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2.5.7; vignette work

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@125222 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 15/12/2016 18:43:47
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 Package: OncoSimulR
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 Type: Package
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 Title: Forward Genetic Simulation of Cancer Progression with Epistasis 
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-Version: 2.5.6
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-Date: 2016-12-14
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+Version: 2.5.7
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+Date: 2016-12-15
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 Authors@R: c(person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),
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 		     email = "rdiaz02@gmail.com"),
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 	      person("Mark", "Taylor", role = "ctb", email = "ningkiling@gmail.com"))
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+Changes in version 2.5.7 (2016-12-15):
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+	- Clarified McFarland parameterization.
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+
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 Changes in version 2.5.6 (2016-12-14):
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 	- Fixed a few typos in help files.
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@@ -3688,15 +3688,56 @@ For the Bozic model [@Bozic2010], however, the birth rate is set to
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 In the original model of @McFarland2013, the effects of drivers
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 contribute to the numerator of the birth rate, and those of the
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 (deleterious) passengers to the denominator as: $\frac{(1 +
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-s)^d}{(1 - s_p)^p}$, where $d$ and $p$ are, respectively, the total
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+s)^d}{(1 + s_p)^p}$, where $d$ and $p$ are, respectively, the total
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 number of drivers and passengers in a genotype, and here the fitness
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 effects of all drivers is the same ($s$) and that of all passengers
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-the same too ($s_p$). However, we can map from this ratio to the
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-usual product of terms by using a different value of $s_p$, that we
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-will call $s_{pp} = -s_p/(1 + s_p)$ (see @McFarland2014-phd, his
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-eq. 2.1 in p.9).  This reparameterization applies to v.2. In v.1 we
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-use the same parameterization as in the original one in
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-@McFarland2013.
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+the same too ($s_p$). Note that, as written above, and as explicitly
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+said in @McFarland2013 (see p. 2911) and @McFarland2014-phd (see
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+p. 9), "(...)  $s_p$ is the fitness disadvantage conferred by a
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+passenger". In other words, the larger the $s_p$ the more
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+deleterious the passenger.
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+
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+This is obvious, but I make it explicit because in our
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+parameterization a positive $s$ means fitness advantage, whereas
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+fitness disadvantages are associated with negative $s$. Of course,
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+if you rewrite the above expression as $\frac{(1 + s)^d}{(1 -
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+s_p)^p}$ then we are back to the "positive means fitness advantage
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+and negative means fitness disadvantage".
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+
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+
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+As @McFarland2014-phd explains (see p.\ 9, bottom), we can rewrite
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+the above expression so that there are no terms in the
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+denominator. McFarland writes it as (I copy verbatim from the fourth
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+and fifth lines from the bottom on his p.\ 9) 
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+$(1 + s_d)^{n_d} (1 - s_p^{'})^{n_p}$ where $s_p^{'} = s_p/(1 + s_p)$.
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+
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+
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+However, if we want to express everything as products (no ratios)
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+and use the "positive s means advantage and negative s means
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+disadvantage" rule, we want to write the above expression as 
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+$(1 + s_d)^{n_d} (1 + s_{pp})^{n_p}$ where $s_{pp} = -s_p/(1 + s_p)$. And
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+this is actually what we do in v.2. There is an example, for
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+instance, in section \@ref(mcf5070) where you will see:
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+
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+```{r mcflparam}
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+sp <- 1e-3 
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+spp <- -sp/(1 + sp)
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+```
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+
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+so we are going from the "(...) $s_p$ is the fitness disadvantage
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+conferred by a passenger" in @McFarland2013 (p. 2911) and
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+@McFarland2014-phd (p. 9) to the expression where we have a product
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+$\prod (1 + s_i)$, with the "positive s means advantage and negative
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+s means disadvantage" rule. This reparameterization applies to
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+v.2. In v.1 we use the same parameterization as in the original one
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+in @McFarland2013, but with the "positive s means advantage and negative
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+s means disadvantage" rule (so we are using expression 
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+$\frac{(1 + s)^d}{(1 - s_p)^p}$).
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+
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+
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+<!-- However, we can map from this ratio to the usual product of terms by -->
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+<!-- using a different value of $s_p$, that we will call $s_{pp} = -->
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+<!-- -s_p/(1 + s_p)$ (see @McFarland2014-phd, his eq. 2.1 in p.9).  -->
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 For death rate, we use the expression that @McFarland2013 (see their
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 p. 2911) use "(...) for large cancers (grown to $10^6$ cells)": $D(N) =
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 \usepackage[%
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-		shash={1031e69},
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-		lhash={1031e697f4a920ae6120c78b3c1f3e818ffcad53},
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+		shash={4dc6adf},
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+		lhash={4dc6adf0f20920ff51825aa8ac8563837d4f1239},
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 		authname={Ramon Diaz-Uriarte (at Coleonyx)},
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 		authemail={rdiaz02@gmail.com},
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-		authsdate={2016-12-13},
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-		authidate={2016-12-13 20:38:33 +0100},
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-		authudate={1481657913},
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+		authsdate={2016-12-15},
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+		authidate={2016-12-15 17:47:46 +0100},
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+		authudate={1481820466},
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 		commname={Ramon Diaz-Uriarte (at Coleonyx)},
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 		commemail={rdiaz02@gmail.com},
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-		commsdate={2016-12-13},
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-		commidate={2016-12-13 20:38:33 +0100},
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-		commudate={1481657913},
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+		commsdate={2016-12-15},
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+		commidate={2016-12-15 17:47:46 +0100},
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+		commudate={1481820466},
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 		refnames={ (HEAD, origin/master, origin/HEAD)}
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 	]{gitsetinfo}
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