pal | oriented programming library for molecular evolution
kandi X-RAY | pal Summary
kandi X-RAY | pal Summary
Mirror of Drummond, A., & Strimmer, K. (2001). PAL: an object-oriented programming library for molecular evolution and phylogenetics.
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- Estimate and estimate the best estimate of the parameters
- Computes the distance of each site pattern in the substitution model
- Calculates the diagonal of the multivariate function
- Optimise the branch lengths
- Sets the branch
- Computes the likelihood of an arc
- Get position of codon alignment
- Gets the position of the codon alignment
- Get the table data
- Gets the states for a particular site
- Deserialize this node
- Computes the likelihood of an arc
- Compute the next gaussian distribution
- This method calculates the extended implementation probabilities of the transitions
- Deserialization
- Calculates the post extended lattice
- Report a set of bootstraps
- Merge by Identifiers
- Build the rate matrix
- Prints information about the substitution
- Checks if muChanges are valid
- Test the test harness
- Parse a Demographic model from a DOM document
- Generates a tree for the clusters
- Computes the lv value
- Prints the test tree
pal Key Features
pal Examples and Code Snippets
Community Discussions
Trending Discussions on pal
QUESTION
I'm aiming to reproduce an animated figure by Ed Hawkins on climate change in R with gganimate. The figure is called climate spiral. While a static ggplot figure shows the correct order of lines by year (the most recent data on top), the animated plot with transition_reveal() results in a wrong order of the lines.
Here is a reproducible example code with synthetic data:
...ANSWER
Answered 2022-Mar-24 at 04:25This isn't the answer per se. This is the why. You'll have to tell me what you prefer given this information for me to give you a solution.
I tried a few things—each of which I was just sure would work but did not. So, I wanted to see what was happening in ggplot. My hunch proved correct. Your data is in order of value_yr in the png, not year.
I repeat this question at the end:
Either you can put the animation in order of
value_yror you can put the color inggplotin order by year. Which would you prefer?
How do I know? I extracted the assigned colors in the object.
QUESTION
I built upon this thread to plot a spatial heatmap. The difference is that I do not want to compute the density of points because I already have the value for the level of "heat". In detail I want to plot the population density of the canton of Berne (Switzerland) with colour gradients.
The population data is from the Swiss statistical office and counts the inhabitants per hectare (100m x 100m squares), downloadable here (the "STATPOP2020.csv" file). Building on jlhoward answer in thread my code so far is:
...ANSWER
Answered 2022-Mar-20 at 14:15The problem, as you have already established, is that you want a contour map that represents population density, not the density of measurements, which is what stat_density_2d does. It is possible to create such an object in R, but it is difficult when the measurements are not spaced regularly on a grid (as is the case with this data). It may be best to use geom_point here for that reason:
QUESTION
Java 11, Spring, Hibernate & MySQL here. I have some tables:
...ANSWER
Answered 2022-Feb-26 at 09:42I wasn't able to replicate your exact exceptions, but after tinkering a bit, i made it work, locally at least...
QUESTION
I am working with the R programming language.
Using the "leaflet" library, I made the following 3 maps:
...ANSWER
Answered 2022-Feb-23 at 08:34Leaflet has the concept of overlay groups (see here)
QUESTION
I recently asked this question about how to colour nodes by variable. And the code works great. However, I'm back trying to colour the terminal nodes separately. For example, if I create some data, then turn them into tidygraph objects and plot them using ggraph then I get something like this:
...ANSWER
Answered 2022-Feb-21 at 15:11If I understand correctly, you want to apply a different colour mapping to
the terminal nodes, mapping value to colour rather than name, and using
a different colour scale altogether. ggplot2 doesn’t support that directly,
but you can use e.g. ggnewscale to apply a different scale for the rest
of the plot.
I simplified your example a bit to focus on the new scale application:
QUESTION
I had to write a program in c as a homework assignment. The program checks if the inputed string is a palindrome. Unfortunately I am getting a segmentation fault error when executing my program.
According to my knowledge segmentation fault means I am accessing memory that does not belong to me.
After some trying I found out, that I get that error "during" the marked scanf function. Please help.
This is the source-code:
...ANSWER
Answered 2022-Feb-01 at 17:32the for loop in fStrRev is what's causing you segmentation fault
QUESTION
I am trying to work with flash memory on MPC5748G - a microcontroller from NXP running FreeRTOS 10.0.1, and I get some behaviour that I can't understand.
I am allocating memory manually, and the assignment seems not to work. However, I can reach the value at the address when using 'printf' - but only from the same function. (I'm using the copy of a pointer, to make sure that some sore of compiler optimisation doesn't take place)
...ANSWER
Answered 2022-Feb-16 at 16:50The problem was writing to FLASH memory - it hasn't been correctly initialized.
The proper way to write to flash on MPC5748g using the SDK 3.0.3 is following:
- save flash controller cache
- initialise flash
- check and protect UT block
- unblock an address space
- erase a block in this space
- check if the space block is blank
- program the block
- verify if the block is programmed correctly
- check sum of the programmed data
- restore flash controller cache
The strange behaviour of printf and pointer was due to compiler optimization. After changing the compiler flags to -O0 (no optimization), the error was consistent.
The same consistent error can be achieved when marking the pointers as 'volatile'.
QUESTION
I am trying to crease a grid of points corresponding to luminescence values in a 384-well plate experiment. I am drawing the plate as a .png file and overlaying the grid such that each point should sit in one well of the plate. Example code and data provided.
Is it possible to do this with ggplot2?
I am using the following code (example data provided):
...ANSWER
Answered 2022-Feb-14 at 16:50By manually adjusting the position of the image with xmin/xmax & ymin/ymax, fixing the pitch of rows and columns with coord_fixed(clip = "off) and expanding the plot.margin in theme I was able to get something that seems like it will work.
QUESTION
I am trying to plot a scatter plot with 22 variables, so they all need to have different markers. I thought of repeating some shapes and colors from RColorBrew, and everything works fine, except for the legend that does not update with the colors I selected (please see image below). I also attached a working example below. What could I possibly be doing wrong?
...ANSWER
Answered 2022-Jan-30 at 22:16There are two issues:
I you want to have your colors make use of
scale_color_manualand mapyon thecoloraes as you did with shapeThe reason your legend does not get colored is that you have set
guides(color = "none")
QUESTION
If I copy paste the example given on Seaborn website to make a "Ridge Plot", the code fails in two different points:
...ANSWER
Answered 2022-Jan-19 at 18:52You can replace g.figure with g.fig. g.figure is intended to be the new name for the same variable. refline() is new in seaborn 0.11.2 (the website supposes you run the last published version). You could replace the call to g.refline() with g.map(plt.axhline, y=0, linewidth=2, linestyle="-", color=None, clip_on=False).
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install pal
You can use pal like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the pal component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .
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