clade | Simple taxonomy management tool and document classifier

 by   flaxsearch Java Version: Current License: Non-SPDX

kandi X-RAY | clade Summary

kandi X-RAY | clade Summary

clade is a Java library. clade has no bugs, it has no vulnerabilities and it has low support. However clade build file is not available and it has a Non-SPDX License. You can download it from GitHub.

flax clade poc is a proof-of-concept open source taxonomy management and document classification system, based on apache solr. in its current state it should be considered pre-alpha. as open-source software you are welcome to try, use, copy and modify clade as you like. we would love to hear any constructive suggestions you might have. clade taxonomies have a tree structure, with a single top-level category (e.g. in the example data, "social psychology"). there is no distinction between parent and child nodes (except that the former has children) and the hierachical structure of the taxonomy is completely orthogonal from the node data. the structure may be freely edited. each node represents a category, which is represented by a set of "keywords" (words or phrases) which should be present in a document belonging to that category. not all the keywords have to be present - they are joined with boolean or rather than and. a document may belong to multiple categories, which are ranked according to standard solr (tf-idf) scoring. it is
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            kandi-support Support

              clade has a low active ecosystem.
              It has 50 star(s) with 19 fork(s). There are 16 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 1 open issues and 2 have been closed. There are 2 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of clade is current.

            kandi-Quality Quality

              clade has no bugs reported.

            kandi-Security Security

              clade has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              clade has a Non-SPDX License.
              Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

            kandi-Reuse Reuse

              clade releases are not available. You will need to build from source code and install.
              clade has no build file. You will be need to create the build yourself to build the component from source.
              Installation instructions are not available. Examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed clade and discovered the below as its top functions. This is intended to give you an instant insight into clade implemented functionality, and help decide if they suit your requirements.
            • Returns a collection of features for the feature .
            • Get the next input stream .
            • Translates a string literal .
            • Private helper method to print tree .
            • moved from the current position
            • transform a node of a CC
            • Creates an instance of Counter from a map .
            • Returns the k - sequences for the given sequence model .
            • Get the next step .
            • Load a TextClassifier from a text file
            Get all kandi verified functions for this library.

            clade Key Features

            No Key Features are available at this moment for clade.

            clade Examples and Code Snippets

            No Code Snippets are available at this moment for clade.

            Community Discussions

            QUESTION

            How to limit the size of the partition per class in R (starting from imbalanced dataset)
            Asked 2022-Apr-02 at 22:47

            I'd like to partition an imbalanced dataset. My current dataset has 7 classes, some with 10.000 samples and some with 500. I'd basically like to limit the data frame size to 500 observations per class (so 500 observations * 7 classes), for example, so all classes have around 500 observations instead of having some with 10.000, others with 2.000, etc.

            Currently, I'm doing the partition with caret package like this:

            ...

            ANSWER

            Answered 2022-Apr-02 at 22:39

            Consider a base solution using by (wrapper to tapply) to run operations across factor-split subsets:

            Source https://stackoverflow.com/questions/71721377

            QUESTION

            Create bar plot in ggplot2 - Place data frame values instead of count
            Asked 2022-Jan-14 at 17:27

            I'd like to place this data onto a bar plot using ggplot2

            where the column "Clades" would be placed on the X axis and the values from each column (such as the values of 19A, for example) would be place on Y axis

            I'm trying something like this:

            ...

            ANSWER

            Answered 2022-Jan-14 at 17:21

            As cazman said in the comments, you need to get your data in long form for it to work with ggplot2 (efficiently).

            First, use pivot_longer(), and then use ggplot2:

            Source https://stackoverflow.com/questions/70714189

            QUESTION

            insert a legend to a distinct graph
            Asked 2021-Oct-25 at 13:01

            I have one phylogenetic tree as picture below.

            I did make a fake dataframe to get the legend, and now I would like to insert that legend to the center of phylogenetic tree. I used grid.arrange but I could not move the legend position.

            The fake legend that I created

            ...

            ANSWER

            Answered 2021-Oct-25 at 13:01

            The new ggdraw function from cowplot provides one option.

            It accepts any grob, not just ggplot objects.

            Source https://stackoverflow.com/questions/69704283

            QUESTION

            why getting Error in abs(x) : non-numeric argument to mathematical function in ggplot?
            Asked 2021-Aug-28 at 13:27

            Here is the .tsv file for the following script.

            Source code:

            ...

            ANSWER

            Answered 2021-Aug-28 at 13:27

            The results of your df$date reassignment is a list, not a vector. This can be fixed in a number of ways:

            Source https://stackoverflow.com/questions/68956090

            QUESTION

            How to apply a function to a dataframe column in R?
            Asked 2021-Aug-27 at 08:00

            I'm describing my problem below:

            Data Frame:

            ...

            ANSWER

            Answered 2021-Aug-27 at 07:29

            Instead of df["date"], use df$date will work.

            Source https://stackoverflow.com/questions/68949423

            QUESTION

            Formatting phylogeny to map projection (`phylo.to.plot`, or alternate method) in R
            Asked 2021-Jul-06 at 12:34

            I am hoping someone can help me with the formating from phylo.to.plot() or suggest another method that can produce a similar output.

            I have followed tutorial(s) here to produce an output but it seems difficult to alter the resulting figures.

            Briefly these are my questions. I will expand further below.

            1. How to plot a subregion of a "WorldHires" map, not entire region?
            2. Change the shape of the points on the map, but maintain the colour?

            Reproducible example:

            Here is a very basic tree with some randomly assigned geographic locations

            ...

            ANSWER

            Answered 2021-Jul-06 at 12:34

            I improved (somewhat) on my comments by using the map you made in your question. Here's the code:

            Source https://stackoverflow.com/questions/68021264

            QUESTION

            Is it possible to name a column of a tibble using a variable containing a character vector (string)?
            Asked 2021-Jun-28 at 22:10

            Is there a way to name the column of a tibble using a variable? I want to name the first column below Clade for example. I tried paste() and assign(), but neither function seems to do what I want.

            ...

            ANSWER

            Answered 2021-Jun-28 at 22:10

            You can use the following solution:

            • In order to have column names which are variable stored as string we make use of bang bang operator !! which force the evaluation of it succeeding name
            • We also need to use walrus := instead of = which are equivalent and prompts you to supply name (as is the case with our variable name) on it LHS (left hand side)

            Source https://stackoverflow.com/questions/68170333

            QUESTION

            delete line after previous line match
            Asked 2021-Jun-21 at 21:05

            This might be very straightforward but I am having bit of trouble while deleting unwanted line in my text file:

            ...

            ANSWER

            Answered 2021-Jun-21 at 19:55

            I don't know about the Python code but if you join your list into a giant regex boolean then you can do this:

            regex

            Source https://stackoverflow.com/questions/68073801

            QUESTION

            Plot selected points with different colors, on graphs filled with different shapes
            Asked 2020-Dec-22 at 09:44

            I am currently trying to plot a point graph using ggplot2. The data is of 3 categories, but for each of the categories, there are some selected points I would like to highlight (or make them show differently in the graph). There is no any special characteristics like what I manage to check on the previous examples (eg. last point of the category, point outside range,....).

            Attached is the general view of the graph I have got currently, where each category was represented by default shapes.

            The struggle is, how can I highlight the selected point on the graph, with the same shape used for each of the categories, but with different colors? So each of the point will be the same, just that the selected points are with colors other than black. I have 15 selected points for each of the categories to plot on.

            Is this possible to do with ggplot2?

            I cannot reach any case similar with mine, but instead some previous examples on manually assigning colors on the plot. I was just trying out to plot the categories with different colors instead of shapes, and use scale_fill_manual to plot the points in 2 different colors (base color and color for selected points), but it doesn't work, 6 colors appeared instead.

            ...

            ANSWER

            Answered 2020-Dec-22 at 09:44

            To achieve your desired result you could map your variable Selected on color and Genes on shape.

            As a first step I recoded Selected as I was not sure whether it contains missing or empty strings. If you don't want to have a color legend you could do so by adding guides(color=FALSE).

            Source https://stackoverflow.com/questions/65404239

            QUESTION

            How to add output "non_assigned" when there is no match in grep?
            Asked 2020-Oct-21 at 19:38

            When I run a command (COMMAND) on one line of my input file (input.txt) I get an associated result where only one line is interesting, always starting by the world phylum.

            For instance:

            ...

            ANSWER

            Answered 2020-Oct-21 at 19:38

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install clade

            You can download it from GitHub.
            You can use clade 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 clade 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 .

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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            CLONE
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            https://github.com/flaxsearch/clade.git

          • CLI

            gh repo clone flaxsearch/clade

          • sshUrl

            git@github.com:flaxsearch/clade.git

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