diff --git a/docs/catalog.rst b/docs/catalog.rst index 5e4052af8..a4fcb1f26 100644 --- a/docs/catalog.rst +++ b/docs/catalog.rst @@ -29,7 +29,7 @@ and saves the output to a file called ``test.trees``: .. code-block:: console - $ stdpopsim HomSap -c chr22 -o test.trees -g HapmapII_GRCh37 --model ooa_3 2 2 2 + $ stdpopsim HomSap -c chr22 -o test.trees -g HapMapII_GRCh37 --model OutOfAfrica_3G09 2 2 2 (To learn more about using ``stdpopsim`` via the command-line, read our :ref:`sec_tutorial` about it.) diff --git a/docs/tutorial.rst b/docs/tutorial.rst index e4993b891..b7b859102 100644 --- a/docs/tutorial.rst +++ b/docs/tutorial.rst @@ -70,7 +70,7 @@ This gives all of the possible demographic models we could simulate. We choose the two population out-of-Africa :ref:`model ` from `Tennesen et al. (2012) `_ . By looking at the model help we -find that the name for this model is ``ooa_2`` and that we can specify it using +find that the name for this model is ``OutOfAfrica_2T12`` and that we can specify it using the ``--model`` option. We choose to draw two samples from the African population and three samples from the European population. To increase simulation speed we can also chose to simulate a sequence a fraction of the @@ -81,7 +81,7 @@ uniform recombination map. The command now looks like this: .. code-block:: console - $ stdpopsim HomSap -c chr22 -l 0.05 -o foo.ts --model ooa_2 2 3 + $ stdpopsim HomSap -c chr22 -l 0.05 -o foo.ts --model OutOfAfrica_2T12 2 3 Note that there are now two numbers after the model option. This is because the model simulates two populations so we have to specify a number of samples to @@ -98,14 +98,14 @@ the ``-l`` option. (NOTE: this may a minute or so to run). .. code-block:: console - $ stdpopsim HomSap -g HapmapII_GRCh37 -c chr22 -o foo.ts --model ooa_2 2 3 + $ stdpopsim HomSap -g HapMapII_GRCh37 -c chr22 -o foo.ts --model OutOfAfrica_2T12 2 3 For reproducibility we can also choose set seed for the simulator using the ``-s`` flag. .. code-block:: console - $ stdpopsim HomSap -s 1046 -g HapmapII_GRCh37 -c chr22 -o foo.ts --model ooa_2 2 3 + $ stdpopsim HomSap -s 1046 -g HapMapII_GRCh37 -c chr22 -o foo.ts --model OutOfAfrica_2T12 2 3 Lastly, the CLI also outputs the relevant citations for both the simulator used and the resources used for simulation scenario. @@ -262,8 +262,8 @@ This prints detailed information about all of the available models to the terminal. In this tutorial, we will use the model of African-American admixture from `2011 Browning et al `_. -From the help output (or the :ref:`Catalog `), -we can see that this model has id ``america``, +From the help output (or the :ref:`Catalog `), +we can see that this model has id ``AmericanAdmixture_4B11``, and allows samples to be drawn from 4 contemporary populations representing African, European, Asian and African-American groups. @@ -272,7 +272,7 @@ are available: .. command-output:: stdpopsim HomSap --help-genetic-maps -Let's go with ``HapmapII_GRCh37``. +Let's go with ``HapMapII_GRCh37``. The next command simulates 4 samples of chromosome 1 from each of the four populations, and saves the output to a file called ``afr-america-chr1.trees``. For the purposes of this tutorial, we'll also specify a random seed using the @@ -281,8 +281,8 @@ For the purposes of this tutorial, we'll also specify a random seed using the .. code-block:: console - $ stdpopsim HomSap -c chr1 -o afr-america-chr1.trees -s 13 -g HapmapII_GRCh37\ - --model america 4 4 4 4 + $ stdpopsim HomSap -c chr1 -o afr-america-chr1.trees -s 13 -g HapMapII_GRCh37\ + --model AmericanAdmixture_4B11 4 4 4 4 -------------------------- 2. Calculating divergences