Recon is an algorithm for generating a description of a population from a sample (see Section 2, Terminology).
More precisely, it uses the distribution of species counts in a sample to estimate the distribution of species sizes in the population from which the sample was drawn.
The code provided in this directory:
A species is group made up of one or more individuals. The number of individuals of a given species is that species' size. A sample is a set of individuals from one or more species that is drawn randomly from a population. Species represented in the population that are not represented in the sample are called missing species.
Diversity refers to any of a set of measures of the frequency distribution in the population. They can be thought of as effective numbers of species in the population. The Hill numbers (qD, read "D-q") are a family of diversity measures defined by the parameter q, which determines the degree to which diversity measures are weighted toward larger species. For example, 0D is species richness, a diversity measure that weights all species equally (and so is just a count of the number of different species). infD is the reciprocal of the Berger-Parker Index, the effective number of species if all species were the size of the largest species. Simple mathematical transformations of Shannon entropy (q=1), Gini-Simpson Index (q=2), and other common diversity measures correspond to different Hill numbers.
Given a set of observations of species frequency in the sample, outputs a set of parameters that describe the maximum-likelihood species frequency distribution in the parent population, without overfitting.
python recon.py [-c -d BIN_SIZE -l PARAMETER_LIMIT -t THRESHOLD -v -r] FILE_OUT DATA_FILE
python recon.py -l 10 -t 30 test.out recon_test_data.txt
A fit file with parameters that describe the parent population. Diversity measurements for the population can be output and displayed from this file (see section 5, Displaying results). These parameters are called "weights" and "means." The weights w_j give the proportion of species in the population that have j individuals. The means are Poisson parameters; they give the mean number of individuals a species of size j contributes to the sample.
FILE_OUT the filename to be used for output. Note that if this file exists it will not be overwritten; instead, recon will exit with an error message.
DATA_FILE a text file containing the number of individuals of each species seen in the sample (i.e., the species sizes in the sample).
The default format is a tab-delimited file with lines of the form
species name species size
with a newline character delimiting lines. Species size is an integer. Sample data in this format can be found in the file recon_test_data.txt; in it, species1 has 1 individual, species2 has 1 individual, etc. up to species100; species 101 has 2 individuals, etc.
-c The -c option allows recon to read an alternative tab-delimited format with lines of the form
species size number of species of this size
Both values are integers. Example data in this format can be found in recon_test_data_distribution_in_file.txt; this is the same data as in recon_test_data.txt, just in the alternative format. (Note that Recon does not need species names.) The number of species of size 1 (i.e., the number of species with one individual each) in the sample is 100, the number of species of size 2 is 30, etc.
-d BIN_SIZE (default: 1) Average number of observations per individual. In many circumstances, each individual in the sample will be observed and counted once. However, there are cases where each individual in the sample will be observed and counted multiple times. BIN_SIZE allows for this possibility.
-l PARAMETER_LIMIT (default: 20) The maximum number of parameters that the algorithm will use to fit the data (default, 20). The recon algorithm will continue adding parameters until the (corrected) Akaike Information Criterion indicates that additional parameters are not justified. In practice the limit of 20 is rarely reached.
-t THRESHOLD (default: 50) The -t option allows you to modify THRESHOLD, the size above which sampling error is considered small, which means that Recon will assume the frequency of species of this size or greater in the population is the same as the frequency in the sample. It defaults to 50, but 30 usually gives good results. This is because if, in a sample from a well mixed population, species A is seen 30 times in a sample it is very unlikely that there is another species B which is the same size as A in the parent population but is missing or very poorly reperesented in the sample. Smaller values will give faster run times but less accurate results.
-v The -v option produces verbose output. It will print the starting and finishing parameters of every step that recon takes during the fit. This may typically be tens of thousands of lines.
Given a fit file (either the output from Section 4 or any population description in that format), outputs a table of diversity measures as Hill numbers (see Section 3, Terminology).
python recon.py -T -b ERROR_BAR_PARAMETERS FILE_OUT FILE_IN1 [FILE_IN2 FILE_IN3 ...]
python recon.py -T -b error_bar_params.txt error_test.out test.out
A table of Hill numbers for the reconstructed distribution, one row for each input file (see FILE_IN1 below). The columns labelled "obs" show the Hill numbers from the sample. The columns labeled "MLE" (maximum-likelihood estimate) show the Hill numbers Recon has estimated for the population. Since 0D_MLE is the estimate of the species richness in the parent population, the estimated missing species is 0D_MLE - 0D_obs.
-T Tells Recon to output a table of diversity measures.
-b ERROR_BAR_PARAMETERS A file that contains parameters for constructing error bars on fits. The supplied file error_bar_params.txt can be used. Alternatively, Recon can generate an error bar parameter file from a set of gold standard fits.
FILE_OUT The desired name of the output file.
FILE_IN1 The input file. A fit file output from the fit in section 4, Running Recon.
[FILE_IN2, FILE_IN3 ...] These are additional input files. Each file will generate one row in the output table.
Using Recon to generate an error bar parameter file based on from a set of fits on data for which the number of missing species is known.
python recon.py -e FILE_OUT ERROR_BAR_FIT_DIRECTORY
python recon.py -e error_bars_test.out Test_dir
An error bar parameter file.
-e Tells recon to make an error bar parameter file.
FILE_OUT The name of the new error bar parameter file
ERROR_BAR_FIT_DIRECTORY The name of a directory that contains the fits with known missing species. The known missing species are encoded in the weights and means of the population.
Generates a power table with the minimum sample size required to be able to detect differences of a given magnitude in a given Hill number for two populations. That is, if you have two populations, and want to be able detect a difference in 1D of x%, the table tells you how big your samples have to be.
python recon.py -q HILL_NUMBER [-m MINIMUM_NUMBER_OF_DOUBLETS] FILE_OUT ERROR_BAR_PARAMETERS
python recon.py -p -q 0 power.out error_bar_params.txt
The rows and columns of the output table show the minimum fold differences that can be detected for different population sizes. At present these are hardcoded (lines 1605 and 1611); future versions will implement command-line control.
-q HILL_NUMBER The Hill number for which the power calculation is carried out.
FILE_OUT The desired name of the output file.
ERROR_BAR_PARAMETERS A file that contains parameters for constructing error bars on fits. The supplied file error_bar_params.txt can be used. Alternatively, Recon can generate an error bar parameter file from a set of gold standard fits.
MINIMUM_NUMBER_OF_DOUBLETS is an additional statistical minimum required for good results. The default of 100 should be good for most purposes.
This allows resampling a model. The output gives the maximum likelihood observed species size distribution of samples from the model. This is the distribution that Recon attempts to make as close as possible to the observed species size distribution. The closeness of the fits can be compared to measure the goodness of fit.
python recon.py -r FILE_OUT FILE_IN
python recon.py -r resample.out test.out
A list of species sizes up to the threshold that was used in the original fit is outputted, together with a count of species for each size. Output is written both to standard output and to FILE_OUT.
FILE_OUT The desired name of the output file.
FILE_IN A file that contains model fitted parameters as output from a previously completely Recon fit.
Correspondence should be addressed to Ramy Arnaout at rarnaout at gmail dot com.
PLEASE READ THIS AGREEMENT. ANY USE OF THE SOFTWARE OR ANY OF THE SOURCE CODE, OR REPRODUCTION OR MODIFICATION OF THE SOFTWARE OR SOURCE CODE INDICATES YOUR ACCEPTANCE OF THE TERMS OF THIS AGREEMENT. IF YOU DO NOT AGREE, DO NOT USE, COPY, OR MODIFY THE SOFTWARE. YOU MAY PRINT THIS AGREEMENT FOR YOUR RECORDS.
THIS SOURCE CODE SOFTWARE LICENSE (the “Agreement”) is between Beth Israel Deaconess Medical Center, Inc. (“BIDMC”) and you (“Licensee”) as of the date that you accept these terms by clicking “Agree” below (“Effective Date”). You agree as follows:
(a) “Derivative” means any translation, adaptation, alteration, transformation, or modification, including inclusion as part of another software program or product, of the Software. (b) “Embedded Terms” means any terms and conditions of this Agreement embedded in the Source Code. (c) “Intellectual Property Rights” means all patents, patent rights, patent applications, copyrights, copyright registrations, trade secrets, trademarks and service marks (including, where applicable, all derivative works of the foregoing). (d) “Object Code” means computer programs assembled, compiled, or converted to magnetic or electronic binary form, which are readable and useable by computer equipment. (e) “Software” means the software program known as, “Recon: Reconstruction of Estimated Communities from Observed Numbers”, including its Object Code and Source Code. (f) “Source Code” means computer programs written in higher-level programming languages and readable by humans.
Subject to the terms and conditions of this Agreement, BIDMC grants to Licensee a no cost, personal, non-exclusive, non-transferable, limited license (without the right to sublicense) to download the Software, and to copy, make Derivatives and use the Software for Licensee’s internal academic and research purposes during the term of this Agreement. Any rights not expressly granted in this Agreement are expressly reserved. (a) Derivatives. Licensee agrees that from time to time, or upon request by BIDMC, Licensee will deliver all Derivatives to BIDMC and hereby grants to BIDMC a no cost, personal, perpetual, irrevocable, non-exclusive, non- transferable, limited license (with the right to sublicense) to download the Derivatives, to copy, distribute and make Derivatives of the Derivative, and to use the Derivative for BIDMC’s internal academic and research purposes. (b) Commercial Restrictions on Use of the Software. The following are prohibited without obtaining a commercial license from the Office of Technology Ventures at BIDMC: (i) Using the Software or any Derivative to produce any commercial product or to provide any commercial service. (ii) Charging a fee for use of the Software or any Derivative for any purpose. (iii) Distributing the Software or any Derivative to any other party, unless the distribution is made subject to this Agreement and the recipient “Agrees” to this Agreement through the website: https://github.com/ArnaoutLab/Recon (c) Patents. BIDMC does not grant through this Agreement any licenses under any BIDMC patent or patent application. (d) Intellectual Property Rights Notices; Embedded Terms. Licensee is prohibited from removing or altering any of the Intellectual Property Rights notice(s) and any Embedded Terms embedded in the Software. Licensee must reproduce the unaltered Intellectual Property Rights notice(s) and the Embedded Terms in any full or partial copies of the Source Code that Licensee makes. (e) Export Compliance. Licensee acknowledges and agrees that U.S. export control laws and other applicable export and import laws govern download and use of the Software. Licensee will neither export nor re-export, directly or indirectly, the Software in violation of U.S. laws or use the Software for any purpose prohibited by U.S. laws. ￼￼￼￼￼￼￼￼￼￼￼￼￼
(a) Disclaimer of Warranties. THE SOFTWARE IS DELIVERED “AS IS.” BIDMC MAKES NO OTHER WARRANTIES WHATSOEVER, EXPRESS OR IMPLIED, WITH REGARD TO THE SOFTWARE PROVIDED UNDER THIS AGREEMENT, IN WHOLE OR IN PART. BIDMC EXPLICITLY DISCLAIMS ALL WARRANTIES OF NON-INFRINGEMENT, MERCHANTABILITY AND OF FITNESS FOR A PARTICULAR PURPOSE. BIDMC EXPRESSLY DOES NOT WARRANT THAT THE SOFTWARE, IN WHOLE OR IN PART, WILL BE ERROR FREE, OPERATE WITHOUT INTERRUPTION OR MEET LICENSEE’S REQUIREMENTS. (b) Limited Liability; No Consequential Damages. THE TOTAL LIABILITY OF BIDMC, ITS AFFILIATES, TRUSTEES, OFFICERS, AND EMPLOYEES IN CONNECTION WITH THE SOFTWARE, OR ANY OTHER MATTER RELATING TO THIS AGREEMENT (WHATEVER THE BASIS FOR THE CAUSE OF ACTION) WILL NOT EXCEED IN THE AGGREGATE OVER THE TERM OF THE AGREEMENT $100. IN NO EVENT WILL BIDMC , ITS AFFILIATES, TRUSTEES, OFFICERS, AND EMPLOYEES BE LIABLE FOR ANY SPECIAL, INCIDENTAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR DAMAGES FOR LOST PROFITS, WHETHER BASED ON BREACH OF CONTRACT, TORT (INCLUDING NEGLIGENCE), PRODUCT LIABILITY, OR OTHERWISE. (c) Failure of Essential Purpose. THE LIMITATIONS SPECIFIED IN THIS SECTION WILL SURVIVE AND APPLY EVEN IF ANY REMEDY SPECIFIED IN THIS AGREEMENT IS FOUND TO HAVE FAILED OF ITS ESSENTIAL PURPOSE.
(a) Right of Termination. BIDMC may, for any reason or no reason, upon written notice sent to the contact information Licensee provides upon clicking “agree”, immediately terminate this Agreement. This Agreement will automatically terminate upon any breach by Licensee of any of the terms or conditions of this Agreement. BIDMC shall not be liable to Licensee or any third party for any termination of this Agreement. (b) Licensee Derivatives. Upon termination or expiration of this Agreement, Licensee shall promptly deliver to BIDMC the Source Code and Object Code of Licensee’s Derivatives and shall immediately cease all use of the Software.
Without BIDMC’s prior written consent, Licensee will not identify BIDMC in any promotional statement, or otherwise use the name of any BIDMC employee or any trademark, service mark, trade name, or symbol of BIDMC.
This Agreement and the rights and obligations hereunder are personal to Licensee, and may not be assigned or otherwise transferred, in whole or in part, without BIDMC’s prior written consent. Any attempt to do otherwise shall be void and of no effect. BIDMC has the right to assign this Agreement or any rights or obligations hereunder to any third party. This Agreement shall be binding upon, and inure to the benefit of, the successors, representatives and permitted assigns of the parties.
This Agreement and all disputes and controversies related to this Agreement, are governed by and construed under the laws of the Commonwealth of Massachusetts, without regard to the choice of law provisions. The state and federal courts located in the Commonwealth of Massachusetts are the exclusive forum for any action between the parties relating to this Agreement. Licensee submits to the jurisdiction of such courts, and waives any claim that such a court lacks jurisdiction over Licensee or constitutes an inconvenient or improper forum. The United Nations Convention on the International Sale of Goods (CISG) shall not apply to the interpretation or enforcement of this Agreement.
This Agreement is originally written in the English language and the English language version shall control over any translations.
This Agreement constitutes the entire agreement, and supersedes all prior and contemporaneous agreements or understandings (oral or written), between the parties about the subject matter of this Agreement. Licensee has no right to waive or modify any of this Agreement without the written consent of BIDMC. No waiver, consent or modification of this Agreement shall bind either party unless in writing and signed by the party granting the waiver. The failure of either party to enforce its rights under this Agreement at any time for any period will not be construed as a waiver of such rights. If any provision of this Agreement is determined to be illegal or unenforceable, that provision will be limited or eliminated to the minimum extent necessary so that this Agreement will otherwise remain in full force and effect and enforceable.
Last Updated June 23, 2015 © 2015 Beth Israel Deaconess Medical Hospital, Inc. All rights reserved.