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| estimate_Genome_peakp | Function to fit 2p peak model, with p forms |
| eval_model | Evaluate distinct model forms, in order to resolve ambiguity of which peak is the homozygous peak |
| nls_peak | Uses nlsLM to fit 2p peak model |
| predict1_0 | Produce model estimated (p=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict1_0_unique | Produce model estimated (p=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict1_1 | Produce model estimated (p=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict1_1_unique | Produce model estimated (p=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict2_0 | Produce model estimated (p=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict2_0_unique | Produce model estimated (p=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict2_1 | Produce model estimated (p=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict2_1_unique | Produce model estimated (p=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict3_0 | Produce model estimated (p=3) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict3_0_unique | Produce model estimated (p=3, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict3_1 | Produce model estimated (p=3) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict3_1_unique | Produce model estimated (p=3, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict4_0 | Produce model estimated (p=4, full model) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict4_0_unique | Produce model estimated (p=4, full model, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict4_1 | Produce model estimated (p=4, topology=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict4_1_unique | Produce model estimated (p=4, topology=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict4_2 | Produce model estimated (p=4, topology=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict4_2_unique | Produce model estimated (p=4, topology=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict5_0 | Produce model estimated (p=5, full model) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict5_0_unique | Produce model estimated (p=5, full model, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict5_1 | Produce model estimated (p=5, topology=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict5_1_unique | Produce model estimated (p=5, topology=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict5_2 | Produce model estimated (p=5, topology=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict5_2_unique | Produce model estimated (p=5, topology=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict5_3 | Produce model estimated (p=5, topology=3) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict5_3_unique | Produce model estimated (p=5, topology=3, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict5_4 | Produce model estimated (p=5, topology=4) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict5_4_unique | Produce model estimated (p=5, topology=4, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict5_5 | Produce model estimated (p=5, topology=5) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict5_5_unique | Produce model estimated (p=5, topology=5, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_0 | Produce model estimated (p=6, full model) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_0_unique | Produce model estimated (p=6, full model, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_1 | Produce model estimated (p=6, topology=1) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_10 | Produce model estimated (p=6, topology=10) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_10_unique | Produce model estimated (p=6, topology=10, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_11 | Produce model estimated (p=6, topology=11) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_11_unique | Produce model estimated (p=6, topology=11, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_12 | Produce model estimated (p=6, topology=12) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_12_unique | Produce model estimated (p=6, topology=12, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_13 | Produce model estimated (p=6, topology=13) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_13_unique | Produce model estimated (p=6, topology=13, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_14 | Produce model estimated (p=6, topology=14) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_14_unique | Produce model estimated (p=6, topology=14, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_15 | Produce model estimated (p=6, topology=15) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_15_unique | Produce model estimated (p=6, topology=15, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_16 | Produce model estimated (p=6, topology=16) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_16_unique | Produce model estimated (p=6, topology=16, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_1_unique | Produce model estimated (p=6, topology=1, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_2 | Produce model estimated (p=6, topology=2) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_2_unique | Produce model estimated (p=6, topology=2, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_3 | Produce model estimated (p=6, topology=3) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_3_unique | Produce model estimated (p=6, topology=3, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_4 | Produce model estimated (p=6, topology=4) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_4_unique | Produce model estimated (p=6, topology=4, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_5 | Produce model estimated (p=6, topology=5) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_5_unique | Produce model estimated (p=6, topology=5, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_6 | Produce model estimated (p=6, topology=6) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_6_unique | Produce model estimated (p=6, topology=6, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_7 | Produce model estimated (p=6, topology=7) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_7_unique | Produce model estimated (p=6, topology=7, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_8 | Produce model estimated (p=6, topology=8) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_8_unique | Produce model estimated (p=6, topology=8, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_9 | Produce model estimated (p=6, topology=9) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| predict6_9_unique | Produce model estimated (p=6, topology=9, unique portion) y-coordinates of the kmer spectra given the kmer size, repetitiveness, average polyploid kmer coverage, bias, and x-coordinates of the kmer spectra. |
| report_results | Report results and make plots |
| score_model | Score nlsLM model by number and percent of residual errors after excluding sequencing errors |