approach a state where it violates the ASM assumptions (smaller values allow greater violation). |
| id_cols | List of strings. Specifies the column names that should be treated as identifiers (will be returned in output). |
| mult_seq | Vector. Describes the multiplication factors to take into account for gamma.T. |
| verbose | Boolean. Should warnings be returned? |
Dataframe of estimated critical times for the input DRT data and a range of gamma.T values.
estimate_conj_rate for estimation of the
conjugation rates.
Other critical time functions:
estimate_crit_time()
scan_crit_time(DRT_example)#> ID mult_factor gamma.D gamma.T tcrit1 tcrit2 tcrit3 min_tcrit #> 1 A1 1e-02 9.004904e-10 9.004904e-12 14.500 11.6 14.10 11.600 #> 2 A1 1e-01 9.004904e-10 9.004904e-11 12.200 11.6 12.90 11.600 #> 3 A1 1e+00 9.004904e-10 9.004904e-10 9.900 11.6 11.60 9.900 #> 4 A1 1e+01 9.004904e-10 9.004904e-09 7.600 11.6 10.30 7.600 #> 5 A1 1e+02 9.004904e-10 9.004904e-08 5.300 11.6 9.01 5.300 #> 6 A1 1e+03 9.004904e-10 9.004904e-07 3.000 11.6 7.73 3.000 #> 7 A1 1e+04 9.004904e-10 9.004904e-06 0.693 11.6 6.45 0.693 #> 8 A1 1e+05 9.004904e-10 9.004904e-05 -1.610 11.6 5.17 -1.610 #> 9 A2 1e-02 9.004904e-10 9.004904e-12 14.500 11.6 14.10 11.600 #> 10 A2 1e-01 9.004904e-10 9.004904e-11 12.200 11.6 12.90 11.600 #> 11 A2 1e+00 9.004904e-10 9.004904e-10 9.900 11.6 11.60 9.900 #> 12 A2 1e+01 9.004904e-10 9.004904e-09 7.600 11.6 10.30 7.600 #> 13 A2 1e+02 9.004904e-10 9.004904e-08 5.300 11.6 9.01 5.300 #> 14 A2 1e+03 9.004904e-10 9.004904e-07 3.000 11.6 7.73 3.000 #> 15 A2 1e+04 9.004904e-10 9.004904e-06 0.693 11.6 6.45 0.693 #> 16 A2 1e+05 9.004904e-10 9.004904e-05 -1.610 11.6 5.17 -1.610 #> 17 A3 1e-02 8.008783e-10 8.008783e-12 14.600 11.8 14.20 11.800 #> 18 A3 1e-01 8.008783e-10 8.008783e-11 12.300 11.8 12.90 11.800 #> 19 A3 1e+00 8.008783e-10 8.008783e-10 10.000 11.8 11.60 10.000 #> 20 A3 1e+01 8.008783e-10 8.008783e-09 7.720 11.8 10.40 7.720 #> 21 A3 1e+02 8.008783e-10 8.008783e-08 5.420 11.8 9.08 5.420 #> 22 A3 1e+03 8.008783e-10 8.008783e-07 3.110 11.8 7.80 3.110 #> 23 A3 1e+04 8.008783e-10 8.008783e-06 0.810 11.8 6.52 0.810 #> 24 A3 1e+05 8.008783e-10 8.008783e-05 -1.490 11.8 5.24 -1.490#> ID t mult_factor gamma.D gamma.T tcrit1 tcrit2 tcrit3 min_tcrit #> 1 A1 7 1.000000 9.004904e-10 9.004904e-10 9.90 11.6 11.60 9.90 #> 2 A1 7 1.258925 9.004904e-10 1.133650e-09 9.67 11.6 11.40 9.67 #> 3 A1 7 1.584893 9.004904e-10 1.427181e-09 9.44 11.6 11.30 9.44 #> 4 A1 7 1.995262 9.004904e-10 1.796715e-09 9.21 11.6 11.20 9.21 #> 5 A1 7 10.000000 9.004904e-10 9.004904e-09 7.60 11.6 10.30 7.60 #> 6 A1 7 100.000000 9.004904e-10 9.004904e-08 5.30 11.6 9.01 5.30 #> 7 A1 7 1000.000000 9.004904e-10 9.004904e-07 3.00 11.6 7.73 3.00 #> 8 A1 7 12.589254 9.004904e-10 1.133650e-08 7.37 11.6 10.20 7.37 #> 9 A1 7 125.892541 9.004904e-10 1.133650e-07 5.07 11.6 8.88 5.07 #> 10 A1 7 15.848932 9.004904e-10 1.427181e-08 7.14 11.6 10.00 7.14 #> 11 A1 7 158.489319 9.004904e-10 1.427181e-07 4.84 11.6 8.76 4.84 #> 12 A1 7 19.952623 9.004904e-10 1.796715e-08 6.91 11.6 9.91 6.91 #> 13 A1 7 199.526231 9.004904e-10 1.796715e-07 4.61 11.6 8.63 4.61 #> 14 A1 7 2.511886 9.004904e-10 2.261930e-09 8.98 11.6 11.10 8.98 #> 15 A1 7 25.118864 9.004904e-10 2.261930e-08 6.68 11.6 9.78 6.68 #> 16 A1 7 251.188643 9.004904e-10 2.261930e-07 4.38 11.6 8.50 4.38 #> 17 A1 7 3.162278 9.004904e-10 2.847601e-09 8.75 11.6 10.90 8.75 #> 18 A1 7 3.981072 9.004904e-10 3.584917e-09 8.52 11.6 10.80 8.52 #> 19 A1 7 31.622777 9.004904e-10 2.847601e-08 6.45 11.6 9.65 6.45 #> 20 A1 7 316.227766 9.004904e-10 2.847601e-07 4.15 11.6 8.37 4.15 #> 21 A1 7 39.810717 9.004904e-10 3.584917e-08 6.22 11.6 9.52 6.22 #> 22 A1 7 398.107171 9.004904e-10 3.584917e-07 3.92 11.6 8.24 3.92 #> 23 A1 7 5.011872 9.004904e-10 4.513143e-09 8.29 11.6 10.70 8.29 #> 24 A1 7 50.118723 9.004904e-10 4.513143e-08 5.99 11.6 9.40 5.99 #> 25 A1 7 501.187234 9.004904e-10 4.513143e-07 3.69 11.6 8.12 3.69 #> 26 A1 7 6.309573 9.004904e-10 5.681710e-09 8.06 11.6 10.50 8.06 #> 27 A1 7 63.095734 9.004904e-10 5.681710e-08 5.76 11.6 9.27 5.76 #> 28 A1 7 630.957344 9.004904e-10 5.681710e-07 3.46 11.6 7.99 3.46 #> 29 A1 7 7.943282 9.004904e-10 7.152849e-09 7.83 11.6 10.40 7.83 #> 30 A1 7 79.432823 9.004904e-10 7.152849e-08 5.53 11.6 9.14 5.53 #> 31 A1 7 794.328235 9.004904e-10 7.152849e-07 3.23 11.6 7.86 3.23 #> 32 A2 7 1.000000 9.004904e-10 9.004904e-10 9.90 11.6 11.60 9.90 #> 33 A2 7 1.258925 9.004904e-10 1.133650e-09 9.67 11.6 11.40 9.67 #> 34 A2 7 1.584893 9.004904e-10 1.427181e-09 9.44 11.6 11.30 9.44 #> 35 A2 7 1.995262 9.004904e-10 1.796715e-09 9.21 11.6 11.20 9.21 #> 36 A2 7 10.000000 9.004904e-10 9.004904e-09 7.60 11.6 10.30 7.60 #> 37 A2 7 100.000000 9.004904e-10 9.004904e-08 5.30 11.6 9.01 5.30 #> 38 A2 7 1000.000000 9.004904e-10 9.004904e-07 3.00 11.6 7.73 3.00 #> 39 A2 7 12.589254 9.004904e-10 1.133650e-08 7.37 11.6 10.20 7.37 #> 40 A2 7 125.892541 9.004904e-10 1.133650e-07 5.07 11.6 8.88 5.07 #> 41 A2 7 15.848932 9.004904e-10 1.427181e-08 7.14 11.6 10.00 7.14 #> 42 A2 7 158.489319 9.004904e-10 1.427181e-07 4.84 11.6 8.76 4.84 #> 43 A2 7 19.952623 9.004904e-10 1.796715e-08 6.91 11.6 9.91 6.91 #> 44 A2 7 199.526231 9.004904e-10 1.796715e-07 4.61 11.6 8.63 4.61 #> 45 A2 7 2.511886 9.004904e-10 2.261930e-09 8.98 11.6 11.10 8.98 #> 46 A2 7 25.118864 9.004904e-10 2.261930e-08 6.68 11.6 9.78 6.68 #> 47 A2 7 251.188643 9.004904e-10 2.261930e-07 4.38 11.6 8.50 4.38 #> 48 A2 7 3.162278 9.004904e-10 2.847601e-09 8.75 11.6 10.90 8.75 #> 49 A2 7 3.981072 9.004904e-10 3.584917e-09 8.52 11.6 10.80 8.52 #> 50 A2 7 31.622777 9.004904e-10 2.847601e-08 6.45 11.6 9.65 6.45 #> 51 A2 7 316.227766 9.004904e-10 2.847601e-07 4.15 11.6 8.37 4.15 #> 52 A2 7 39.810717 9.004904e-10 3.584917e-08 6.22 11.6 9.52 6.22 #> 53 A2 7 398.107171 9.004904e-10 3.584917e-07 3.92 11.6 8.24 3.92 #> 54 A2 7 5.011872 9.004904e-10 4.513143e-09 8.29 11.6 10.70 8.29 #> 55 A2 7 50.118723 9.004904e-10 4.513143e-08 5.99 11.6 9.40 5.99 #> 56 A2 7 501.187234 9.004904e-10 4.513143e-07 3.69 11.6 8.12 3.69 #> 57 A2 7 6.309573 9.004904e-10 5.681710e-09 8.06 11.6 10.50 8.06 #> 58 A2 7 63.095734 9.004904e-10 5.681710e-08 5.76 11.6 9.27 5.76 #> 59 A2 7 630.957344 9.004904e-10 5.681710e-07 3.46 11.6 7.99 3.46 #> 60 A2 7 7.943282 9.004904e-10 7.152849e-09 7.83 11.6 10.40 7.83 #> 61 A2 7 79.432823 9.004904e-10 7.152849e-08 5.53 11.6 9.14 5.53 #> 62 A2 7 794.328235 9.004904e-10 7.152849e-07 3.23 11.6 7.86 3.23 #> 63 A3 7 1.000000 8.008783e-10 8.008783e-10 10.00 11.8 11.60 10.00 #> 64 A3 7 1.258925 8.008783e-10 1.008246e-09 9.79 11.8 11.50 9.79 #> 65 A3 7 1.584893 8.008783e-10 1.269307e-09 9.56 11.8 11.40 9.56 #> 66 A3 7 1.995262 8.008783e-10 1.597962e-09 9.33 11.8 11.30 9.33 #> 67 A3 7 10.000000 8.008783e-10 8.008783e-09 7.72 11.8 10.40 7.72 #> 68 A3 7 100.000000 8.008783e-10 8.008783e-08 5.42 11.8 9.08 5.42 #> 69 A3 7 1000.000000 8.008783e-10 8.008783e-07 3.11 11.8 7.80 3.11 #> 70 A3 7 12.589254 8.008783e-10 1.008246e-08 7.49 11.8 10.20 7.49 #> 71 A3 7 125.892541 8.008783e-10 1.008246e-07 5.18 11.8 8.95 5.18 #> 72 A3 7 15.848932 8.008783e-10 1.269307e-08 7.26 11.8 10.10 7.26 #> 73 A3 7 158.489319 8.008783e-10 1.269307e-07 4.95 11.8 8.82 4.95 #> 74 A3 7 19.952623 8.008783e-10 1.597962e-08 7.03 11.8 9.97 7.03 #> 75 A3 7 199.526231 8.008783e-10 1.597962e-07 4.72 11.8 8.69 4.72 #> 76 A3 7 2.511886 8.008783e-10 2.011715e-09 9.10 11.8 11.10 9.10 #> 77 A3 7 25.118864 8.008783e-10 2.011715e-08 6.80 11.8 9.84 6.80 #> 78 A3 7 251.188643 8.008783e-10 2.011715e-07 4.49 11.8 8.57 4.49 #> 79 A3 7 3.162278 8.008783e-10 2.532599e-09 8.87 11.8 11.00 8.87 #> 80 A3 7 3.981072 8.008783e-10 3.188354e-09 8.64 11.8 10.90 8.64 #> 81 A3 7 31.622777 8.008783e-10 2.532599e-08 6.57 11.8 9.72 6.57 #> 82 A3 7 316.227766 8.008783e-10 2.532599e-07 4.26 11.8 8.44 4.26 #> 83 A3 7 39.810717 8.008783e-10 3.188354e-08 6.34 11.8 9.59 6.34 #> 84 A3 7 398.107171 8.008783e-10 3.188354e-07 4.03 11.8 8.31 4.03 #> 85 A3 7 5.011872 8.008783e-10 4.013900e-09 8.41 11.8 10.70 8.41 #> 86 A3 7 50.118723 8.008783e-10 4.013900e-08 6.11 11.8 9.46 6.11 #> 87 A3 7 501.187234 8.008783e-10 4.013900e-07 3.80 11.8 8.18 3.80 #> 88 A3 7 6.309573 8.008783e-10 5.053200e-09 8.18 11.8 10.60 8.18 #> 89 A3 7 63.095734 8.008783e-10 5.053200e-08 5.88 11.8 9.33 5.88 #> 90 A3 7 630.957344 8.008783e-10 5.053200e-07 3.57 11.8 8.05 3.57 #> 91 A3 7 7.943282 8.008783e-10 6.361602e-09 7.95 11.8 10.50 7.95 #> 92 A3 7 79.432823 8.008783e-10 6.361602e-08 5.65 11.8 9.21 5.65 #> 93 A3 7 794.328235 8.008783e-10 6.361602e-07 3.34 11.8 7.93 3.34