paper: Update paper with latest changes

[mhovd]

No description provided.

[mhovd]

This PR is not meant to be merged until the (eventual) acceptance of the paper.
It is meant to keep track of changes between the main and joss branch.

[github-actions]

Bencher Report

Branch	joss
Testbed	mhovd-pgx

Click to view all benchmark results

Benchmark	Latency	Benchmark Result nanoseconds (ns) (Result Δ%)	Upper Boundary nanoseconds (ns) (Limit %)
Analytical vs ODE/One-compartment IV/Analytical	📈 view plot 🚷 view threshold	783.05 ns (-4.26%) Baseline: 817.89 ns	883.81 ns (88.60%)
Analytical vs ODE/One-compartment IV/ODE	📈 view plot 🚷 view threshold	18,753.00 ns (+0.75%) Baseline: 18,613.32 ns	19,648.46 ns (95.44%)
Analytical vs ODE/One-compartment oral/Analytical	📈 view plot 🚷 view threshold	731.68 ns (-9.53%) Baseline: 808.74 ns	903.83 ns (80.95%)
Analytical vs ODE/One-compartment oral/ODE	📈 view plot 🚷 view threshold	26,370.00 ns (-1.89%) Baseline: 26,877.39 ns	28,148.63 ns (93.68%)
Analytical vs ODE/Two-compartment IV/Analytical	📈 view plot 🚷 view threshold	855.70 ns (-2.66%) Baseline: 879.07 ns	963.80 ns (88.78%)
Analytical vs ODE/Two-compartment IV/ODE	📈 view plot 🚷 view threshold	27,822.00 ns (+0.22%) Baseline: 27,759.93 ns	29,258.79 ns (95.09%)
Analytical vs ODE/Two-compartment oral/Analytical	📈 view plot 🚷 view threshold	923.01 ns (-1.39%) Baseline: 936.05 ns	1,027.42 ns (89.84%)
Analytical vs ODE/Two-compartment oral/ODE	📈 view plot 🚷 view threshold	30,426.00 ns (-1.06%) Baseline: 30,750.89 ns	32,228.29 ns (94.41%)
Conditional dose modification	📈 view plot 🚷 view threshold	1,223.40 ns (+0.93%) Baseline: 1,212.15 ns	1,263.77 ns (96.81%)
Create large dataset (100 subjects)	📈 view plot 🚷 view threshold	55,479.00 ns (+1.54%) Baseline: 54,640.21 ns	56,672.40 ns (97.89%)
Data expand complex (1h intervals)	📈 view plot 🚷 view threshold	27,459.00 ns (-1.68%) Baseline: 27,928.29 ns	29,498.72 ns (93.09%)
Data expand simple (1h intervals)	📈 view plot 🚷 view threshold	494.00 ns (+0.89%) Baseline: 489.65 ns	509.70 ns (96.92%)
Data expand with additional time	📈 view plot 🚷 view threshold	37,766.00 ns (-2.27%) Baseline: 38,641.61 ns	40,942.34 ns (92.24%)
Filter exclude subjects	📈 view plot 🚷 view threshold	30,925.00 ns (+0.32%) Baseline: 30,825.79 ns	31,552.75 ns (98.01%)
Filter include subjects	📈 view plot 🚷 view threshold	7,899.60 ns (-0.66%) Baseline: 7,951.98 ns	8,423.03 ns (93.79%)
Modify all bolus doses	📈 view plot 🚷 view threshold	1,152.00 ns (-2.16%) Baseline: 1,177.44 ns	1,226.25 ns (93.95%)
Modify all infusion doses	📈 view plot 🚷 view threshold	1,204.00 ns (-0.63%) Baseline: 1,211.60 ns	1,260.70 ns (95.50%)
SubjectBuilder multi-occasion	📈 view plot 🚷 view threshold	261.56 ns (-1.21%) Baseline: 264.77 ns	275.04 ns (95.10%)
SubjectBuilder simple	📈 view plot 🚷 view threshold	105.13 ns (+0.74%) Baseline: 104.36 ns	109.16 ns (96.31%)
SubjectBuilder with covariates	📈 view plot 🚷 view threshold	290.16 ns (+4.58%) Baseline: 277.44 ns	295.40 ns (98.23%)
nca_auc_cmax_metrics	📈 view plot 🚷 view threshold	569.02 ns (-2.77%) Baseline: 585.20 ns	621.63 ns (91.54%)
nca_population/10	📈 view plot 🚷 view threshold	47,493.00 ns (+1.44%) Baseline: 46,816.78 ns	49,529.26 ns (95.89%)
nca_population/100	📈 view plot 🚷 view threshold	124,910.00 ns (+2.22%) Baseline: 122,193.33 ns	126,877.78 ns (98.45%)
nca_population/500	📈 view plot 🚷 view threshold	411,720.00 ns (+1.31%) Baseline: 406,411.11 ns	425,822.32 ns (96.69%)
nca_single_subject	📈 view plot 🚷 view threshold	1,004.30 ns (-0.29%) Baseline: 1,007.18 ns	1,028.06 ns (97.69%)
one_compartment	📈 view plot 🚷 view threshold	22,471.00 ns (+0.46%) Baseline: 22,367.54 ns	24,724.29 ns (90.89%)
one_compartment_covariates	📈 view plot 🚷 view threshold	28,642.00 ns (-0.37%) Baseline: 28,748.82 ns	31,181.52 ns (91.86%)
readme 20	📈 view plot 🚷 view threshold	332,090.00 ns (+1.14%) Baseline: 328,344.64 ns	350,374.93 ns (94.78%)
two_compartment	📈 view plot 🚷 view threshold	24,195.00 ns (+0.91%) Baseline: 23,976.25 ns	25,945.68 ns (93.25%)

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