diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-19 15:41:24 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-11-19 15:41:24 +0100 |
| commit | db9ae6a0c9cecb92048fde6f06af1da183c09b5f (patch) | |
| tree | f0ea97545549c71bd7aa3d13afed422fd402f0e6 /docs/dev/reference/mmkin.html | |
| parent | 6441a9f35d66f2c4d38c0036f99cd8f509d76f3b (diff) | |
Depend on parallel, doc improvements
By depending on parallel instead of importing it, functions to set up
and stop a cluster are always available when mkin is loaded.
The use of multicore processing in mmkin on Windows is now documented in
the help file, which brings mkin closer to a version 1.0 #9.
Diffstat (limited to 'docs/dev/reference/mmkin.html')
| -rw-r--r-- | docs/dev/reference/mmkin.html | 28 |
1 files changed, 25 insertions, 3 deletions
diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html index b0ca90f0..4786b02e 100644 --- a/docs/dev/reference/mmkin.html +++ b/docs/dev/reference/mmkin.html @@ -227,9 +227,9 @@ plotting.</p></div> <span class='va'>time_default</span> </div><div class='output co'>#> user system elapsed -#> 4.706 0.488 1.375 </div><div class='input'><span class='va'>time_1</span> +#> 4.664 0.433 1.317 </div><div class='input'><span class='va'>time_1</span> </div><div class='output co'>#> user system elapsed -#> 5.232 0.005 5.238 </div><div class='input'> +#> 5.326 0.001 5.330 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink @@ -252,7 +252,29 @@ plotting.</p></div> <span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span> <span class='co'># allow to plot the observed variables separately</span> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='fl'>1</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> +</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='co'># On Windows, we can use multiple cores by making a cluster using the parallel</span> +<span class='co'># package, which gets loaded with mkin, and passing it to mmkin, e.g.</span> +<span class='va'>cl</span> <span class='op'><-</span> <span class='fu'>makePSOCKcluster</span><span class='op'>(</span><span class='fl'>12</span><span class='op'>)</span> +<span class='va'>f</span> <span class='op'><-</span> <span class='fu'>mmkin</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, + <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>A <span class='op'>=</span> <span class='va'>FOCUS_2006_A</span>, B <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, C <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span>, D <span class='op'>=</span> <span class='va'>FOCUS_2006_D</span><span class='op'>)</span>, + cluster <span class='op'>=</span> <span class='va'>cl</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> +</div><div class='output co'>#> <mmkin> object +#> Status of individual fits: +#> +#> dataset +#> model A B C D +#> SFO OK OK OK OK +#> FOMC C OK OK OK +#> DFOP OK OK OK OK +#> +#> OK: No warnings +#> C: Optimisation did not converge: +#> false convergence (8)</div><div class='input'><span class='co'># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span> +<span class='co'># dataset is really SFO, and the FOMC fit is overparameterised</span> +<span class='fu'>stopCluster</span><span class='op'>(</span><span class='va'>cl</span><span class='op'>)</span> +<span class='co'># }</span> </div></pre> </div> |