1. 29 Mar, 2021 1 commit
2. 20 Mar, 2021 2 commits
• tk/Mutsel_simulator_cpg: initial speed assessment · 8f248d0d
Philippe Veber authored
```using (debugged) implementation in phylogenetics, perform simulation
for 500 to 2000 sites. Quadratic complexity is expected here, to
observe it I use the log transform from

t = K n^2

to
log t = 2 log n + log K

Running times are only nearly quadratic:

> df <- data.frame(n = c(500,1000,1300,2000), t = c(5.15,18.48,28.63,68.07)) ; fit <- lm(log2(t) ~ log2(n), data = df) ; summary(fit)

Call:
lm(formula = log2(t) ~ log2(n), data = df)

Residuals:
1         2         3         4
0.015095  0.007796 -0.061122  0.038231

Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -14.24278    0.36390  -39.14 0.000652 ***
log2(n)       1.85062    0.03608   51.30 0.000380 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0.05237 on 2 degrees of freedom
Multiple R-squared:  0.9992,	Adjusted R-squared:  0.9989
F-statistic:  2631 on 1 and 2 DF,  p-value: 0.0003798

> df <- data.frame(n = c(500,1000,1300,2000), t = c(5.15,18.48,28.63,68.07)) ; fit <- lm(t ~ I(n^2), data = df) ; summary(fit)

Call:
lm(formula = t ~ I(n^2), data = df)

Residuals:
1       2       3       4
-0.1138  0.6815 -0.7004  0.1327

Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 1.086e+00  5.581e-01   1.945 0.191208
I(n^2)      1.671e-05  2.501e-07  66.822 0.000224 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0.702 on 2 degrees of freedom
Multiple R-squared:  0.9996,	Adjusted R-squared:  0.9993
F-statistic:  4465 on 1 and 2 DF,  p-value: 0.0002239```
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