Recent Changes for "3. Editing XML Input File" - Bodega Phylogenetics Wiki

3. Editing XML Input File

2009-03-21 12:42:41

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- What gives? As suggested by the error message, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have just defined, which is described in the error message as an {{{‘initial state is incompatible with one or more 'hard' constraints (on monophyly or bounds on parameter values)’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and caused the initial state of the chain to have a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which we will describe in the ["4. Specifying a Starting Tree" next] part of the tutorial	+ What gives? As suggested by the error message, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have just defined, which is described in the error message as an {{{‘initial state is incompatible with one or more 'hard' constraints (on monophyly or bounds on parameter values)’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and caused the initial state of the chain to have a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which we will describe in the ["4. Specifying a Starting Tree" next] part of the tutorial.

3. Editing XML Input File

2009-03-21 12:42:04

Differences for 3. Editing XML Input File

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- What gives? As suggested by the error message, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have just defined, which is described in the error message as an {{{‘initial state is incompatible with one or more 'hard' constraints (on monophyly or bounds on parameter values)’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and caused the initial state of the chain to have a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which we will describe in the ["4. Specifying a Starting Tree" next tutorial].	+ What gives? As suggested by the error message, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have just defined, which is described in the error message as an {{{‘initial state is incompatible with one or more 'hard' constraints (on monophyly or bounds on parameter values)’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and caused the initial state of the chain to have a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which we will describe in the ["4. Specifying a Starting Tree" next] part of the tutorial

3. Editing XML Input File

2009-03-21 10:46:14

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- ===== Step 1: Defining a clade =====	+ ==== + ===== '''Step 1: Defining a clade''' =====
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- ===== Step 2: Monitoring the monophyly of the specified clade =====	+ ==== + ===== '''Step 2: Monitoring the monophyly of the specified clade''' =====
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- ===== Step 3: Monitoring the age of the specified clade =====	+ ==== + ===== '''Step 3: Monitoring the age of the specified clade''' =====
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- ===== Step 4: Enforcing the monophyly of the specified clade =====	+ ==== + ===== '''Step 4: Enforcing the monophyly of the specified clade''' =====
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- ===== Step 5: Calibrating the age of the specified clade =====	+ ==== + ===== '''Step 5: Calibrating the age of the specified clade''' =====
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- ===== Almost (but not quite) ready to roll... =====	+ ===== '''Almost (but not quite) ready to roll...''' =====

3. Editing XML Input File

2009-03-20 03:14:32

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- -->[http://bodegaphylo.wikispot.org/2._Formatting_BEAST_Input_Files Back: Tutorial Part 2] [http://bodegaphylo.wikispot.org/Divergence_Time_Estimation_%28Moore%29 Tutorial Home] [http://bodegaphylo.wikispot.org/4._Specifying_a_Starting_Tree Next: Tutorial Part 4]<-- -->Created by [http://www.phylodiversity.net/bmoore/ Brian Moore]<--	+ -->["2. Formatting BEAST Input Files" Back: Part 2] ["Divergence Time Estimation (Moore)" Tutorial Home] ["4. Specifying a Starting Tree" Next: Part 4]<-- -->Created by [http://www.phylodiversity.net/bmoore/ Brian Moore]<--

3. Editing XML Input File

2009-03-20 02:54:36

Differences for 3. Editing XML Input File

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- What gives? As suggested by the error message, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have just defined, which is described in the error message as an {{{‘initial state is incompatible with one or more 'hard' constraints (on monophyly or bounds on parameter values)’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and caused the initial state of the chain to have a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which we will describe in the next ["4. Specifying a Starting Tree" tutorial].	+ What gives? As suggested by the error message, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have just defined, which is described in the error message as an {{{‘initial state is incompatible with one or more 'hard' constraints (on monophyly or bounds on parameter values)’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and caused the initial state of the chain to have a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which we will describe in the ["4. Specifying a Starting Tree" next tutorial].

3. Editing XML Input File

2009-03-20 02:54:01

Differences for 3. Editing XML Input File

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- What gives? As suggested by the error message, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have just defined, which is described in the error message as an {{{‘initial state is incompatible with one or more 'hard' constraints (on monophyly or bounds on parameter values)’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and caused the initial state of the chain to have a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which we will describe in the next [http://bodegaphylo.wikispot.org/4._Specifying_a_Starting_Tree tutorial].	+ What gives? As suggested by the error message, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have just defined, which is described in the error message as an {{{‘initial state is incompatible with one or more 'hard' constraints (on monophyly or bounds on parameter values)’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and caused the initial state of the chain to have a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which we will describe in the next ["4. Specifying a Starting Tree" tutorial].

3. Editing XML Input File

2009-03-20 02:52:13

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- In our example data set, the fossil previously assigned to {{{'clade_1'}}} has been estimated to be ~45My of age, which defines the minimum age for this clade. Moreover, there is evidence that the stem age of the group to which ''Platanus'' belongs (the 'plane-tree' family Platanaceae) is no more than ~65My of age, which provides a maximum age constraint for {{{'clade_1'}}}. There is little additional fossil information to inform a calibration prior for this group, so we will adopt a fairly vague calibration prior to reflect this uncertainty, and constrain the MRCA of {{{'clade_1'}}} to a uniform calibration prior bounded between 45 to 65 MA. This is achieved via the xml element depicted below:	+ In our example data set, the fossil previously assigned to {{{'clade_1'}}} has been estimated to be ~45My of age, which defines the minimum age for this clade. Moreover, there is evidence that the stem age of the group to which ''Platanus'' belongs (the 'plane-tree' family Platanaceae) is no more than ~65My of age, which provides a maximum age constraint for {{{'clade_1'}}}. There is little additional fossil information to inform a calibration prior for this group, so we will adopt a fairly vague calibration prior to reflect this uncertainty, and constrain the MRCA of clade_1 (which is monitored by the previously defined statistic, {{'clade_1_DTE'}}} to a uniform calibration prior bounded between 45 to 65 MA. This is achieved via the xml element depicted below:
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- We've just completed a series of modifications to our XML file that defines the clade to which the fossil belongs, to monitors and enforces the monophyly of that clade, and monitors and constrains the age of this clade. Are we finally ready to run the BEAST analysis? Not quite yet. Attempting to do so will cause BEAST to generate the following error message:	+ We've just completed a series of modifications to our XML file that defines the clade to which the fossil belongs, monitors and enforces the monophyly of that clade, and monitors and constrains the age of this clade. Are we finally ready to run the BEAST analysis? Not quite yet. Attempting to do so will cause BEAST to generate the following error message:

3. Editing XML Input File

2009-03-20 02:49:32

Differences for 3. Editing XML Input File

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- In our example data set, the fossil previously been assigned to {{{'clade_1'}}} has been estimated to be ~45My of age, which defines the minimum age for this clade. Moreover, there is evidence that the stem age of the group to which ''Platanus'' belongs (the 'plane-tree' family Platanaceae) is no more than ~65My of age, which provides a maximum age constraint for {{{'clade_1'}}}. There is little additional fossil information to inform a calibration prior for this group, so we will adopt a fairly vague calibration prior to reflect this uncertainty, and constrain the MRCA of {{{'clade_1'}}} to a uniform calibration prior bounded between 45 to 65 MA. This is achieved via the xml element depicted below:	+ In our example data set, the fossil previously assigned to {{{'clade_1'}}} has been estimated to be ~45My of age, which defines the minimum age for this clade. Moreover, there is evidence that the stem age of the group to which ''Platanus'' belongs (the 'plane-tree' family Platanaceae) is no more than ~65My of age, which provides a maximum age constraint for {{{'clade_1'}}}. There is little additional fossil information to inform a calibration prior for this group, so we will adopt a fairly vague calibration prior to reflect this uncertainty, and constrain the MRCA of {{{'clade_1'}}} to a uniform calibration prior bounded between 45 to 65 MA. This is achieved via the xml element depicted below:

3. Editing XML Input File

2009-03-20 02:47:29

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- i. The test for the monophyly of {{{'clade_1'}}} invokes a {{{'booleanLikelihood'}}} element that returns a value of 1 when its argument is true and a value of 0 when it is false. Specifically, we designate a {{{'booleanLikelihood'}}} statistic, which we designate {{{'clade1_constraint'}}}, that has as its argument the monophyly statistic, {{{'clade1_constraint'}}}. This is achieved by means of the xml element depicted below:	+ i. The test for the monophyly of {{{'clade_1'}}} invokes a {{{'booleanLikelihood'}}} element that returns a value of 1 when its argument is true and a value of 0 when it is false. Specifically, we designate a {{{'booleanLikelihood'}}} statistic, which we designate {{{'clade1_constraint'}}}, that has as its argument the monophyly statistic, {{{'clade1_monophyly'}}}. This is achieved by means of the xml element depicted below:

3. Editing XML Input File

2009-03-17 16:37:48

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	+

3. Editing XML Input File

2009-03-17 16:34:44

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- This entails 5 main steps: (1) defining the clade to which the fossil calibration applies, (2) monitoring and (3) enforcing the monophyly of that clade, (4) monitoring the age of that clade, and (5) assigning a prior probability density to describe the age of the fossil.	+ This entails 5 main steps: (1) defining the clade to which the fossil has been assigned, (2) monitoring and (3) enforcing the monophyly of that clade, (4) monitoring the age of that clade, and (5) assigning a prior probability density to describe the age of the fossil.

3. Editing XML Input File

2009-03-17 16:33:19

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- We've now made a series of modifications to our XML file to define the clade to which the fossil has been assigned, to monitor and enforce the monophyly of that clade, and to monitor and constraint the age of the calibrated clade. Are we finally ready to run the BEAST analysis? Not quite yet. Attempting to do so will cause BEAST to generate the following error message:	+ We've just completed a series of modifications to our XML file that defines the clade to which the fossil belongs, to monitors and enforces the monophyly of that clade, and monitors and constrains the age of this clade. Are we finally ready to run the BEAST analysis? Not quite yet. Attempting to do so will cause BEAST to generate the following error message:
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- What gives? As suggested by the error message, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have defined, which results in an {{{‘initial state is incompatible with one or more 'hard' constraints (on monophyly or bounds on parameter values. This will result in Priors with zero probability’}}}. - - and as in, (4) assigning a prior probability density to describe the age of the fossil, (5) and specifying a starting tree that satisfies the resulting temporal and phylogenetic constraintsHaving made the necessary modifications to our xml file How to enforce the monophyly of a specified clade {{{‘text here’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and resulted in a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which is described in the next [http://bodegaphylo.wikispot.org/4._Specifying_a_Starting_Tree tutorial].	+ What gives? As suggested by the error message, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have just defined, which is described in the error message as an {{{‘initial state is incompatible with one or more 'hard' constraints (on monophyly or bounds on parameter values)’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and caused the initial state of the chain to have a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which we will describe in the next [http://bodegaphylo.wikispot.org/4._Specifying_a_Starting_Tree tutorial].

3. Editing XML Input File

2009-03-17 16:28:00

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- and as in, (4) assigning a prior probability density to describe the age of the fossil, (5) and specifying a starting tree that satisfies the resulting temporal and phylogenetic constraintsHaving made the necessary modifications to our xml file How to enforce the monophyly of a specified clade {{{‘text here’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and resulted in a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which is described in the next [http://bodegaphylo.wikispot.org/4._Specifying_a_Starting_Tree Next: tutorial].	+ and as in, (4) assigning a prior probability density to describe the age of the fossil, (5) and specifying a starting tree that satisfies the resulting temporal and phylogenetic constraintsHaving made the necessary modifications to our xml file How to enforce the monophyly of a specified clade {{{‘text here’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and resulted in a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which is described in the next [http://bodegaphylo.wikispot.org/4._Specifying_a_Starting_Tree tutorial].

3. Editing XML Input File

2009-03-17 16:27:37

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- ===== Almost (but not quite) there... =====	+ ===== Almost (but not quite) ready to roll... =====
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- What gives? Essentially, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have defined, which results in	+ What gives? As suggested by the error message, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have defined, which results in an {{{‘initial state is incompatible with one or more 'hard' constraints (on monophyly or bounds on parameter values. This will result in Priors with zero probability’}}}.
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- and as in, (4) assigning a prior probability density to describe the age of the fossil, (5) and specifying a starting tree that satisfies the resulting temporal and phylogenetic constraintsHaving made the necessary modifications to our xml file How to enforce the monophyly of a specified clade {{{‘text here’}}}. - i. Commenting out the coalescent starting tree part 1: the constantSize element {{{‘ text here’}}}. - \|\|<:>[[Image(tree_block1.png, noborder)]]\|\| - i. Commenting out the coalescent starting tree part 2: the coalescentTree element {{{‘ text here’}}}. - \|\|<:>[[Image(tree_block2.png, noborder)]]\|\| - i. Specifying a newick tree element {{{‘ text here’}}}. - \|\|<:>[[Image(newick_block.png, noborder)]]\|\| - i. Modifying the treeModel element {{{‘ text here’}}}. - \|\|<:>[[Image(tree_block3.png, noborder)]]\|\|	+ and as in, (4) assigning a prior probability density to describe the age of the fossil, (5) and specifying a starting tree that satisfies the resulting temporal and phylogenetic constraintsHaving made the necessary modifications to our xml file How to enforce the monophyly of a specified clade {{{‘text here’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and resulted in a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which is described in the next [http://bodegaphylo.wikispot.org/4._Specifying_a_Starting_Tree Next: tutorial].

3. Editing XML Input File

2009-03-17 16:18:59

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3. Editing XML Input File

2009-03-17 16:18:52

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3. Editing XML Input File

2009-03-17 16:18:23

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- This entails 5 main steps: (1) defining the clade to which the fossil calibration applies, (2) enforcing the monophyly of that clade, (3) monitoring the age of that clade, (4) assigning a prior probability density to describe the age of the fossil, (5) and specifying a starting tree that satisfies the resulting temporal and phylogenetic constraints.	+ This entails 5 main steps: (1) defining the clade to which the fossil calibration applies, (2) monitoring and (3) enforcing the monophyly of that clade, (4) monitoring the age of that clade, and (5) assigning a prior probability density to describe the age of the fossil.
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	+ ===== + ===== Almost (but not quite) there... ===== + We've now made a series of modifications to our XML file to define the clade to which the fossil has been assigned, to monitor and enforce the monophyly of that clade, and to monitor and constraint the age of the calibrated clade. Are we finally ready to run the BEAST analysis? Not quite yet. Attempting to do so will cause BEAST to generate the following error message: + \|\|<:>[[Image(error1.png, noborder)]]\|\|
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- ===== Almost (but not quite) there... ===== - How to enforce the monophyly of a specified clade {{{‘text here’}}}.	+ What gives? Essentially, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have defined, which results in + + and as in, (4) assigning a prior probability density to describe the age of the fossil, (5) and specifying a starting tree that satisfies the resulting temporal and phylogenetic constraintsHaving made the necessary modifications to our xml file How to enforce the monophyly of a specified clade {{{‘text here’}}}.

3. Editing XML Input File

2009-03-17 16:06:57

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- In our example data set, the fossil previously been assigned to {{{'clade_1'}}} has been estimated to be ~45My of age, which defines the minimum age for the MRCA of {{{'clade_1'}}}. Moreover, there is evidence that the stem age of the group to which ''Platanus'' belongs (the plane-tree family Platanaceae) is no more than ~65My of age, which provides a maximum age constraint for {{{'clade_1'}}}. There is little additional fossil information to inform a calibration prior for this group, so we will adopt a fairly vague calibration prior to reflect this uncertainty and constrain the MRCA of {{{'clade_1'}}} to a uniform calibration prior bounded between 45 t0 65 MA. This is achieved via the xml element depicted below:	+ In our example data set, the fossil previously been assigned to {{{'clade_1'}}} has been estimated to be ~45My of age, which defines the minimum age for this clade. Moreover, there is evidence that the stem age of the group to which ''Platanus'' belongs (the 'plane-tree' family Platanaceae) is no more than ~65My of age, which provides a maximum age constraint for {{{'clade_1'}}}. There is little additional fossil information to inform a calibration prior for this group, so we will adopt a fairly vague calibration prior to reflect this uncertainty, and constrain the MRCA of {{{'clade_1'}}} to a uniform calibration prior bounded between 45 to 65 MA. This is achieved via the xml element depicted below:

3. Editing XML Input File

2009-03-17 16:04:58

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- How to specify a prior probability distribution to describe the the age of the specified clade {{{‘text here’}}}.	+ Now that we have defined and constrained the monophyly of {{{'clade_1'}}}, we are finally ready to apply a fossil constraint to this group of species. Formally, this involves explicit specification of our prior beliefs about the age of the MRCA of this clade as a prior probability density (i.e., a 'calibration prior'). BEAST is very flexible in this regard, as it can accommodate a variety of probability distributions (e.g., uniform, normal, lognormal, exponential) to reflect various calibration priors. Although it is ''technically'' straightforward to define a calibration prior, this aspect of the analysis is often the most difficult in practice, and should be considered carefully. + + In our example data set, the fossil previously been assigned to {{{'clade_1'}}} has been estimated to be ~45My of age, which defines the minimum age for the MRCA of {{{'clade_1'}}}. Moreover, there is evidence that the stem age of the group to which ''Platanus'' belongs (the plane-tree family Platanaceae) is no more than ~65My of age, which provides a maximum age constraint for {{{'clade_1'}}}. There is little additional fossil information to inform a calibration prior for this group, so we will adopt a fairly vague calibration prior to reflect this uncertainty and constrain the MRCA of {{{'clade_1'}}} to a uniform calibration prior bounded between 45 t0 65 MA. This is achieved via the xml element depicted below:
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- ===== Specifying a starting tree =====	+ ===== Almost (but not quite) there... =====

3. Editing XML Input File

2009-03-17 15:27:39

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- -->[http://bodegaphylo.wikispot.org/2._Formatting_BEAST_Input_Files Back: Tutorial Part 2] [http://bodegaphylo.wikispot.org/Divergence_Time_Estimation_%28Moore%29 Tutorial Home] [http://bodegaphylo.wikispot.org/4._Running_a_BEAST_Analysis Next: Tutorial Part 4]<-- -->Created by [http://www.phylodiversity.net/bmoore/ Brian Moore]<--	+ -->[http://bodegaphylo.wikispot.org/2._Formatting_BEAST_Input_Files Back: Tutorial Part 2] [http://bodegaphylo.wikispot.org/Divergence_Time_Estimation_%28Moore%29 Tutorial Home] [http://bodegaphylo.wikispot.org/4._Specifying_a_Starting_Tree Next: Tutorial Part 4]<-- -->Created by [http://www.phylodiversity.net/bmoore/ Brian Moore]<--

3. Editing XML Input File

2009-03-13 15:54:28

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- == Introduction ==	+ ==Introduction==
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- We want to monitor the monophyly of the clade that we defined above. This requires adding a {{{'monophylyStatistic'}}} element to the xml file that we will designate {{{'clade1_Monophyly'}}}, which monitors the status of the MRCA of {{{'clade_1'}}} during the MCMC analysis. This is achieved by via the following xml element:	+ We want to monitor the monophyly of the clade that we defined above. This requires adding a {{{'monophylyStatistic'}}} element to the xml file that we will designate {{{'clade1_Monophyly'}}}, which monitors the status of the MRCA of {{{'clade_1'}}} during the MCMC analysis. This is achieved using the xml element below:
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- Next, we want to monitor age of the MRCA of {{{'clade_1'}}} so that we can impose a calibration prior to this node in the phylogeny. This involves adding a {{{'tmrcaStatistic'}}} element to the xml file that we will designate {{{'clade1_DTE'}}}, which monitors the age of the MRCA of {{{'clade_1'}}} during the MCMC analysis. This is achieved by via the xml element depicted below:	+ Next, we want to monitor age of the MRCA of {{{'clade_1'}}} so that we can impose a calibration prior to this node in the phylogeny. This involves adding a {{{'tmrcaStatistic'}}} element to the xml file that we will designate {{{'clade1_DTE'}}}, which monitors the age of the MRCA of {{{'clade_1'}}} during the MCMC analysis. This is achieved via the xml element depicted below:
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- i. The test for the monophyly of {{{'clade_1'}}} invokes a {{{'booleanLikelihood'}}} element that returns a value of 1 when its argument is true and a value of 0 when it is false. Specifically, we designate a {{{'booleanLikelihood'}}} statistic, which we designate {{{'clade1_constraint'}}}, that has as its argument the monophyly statistic, {{{'clade1_constraint'}}}. This is achieved by via the xml element depicted below:	+ i. The test for the monophyly of {{{'clade_1'}}} invokes a {{{'booleanLikelihood'}}} element that returns a value of 1 when its argument is true and a value of 0 when it is false. Specifically, we designate a {{{'booleanLikelihood'}}} statistic, which we designate {{{'clade1_constraint'}}}, that has as its argument the monophyly statistic, {{{'clade1_constraint'}}}. This is achieved by means of the xml element depicted below:
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- i. How to monitor and enforce the monophyly of the specified clade {{{‘text here’}}}. This is achieved by via the xml element depicted below:	+ i. The result of the boolean test for the monophyly of {{{'clade_1'}}}, {{{'clade1_constraint'}}}, is returned in the {{{'prior'}}} element of the xml file. This is achieved via the xml element depicted below:

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2009-03-13 15:47:44

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- -->[http://bodegaphylo.wikispot.org/2._Formatting_BEAST_Input_Files Back: Tutorial Part 2] [http://bodegaphylo.wikispot.org/Divergence_Time_Estimation_%28Moore%29 Tutorial Home] [http://bodegaphylo.wikispot.org/4._Running_a_BEAST_Analysis Next: Tutorial Part 4]<--	+ -->[http://bodegaphylo.wikispot.org/2._Formatting_BEAST_Input_Files Back: Tutorial Part 2] [http://bodegaphylo.wikispot.org/Divergence_Time_Estimation_%28Moore%29 Tutorial Home] [http://bodegaphylo.wikispot.org/4._Running_a_BEAST_Analysis Next: Tutorial Part 4]<-- -->Created by [http://www.phylodiversity.net/bmoore/ Brian Moore]<--

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- How to monitor and enforce the monophyly of the specified clade {{{‘text here’}}}. - i. How to monitor the monophyly of the specified clade {{{‘text here’}}}.	+ Because we wish to apply our fossil calibration to the MRCA of {{{'clade_1'}}}, it is convenient to constrain the monophyly of this clade. This involves two steps. First, we define a boolean test for the monophyly of {{{'clade_1'}}}, which returns a value of zero when its argument is false. Next, we return the result of this test in the {{{'prior'}}} element of the xml file. This ensures that any proposed change to the topology that violates the test will have zero likelihood and so will not be accepted during the MCMC. + i. The test for the monophyly of {{{'clade_1'}}} invokes a {{{'booleanLikelihood'}}} element that returns a value of 1 when its argument is true and a value of 0 when it is false. Specifically, we designate a {{{'booleanLikelihood'}}} statistic, which we designate {{{'clade1_constraint'}}}, that has as its argument the monophyly statistic, {{{'clade1_constraint'}}}. This is achieved by via the xml element depicted below:
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- i. How to monitor and enforce the monophyly of the specified clade {{{‘text here’}}}.	+ i. How to monitor and enforce the monophyly of the specified clade {{{‘text here’}}}. This is achieved by via the xml element depicted below:

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- \|\|<:>[[Image(clade_block.png, noborder)]]\|\|	+ \|\|<:>[[Image(clade_block.png, noborder)]]\|\|
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- How to monitor the age of the specified clade {{{‘text here’}}}.	+ Next, we want to monitor age of the MRCA of {{{'clade_1'}}} so that we can impose a calibration prior to this node in the phylogeny. This involves adding a {{{'tmrcaStatistic'}}} element to the xml file that we will designate {{{'clade1_DTE'}}}, which monitors the age of the MRCA of {{{'clade_1'}}} during the MCMC analysis. This is achieved by via the xml element depicted below:

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- How to specify a subset of species {{{‘text here’}}}. - \|\|<:>[[Image(clade_block.png, noborder)]]\|\|	+ The fossil that we will use to calibrate divergence time estimates for the genus ''Platanus'' has been assigned to a subclade comprising four species, ''P. occidentalis'', ''P. occidentalis'', ''P. orientalis'', and ''P. racemosa''. Previous Bayesian analyses using MrBayes indicate strong support for this clade (i.e., ''{{{Pr}}}'' {{{>0.99}}}). So, the first thing we need to do is define a {{{'taxa'}}} element that includes these four species, which we designate {{{'clade_1'}}}. This is achieved by adding the xml element depicted below: + \|\|<:>[[Image(clade_block.png, noborder)]]\|\|
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- How to monitor the monophyly of a specified clade {{{‘text here’}}}.	+ We want to monitor the monophyly of the clade that we defined above. This requires adding a {{{'monophylyStatistic'}}} element to the xml file that we will designate {{{'clade1_Monophyly'}}}, which monitors the status of the MRCA of {{{'clade_1'}}} during the MCMC analysis. This is achieved by via the following xml element:

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- -->[http://bodegaphylo.wikispot.org/2._Formatting_BEAST_Input_Files#preview Back: Tutorial Part 2] [http://bodegaphylo.wikispot.org/Divergence_Time_Estimation_%28Moore%29 Tutorial Home] [http://bodegaphylo.wikispot.org/4._Running_a_BEAST_Analysis Next: Tutorial Part 4]<--	+ -->[http://bodegaphylo.wikispot.org/2._Formatting_BEAST_Input_Files Back: Tutorial Part 2] [http://bodegaphylo.wikispot.org/Divergence_Time_Estimation_%28Moore%29 Tutorial Home] [http://bodegaphylo.wikispot.org/4._Running_a_BEAST_Analysis Next: Tutorial Part 4]<--

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- Open the 'base' xml file (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler]. Both the base xml file and the manually edited xml file are included in the example data files for the tutorial ([[File(DTE Input Files.zip)]]). Note that the screen captures below include the line numbers in the edited xml file to help you identify the location of the corresponding edits to the xml file.	+ Open the 'base' xml file (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler]. Both the base xml file and the manually edited xml file are included in the example data files for the tutorial: [[File(DTE Input Files.zip)]]. Note that the screen captures below include the line numbers in the edited xml file to help you identify the location of the corresponding edits to the xml file.

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- Open the 'base' xml file (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler]. Both the base xml file and the manually edited xml file are included in the example data files for the tutorial [[File(DTE Input Files.zip)]]. Note that the screen captures below include the line numbers in the edited xml file to help you identify the location of the corresponding edits to the xml file.	+ Open the 'base' xml file (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler]. Both the base xml file and the manually edited xml file are included in the example data files for the tutorial ([[File(DTE Input Files.zip)]]). Note that the screen captures below include the line numbers in the edited xml file to help you identify the location of the corresponding edits to the xml file.

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- Open the 'base' xml file (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler]. Both the base xml file and the manually edited xml file are included in the example data files. Note that the screen captures below include the line numbers in the edited xml file to help you identify the location of the corresponding edits to the xml file.	+ Open the 'base' xml file (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler]. Both the base xml file and the manually edited xml file are included in the example data files for the tutorial [[File(DTE Input Files.zip)]]. Note that the screen captures below include the line numbers in the edited xml file to help you identify the location of the corresponding edits to the xml file.

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- Open the xml file (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler]. Both the 'base' xml file that was generated using BEAUti and the manually edited xml file are included in the example data files, and the screen captures below show the line numbers in the edited xml file.	+ Open the 'base' xml file (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler]. Both the base xml file and the manually edited xml file are included in the example data files. Note that the screen captures below include the line numbers in the edited xml file to help you identify the location of the corresponding edits to the xml file.

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- Open the xml file (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler]. Note that both the 'base' xml file generated using BEAUti and the manually edited xml file are included in the [[File(example data files.zip)]].	+ Open the xml file (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler]. Both the 'base' xml file that was generated using BEAUti and the manually edited xml file are included in the example data files, and the screen captures below show the line numbers in the edited xml file.

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- Open the xml file (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler]. Note that both the 'base' xml file generated using BEAUti and the manually edited xml file are included in the [[File(example data files)]].	+ Open the xml file (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler]. Note that both the 'base' xml file generated using BEAUti and the manually edited xml file are included in the [[File(example data files.zip)]].

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- Open the xml file (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler].	+ Open the xml file (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler]. Note that both the 'base' xml file generated using BEAUti and the manually edited xml file are included in the [[File(example data files)]].
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- ===== Step 2: Monitoring the monophyly of a clade =====	+ ===== Step 2: Monitoring the monophyly of the specified clade =====

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	+ -->[http://bodegaphylo.wikispot.org/2._Formatting_BEAST_Input_Files#preview Back: Tutorial Part 2] [http://bodegaphylo.wikispot.org/Divergence_Time_Estimation_%28Moore%29 Tutorial Home] [http://bodegaphylo.wikispot.org/4._Running_a_BEAST_Analysis Next: Tutorial Part 4]<--

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- BEAUti is very helpful for translating standard NEXUS formatted files to the xml format read by BEAST and facilitates specification for relatively basic analyses. However, to realize the full potential of BEAST, we will ultimately need to become familiar with the xml file format. Here, we describe how to modify the xml file in a text editor to apply a fossil calibration to an internal node of the phylogeny.	+ BEAUti is very helpful for translating standard NEXUS formatted files to the xml format read by BEAST, and facilitates specification of input files for relatively simple analyses. However, to realize the full potential of BEAST, we will ultimately need to become familiar with the xml file format. Here, we describe how to modify the xml file in a text editor to apply a fossil calibration to an internal node of the phylogeny.
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- ===== Step 1 ===== - From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}.	+ ===== Step 1: Defining a clade ===== + How to specify a subset of species {{{‘text here’}}}.
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- ===== Step 2 ===== - From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}. - \|\|<:>[[Image(tree_block1.png, noborder)]]\|\| - - From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}. - \|\|<:>[[Image(tree_block2.png, noborder)]]\|\| - - From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}. - \|\|<:>[[Image(tree_block3.png, noborder)]]\|\| - - - ===== Step 3 ===== - From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}. - \|\|<:>[[Image(newick_block.png, noborder)]]\|\| - - - ===== Step 4 ===== - From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}. - \|\|<:>[[Image(treemodel.png, noborder)]]\|\| - - - ===== Step 5 ===== - From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}.	+ ===== Step 2: Monitoring the monophyly of a clade ===== + How to monitor the monophyly of a specified clade {{{‘text here’}}}.
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- ===== Step 6 ===== - From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}.	+ ===== Step 3: Monitoring the age of the specified clade ===== + How to monitor the age of the specified clade {{{‘text here’}}}.
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- ===== Step 7 ===== - From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}. - \|\|<:>[[Image(boolean_block.png, noborder)]]\|\|	+ ===== Step 4: Enforcing the monophyly of the specified clade ===== + How to monitor and enforce the monophyly of the specified clade {{{‘text here’}}}. + i. How to monitor the monophyly of the specified clade {{{‘text here’}}}. + \|\|<:>[[Image(boolean_block.png, noborder)]]\|\| + i. How to monitor and enforce the monophyly of the specified clade {{{‘text here’}}}. + \|\|<:>[[Image(posterior_block.png, noborder)]]\|\|
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- ===== Step 8 ===== - From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}.	+ ===== Step 5: Calibrating the age of the specified clade ===== + How to specify a prior probability distribution to describe the the age of the specified clade {{{‘text here’}}}.
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	+ + + ===== Specifying a starting tree ===== + How to enforce the monophyly of a specified clade {{{‘text here’}}}. + i. Commenting out the coalescent starting tree part 1: the constantSize element {{{‘ text here’}}}. + \|\|<:>[[Image(tree_block1.png, noborder)]]\|\| + i. Commenting out the coalescent starting tree part 2: the coalescentTree element {{{‘ text here’}}}. + \|\|<:>[[Image(tree_block2.png, noborder)]]\|\| + i. Specifying a newick tree element {{{‘ text here’}}}. + \|\|<:>[[Image(newick_block.png, noborder)]]\|\| + i. Modifying the treeModel element {{{‘ text here’}}}. + \|\|<:>[[Image(tree_block3.png, noborder)]]\|\|

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- Open the xml file that (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler].	+ Open the xml file (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler].

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- Open the xml file that (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/TextWrangler].	+ Open the xml file that (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler].

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- BEAST reads input files written in xml—the extended markup language—that is similar to the more familiar html (hyper-text markup language) used in web applications. This may seem to be an odd choice, as it can be a bit intimidating for users not familiar with xml and tends to be quite verbose. On the other hand, this format does afford great flexibility for specifying almost arbitrarily complex analyses. In any case, if we want to use BEAST, we need to gain some familiarity with this file format, which we hope to achieve through the following exercise.	+ BEAUti is very helpful for translating standard NEXUS formatted files to the xml format read by BEAST and facilitates specification for relatively basic analyses. However, to realize the full potential of BEAST, we will ultimately need to become familiar with the xml file format. Here, we describe how to modify the xml file in a text editor to apply a fossil calibration to an internal node of the phylogeny.
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- There are 2 main steps to formatting an input file for divergence time estimation using BEAST: generating a base file with BEAUti and then modifying it with a text editor. The latter will be described in the part 3 of the tutorial.	+ This entails 5 main steps: (1) defining the clade to which the fossil calibration applies, (2) enforcing the monophyly of that clade, (3) monitoring the age of that clade, (4) assigning a prior probability density to describe the age of the fossil, (5) and specifying a starting tree that satisfies the resulting temporal and phylogenetic constraints.
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- Open the program BEAUti. This is a ‘helper’ application for BEAST that reads the more standard file NEXUS and generates (almost usable) xml files for basic analyses with BEAST.	+ Open the xml file that (previously generated with BEAUti) in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/TextWrangler].

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- \|\|<:>[[Image(newick_block.png, noborder)]]\|\|	+ \|\|<:>[[Image(tree_block1.png, noborder)]]\|\| + + From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}. + \|\|<:>[[Image(tree_block2.png, noborder)]]\|\| + + From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}. + \|\|<:>[[Image(tree_block3.png, noborder)]]\|\|
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- \|\|<:>[[Image(newick_block.png, noborder)]]\|\|	+ \|\|<:>[[Image(newick_block3.png, noborder)]]\|\|
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- \|\|<:>[[Image(tmrca_block.png, noborder)]]\|\|	+ \|\|<:>[[Image(monophyly_block.png, noborder)]]\|\|
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	+ \|\|<:>[[Image(boolean_block.png, noborder)]]\|\| + + + ===== Step 8 ===== + From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}.

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	+ == Introduction == + BEAST reads input files written in xml—the extended markup language—that is similar to the more familiar html (hyper-text markup language) used in web applications. This may seem to be an odd choice, as it can be a bit intimidating for users not familiar with xml and tends to be quite verbose. On the other hand, this format does afford great flexibility for specifying almost arbitrarily complex analyses. In any case, if we want to use BEAST, we need to gain some familiarity with this file format, which we hope to achieve through the following exercise. + + There are 2 main steps to formatting an input file for divergence time estimation using BEAST: generating a base file with BEAUti and then modifying it with a text editor. The latter will be described in the part 3 of the tutorial. + + Open the program BEAUti. This is a ‘helper’ application for BEAST that reads the more standard file NEXUS and generates (almost usable) xml files for basic analyses with BEAST. + + ===== Step 1 ===== + From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}. + \|\|<:>[[Image(clade_block.pdf, noborder)]]\|\| + + + ===== Step 2 ===== + From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}. + \|\|<:>[[Image(monophyly_block.pdf, noborder)]]\|\| + + + ===== Step 3 ===== + From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}. + \|\|<:>[[Image(newick_block.pdf, noborder)]]\|\| + + + ===== Step 4 ===== + From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}. + \|\|<:>[[Image(newick_block.pdf, noborder)]]\|\| + + + ===== Step 5 ===== + From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}. + \|\|<:>[[Image(newick_block.pdf, noborder)]]\|\| + + + ===== Step 6 ===== + From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}. + \|\|<:>[[Image(treemodel_block.pdf, noborder)]]\|\| + + + ===== Step 7 ===== + From the '''File''' menu, select the {{{‘Import NEXUS’}}} option, and navigate to the directory that contains the file {{{‘Platanus_DTE.nex’}}}. + \|\|<:>[[Image(posterior_block.pdf, noborder)]]\|\|