SAMBA: Standardized and Automated MetaBarcoding Analyses workflow
Description of the workflow
The SAMBA workflow, developed by the SeBiMER (Ifremer's Bioinformatics Core Facility) is an open-source modular workflow
to process eDNA metabarcoding data. SAMBA is developped using the NextFlow workflow manager (Di Tommaso et al., 2017). SAMBA is built
around three main parts: data integrity checking, bioinformatics processes and statistical analyses. The SAMBA checking process
allows to verify the integrity of the raw data. All bioinformatics processes are mainly based on the use of the next-generation
microbiome bioinformatics platform QIIME 2 (Bolyen et al., 2019 ; version 2020.2) and on the approach of grouping
sequences in ASV (Amplicon Sequence Variants) using DADA2 (Callahan et al., 2016). It also performs extensives analyses
of the alpha- and beta-diversity using homemade R scripts (R CORE TEAM, 2020). SAMBA offers a real alternative to the complex use of
a suite of command line bioinformatics tools while providing access to state-of-the-art methods and tools in the field.
The SAMBA source code, documentation and installation instructions are freely available at SeBiMER GitHub.
In order to achieve the complete analysis, SAMBA uses a range of state-of-the-art software and methods which you will find the list below :
| Tools and softwares | Version |
|---|---|
| SAMBA | {{d.soft.samba}} |
| Required | |
| Nextflow | {{d.soft.nextflow}} |
| Included in SAMBA | |
| QIIME 2 | {{d.soft.qiime2}} |
| R | {{d.soft.R}} |
| microDecon | {{d.soft.microdecon}} |
| DESeq2 | {{d.soft.DESeq2}} |
| metagenomeSeq | {{d.soft.metagenomeSeq}} |
| microbiome | {{d.soft.microbiome}} |
| phyloseq | {{d.soft.phyloseq}} |
| vegan | {{d.soft.vegan}} |
| UpSetR | {{d.soft.UpSetR}} |
| Minimap2 | {{d.soft.minimap2}} |
{% if d.steps.stats_only == 'false' %}
Bioinformatic process
{% if d.steps.data_integrity_enable == 'true' %}Data integrity [optional]
This first step allows to analyze the integrity of your data in order to identify
potential problems related to the sequencing processes. It checks:
- that each read is correctly associated with the proper sample (sequence barcode verification)
- that they come from a single sequencer
- the efficiency of forward and reverse PCR amplification
Results
- All data integrity verification are summarized in this csv file
{% endif %} {% if d.steps.longreads == 'false' %}
Importing raw data
The step performs the import of sequencing data directly from DATAREF into
a QIIME 2 specific format. In addition, descriptive statistics of your data are generated
. The SAMBA workflow ran for you the following commands
Results
Output folder
- Sample repartition according to the sequence count
- All descriptive statistics of your samples are available here (html output)
{% if d.steps.cutadapt_enable == 'true' %}
Primers removal
The third step is to remove the primers using the cutadapt plugin available in
QIIME 2. In addition, descriptive statistics of your data are generated.
The following commands made this step possible using the parameters that you have
defined in the parameters configuration file :
User-defined Cutadapt parameters
-
{% if d.singleEnd == 'false' %}
- Mode: Paired-end
- Forward primer sequence: {{d.cutadapt.primerF}}
- Reverse primer sequence: {{d.cutadapt.primerR}}
- Overlap: {{d.cutadapt.overlap}} {% else %}
- Mode: Single-end
- Primer sequence: {d.cutadapt.primerF}} {% endif %}
- Error rate: {{d.cutadapt.errorRate}}
Results
Output folder
- Sample repartition according to the sequence count
- All descriptive statistics of your samples after the trimming are available here (html output)
- The quality of your data before any quality filtering step is viewable here (html output)
{% endif %}
Sequence quality control and feature table construction
The following step of the workflow is to filter the quality of the sequences according
to the parameters defined yourself by having considered the quality of your data in the
previous step. Also to assemble the forward and reverse sequences, and to identify and remove the
chimeras. To performed this step, the DADA2 R package was used through QIIME 2
using the following commands and your parameters :
User-defined DADA2 parameters
-
{% if d.singleEnd == 'false' %}
- Mode: Paired-end
- Number of bases trimmed in 5' of forward reads: {{d.dada2.FtrimLeft}}
- Number of bases trimmed in 5' of reverse reads: {{d.dada2.RtrimLeft}}
- Length to trim forward reads (0 for no trimming): {{d.dada2.FtruncLen}}
- Length to trim reverse reads (0 for no trimming): {{d.dada2.RtruncLen}}
- Max error rate allowed in forward reads: {{d.dada2.FmaxEE}}
- Max error rate allowed in reverse reads: {{d.dada2.RmaxEE}} {% else %}
- Mode: Single-end
- Number of bases trimmed in 5' of reads: {{d.dada2.trimLeft}}
- Length to trim reads: {{d.dada2.FtruncLen}}
- Max error rate allowed: {{d.dada2.FmaxEE}} {% endif %}
- Minimal quality score allowed: {{d.dada2.minQ}}
- Method for chimeras detection: {{d.dada2.chimeras}}
Results
Output folder
- The dynamics of the different step of filtering can be visualized in this html file and are also available in a tabulated file
- Distribution of sequences in samples
- Feature details are available here (html output)
- Details about the samples can be found by going to this interactive html page
- Finally, you can retrieved the reference sequences of your ASVs in this fasta
A total of {{ r.dada2.asv_count }} ASVs was obtained at this step
{% if d.steps.dbotu3_enable == 'true' %}
ASV clustering [optional]
The following step of the workflow is to cluster ASV according to sequence similarity and
abundance profil. This allow to takes into account the overestimation of diversity
produced by DADA2. It also reduces possible PCR errors. To performed this step,
the dbOTU3 algorithm was used through QIIME 2 using the following commands and the parameters :
User-defined dbOTU3 parameters
- Genetic criterion: {{d.dbotu3.gen_crit}}
- Abundance criterion: {{d.dbotu3.abund_crit}}
- Pvalue criterion: {{d.dbotu3.pval_crit}}
Results
Output folder
- Overview of the results available here (html output)
- Feature details are available here (html output)
- Details about the samples can be found by going to this interactive html page
- Finally, you can retrieved the reference sequences of your ASVs in this fasta
A total of {{ r.dbotu3.asv_count }} ASVs remain after this step. dbOTU3 allowed to cluster {{ r.dbotu3.clustering }} ASVs with others ASVs (i.e. about {{ r.dbotu3.clustering_perc }}% clustering).
{% endif %} {% endif %}
Taxonomic assignation
{% if d.steps.longreads == 'false' %}
The taxonomic assignation performed during the fourth step of the workflow allowed to
affiliate each ASV to a taxonomy by using as reference the database defined by yourself.Commands executed
User-defined QIIME 2 parameters
- Minimal confidence allowed: {{d.taxonomy.confidence}}
- Taxonomic database used: {{d.taxonomy.database}}
Results
Output folder
{% else %}
The taxonomic assignation allowed to affiliate each read to a taxonomy by using as reference the database defined by yourself.
User-defined Minimap2 and Taxonomy parameters
- Sequencing technology: {{d.lr.lr_type}}
- Minimal rank level: {{d.lr.lr_rank}}
- Reference database: {{d.lr.lr_tax_fna}}
- Reference taxonomy: {{d.lr.lr_tax_flat}}
Results
Output folder
- The result of the taxonomic affiliation is available in tabulated formats
{% if d.steps.filtering_tax_enable == 'true' %}
Taxonomy filtering [optional]
This step allows you to filter the ASV table and ASV sequences based on the taxonomy assignation and remove user-defined taxa.
User-defined 'Taxonomy filtering' parameters
- List of taxa to exclude: {{d.tax_filtering.tax_to_exclude}}
Results
Output folder
- ASV table: taxonomy filtered ASV table
- Representative sequence: taxonomy filtered ASV sequences
- Descriptive statistics after the filtering step: html file
A total of {{ r.tax_filtering.asv_rm }} ASVs, assigned to taxa to exclude, were removed. It remains {{ r.tax_filtering.asv_count }} ASVs.
{% endif %} {% if d.steps.microDecon_enable == 'true' %}
Samples decontamination (microDecon) [optional]
If you have sequenced control samples, this step allows you to decontaminate your samples from the sequences identified in these controls. This step is carried out using microDecon and a homemade R script.
User-defined microDecon parameters
- Control list: {{d.microdecon.control_list}}
- Number of blanks: {{d.microdecon.nb_controls}}
- Number of samples: {{d.microdecon.nb_samples}}
Results
Output folder
- New ASV table: decontaminated table
- Representative sequence: decontaminated ASV sequence
- All ASVs listed here were removed because they were in the majority in the control samples
- For all ASVs listed here, a proportion of sequences were removed in each sample. Note that this file also contains the ASVs unique to the controls which have therefore been removed.
A total of {{ r.microdecon.asv_count }} ASVs remain after this step. MicroDecon removed {{ r.microdecon.asv_rm }} ASVs ({{ r.microdecon.asv_rm_ctrl }} ASVs were unique to controls).
{% endif %} {% if d.steps.picrust2_enable == 'true' %}
Functional predictions (PICRUSt2) [optional]
This optional step allows you to predic the functional potential of the communities using PICRUSt2
User-defined PICRUSt2 parameters
- HSP method: {{d.picrust2.method}}
- Max nsti: {{d.picrust2.nsti}}
Results
Output folder
- EC predictions: EC metagenome predictions
- KO predictions: KO metagenome predictions
- METACYC predictions: METACYC abundance predictions
{% for ec in r.picrust.var_tested %}
{{ec}}
{% endfor %}
{% for ko in r.picrust.var_tested %}
{{ko}}
{% endfor %}
{% for metacyc in r.picrust.var_tested %}
{{metacyc}}
{% endfor %}
{% endif %} {% if d.steps.ancom_enable == 'true' %}
Differential abundance testing using ANCOM
This step allows you to test if there are differentially abundant ASVs depending on the variable of interest that you have specified using the following commands :
Results
Output folder
List of all tested variables :
-
{% for v in r.ancom.var %}
- {{ v }} {% endfor %}
{% for v in r.ancom.var %}
ANCOM analysis based on the {{ v }} variable :
-
- The full analysis is available in the following directories:
ASV level ;
family level ;
genus level
- The reports generated by QIIME 2 are available by following the following links: ASV level ; family level ; genus level
{% if r.ancom[v].base > 0 %} - Number of significantly differentially abundant ASVs: {{r.ancom[v].base}} [Full list] {% else %} - No significantly differentially abundant ASVs {% endif %}
{% if r.ancom[v].family > 0 %} - Number of significantly differentially abundant family: {{r.ancom[v].family}} [Full list] {% else %} - No significantly differentially abundant family {% endif %}
{% if r.ancom[v].genus > 0 %} - Number of significantly differentially abundant genus: {{r.ancom[v].genus}} [Full list] {% else %} - No significantly differentially abundant genus {% endif %}
{% endif %} {% if d.steps.longreads == 'false' %}
Final outputs
This is the last step of the bioinformatic process where the goal is to merge the ASV abundance table with the taxonomy file
Results
{% endif %} {% endif %}
General statistical analyses
{% if d.steps.stats_alpha_enable == 'true' %}Alpha diversity [optional]
-
{% for var in r.alpha_div.var_tested %}
- {{ var }} {% endfor %}
Diversity indices
{% for var in r.alpha_div.var_tested %}
{{var}}
{% endfor %}
Rarefaction curve
Taxonomic diversity
{% if d.steps.longreads == 'false' %} {% for var in r.alpha_div.var_tested %}
- Taxonomic barplots group by {{var}} :
Barplot at the phylum level ; Barplot at the class level ; Barplot at the order level ; Barplot at the family level
- The results of the significance tests carried out for each variable on each diversity indexes can be viewed here
{% endif %} {% if d.steps.stats_beta_enable == 'true' %}
Beta diversity by index [optional]
-
{% for v in r.beta_div.var_tested %}
- {{ v }} {% endfor %}
Beta diversity by variable [optional]
{% for var in r.beta_div.var_tested %}
Ordination and hierarchical clustering for variable: {{var}}
{% for method in d.methods %}
{% for index in d.indices %}
{% endfor %}
{% endfor %}
{% endfor %}
{{index}}
{% for stat in d.stats %}
{% if index != "hclustering" %}
{% else %}
{% endif %}
{% endfor %}
{% endfor %}
Explained variance
{% for method in d.methods %}
{% for stat in d.stats %}
{% endfor %}
{% endfor %} {% endif %} {% if d.steps.stats_desc_comp_enable == 'true' %}
Descriptive comparison [optional]
-
{% for var in r.descriptive_comparison.var_tested %}
- {{ var }} {% endfor %}
{% for var in r.descriptive_comparison.var_tested %}
{% endfor %}
{% endif %}
About
Contributors
SAMBA is developped by Ifremer's Bioinformatics Core Facility (SeBiMER)
(French Research Institute for Exploitation of the Sea).
Citations
You can cite the NextFlow publication as follows:
Paolo Di Tommaso, Maria Chatzou, Evan W. Floden, Pablo Prieto Barja, Emilio Palumbo & Cedric Notredame. (2017).
Nextflow enables reproducible computational workflows.
Nature biotechnology. 35(4), 316-319.
You can cite each tool used in SAMBA as follows:
Benjamin J. Callahan, Paul J. McMurdie, Michael J. Rosen, Andrew W. Han, Amy Jo A. Johnson & Susan P. Holmes. (2016).
DADA2: high-resolution sample inference from Illumina amplicon data
Nature methods. 13(7), 581.
Donald T. McKnight, Roger Huerlimann, Deborah S. Bower, Lin Schwarzkopf, Ross A. Alford & Kyall R. Zenger. (2019).
microDecon: A highly accurate read‐subtraction tool
for the post‐sequencing removal of contamination in metabarcoding studies. Environmental DNA. 1(1), 14-25.
 Reproducible, interactive, scalable and
extensible microbiome data science using QIIME 2. Nature biotechnology. 37(8), 852-857.
Gavin M. Douglas, Vincent J. Maffei, Jesse Zaneveld, Svetlana N. Yurgel, James R. Brown, Christopher M. Taylor, Curtis Huttenhower & Morgan G. I. Langille. (2019).
PICRUSt2: An improved and extensible approach for metagenome inference.
BioRxiv. 672295.
Marcel Martin. (2011). Cutadapt removes adapter
sequences from high-throughput sequencing reads. EMBnet. journal. 17(1), 10-12.
R Core Team. (2020). R: A language and environment for statistical computing.
R Foundation for Statistical Computing, Vienna, Austria.
Scott W. Olesen, Claire Duvallet & Eric J. Alm. (2017). dbOTU3:
A new implementation of distribution-based OTU calling. PloS one. 12(5).
Siddhartha Mandal, Will Van Treuren, Richard A. White, Merete Eggesbø, Rob Knight & Shyamal D. Peddada. (2015).
Analysis of composition of microbiomes: a novel method for studying microbial composition.
Microbial ecology in health and disease, 26(1), 27663.


[click for next game]
[click for next game]
You will be given a number of cards to buy - your "goal."
Each envelop has a specific number of cards in it.
Click on an envelope to add its quantity of cards to your cart.
The number of cards in each envelope will remain hidden the entire game.
(hint: look at how your score changes when you click an envelope.)
To win, you must get the same number of cards in your cart as the goal.
Get more cards than the goal and you lose.
[click to hide instructions]


| 1. | |
| Description: | Title format: [DRAFT_NAME] - Autorex |
| Priority: | Medium |
| 2. | |
| Description: | Statusbar merged/extended gimp and paint features |
| Priority: | High |
| 3. | |
| Description: | Tooltips everywhere: Statusbar features too |
| Priority: | Medium |
| 4. | |
| Description: | When resizing the window and calculating canvas margins - recognise which corner is being dragged and uncover this part of canvas first (to 5px margin from border) |
| Priority: | Low |
| 5. | |
| Description: | private void SystemParameters_StaticPropertyChanged(object sender, PropertyChangedEventArgs e) function is called everytime a system parameter changes, but is only used to detect virtual screen size changes. Could use more backwards compatible solution by monitoring resource key. |
| Priority: | Very low |
| 6. | |
| Description: | Functions using windowInitialised flag can be assigned in Window_ContentRendered function |
| Priority: | High |
| 7. | |
| Description: | Make an installer |
| Priority: | Last thing to do |
| 8. | |
| Description: | Make a menu of tools like in Paint |
| Priority: | Optional |
| 9. | |
| Description: | Make outline opaque |
| Priority: | Medium |
| 10. | |
| Description: | Add ability to set drill thickness |
| Priority: | Medium |
| 11. | |
| Description: | Add menu items: View->unit->um |
| Priority: | Medium |
| 12. | |
| Description: | Add static class with constant string messages to support multiple languages or load te strings from file (better) |
| Priority: | Very low |
| 13. | |
| Descripiton: | Add mechanism (like enumeration) to recognise element types like outline, rectangle(group of lines) etc. |
| Priority: | Low |
| 14. | |
| Description: | Add menu options for opening recent projects with another unrolling menu list Open \n Open recent > |
| Priority: | Medium |
| 15. | |
| Desctipiton: | Add ability to select many shapes |
| Priority: | High |
| 16. | |
| Description: | Add tool to create a single dot |
| Priority: | Medium |
| 8. | |
| Description: | Restructurise code |
| Priority: | Very high |


WITNESS LIST Intergovernmental Relations Committee April 30, 2001 - 8:30A SB 322 FOR: Henneberger, John none listed (TX Low Income Housing Information Service), Austin, TX Langendorf, Jean Project Director (United Cerebral Palsy of TX), Austin, TX Mintz, David Director of Governmental Affairs (TX Apartment Ass.), Austin, TX Ocanas, Reymundo none listed (Community Developer Corporations), Austin, TX Rollins, Sandy Executive Director (TX Tenents' Union), Dallas, TX Schwartz, Jonas Program Specialist (Advocacy Incorporated), Austin, TX Smith, Terral Attorney (El Paso Chamber of Commerce), Austin, TX Talerico, Jeanne TX Ass. of Local Housing (TX Ass. of Local Housing Finance Agencies), Austin, TX AGAINST: Goleman, R. Kinnan Attorney (Gulf Coast Waste Disposal Authority), Austin, TX ON: Hawkins, John Policy Analyst (Sunset Advisory Commission), Austin, TX Maxwell, Susan Public Policy Specialist (TX Council for Developmental Disabilities), Austin, TX Stiner, Daisy Executive Director (TDHCA), Austin, TX Sugrue, J. Michael Real Estate Investment (Affordable Housing in TX Financial & Investor Coalition), Plano, TX Registering, but not testifying: For: Borel, Dennis none listed (Coalition of Texans with Disabilities), Austin, TX Cates, Phil Lobbyist (Granger McDonald), Austin, TX Dunaway, Jim Ass. of Rural Housing Communities (Ass. of Rural Housing Communities-TX), Elgin, TX Garvin, John none listed (TX Affiliation of Affordable Housing), Austin, TX Horton, Colleen none listed (TX Advocates Supporting Kids with Disabilities), Austin, TX Marshall, Susan Policy Analyst (The Arc of TX), Austin, TX Against: Fischer, Bill Apartment Developer (Southwest Housing), Dallas, TX


| status | stageId | executorRunTime | inputBytes | outputBytes | shuffleReadBytes | shuffleWriteBytes |
|---|
| taskId | index | attempt | launch Time | Executor ID | host | taskLocality | speculative |
|---|
| id | hostPort | rddBlocks | memoryUsed | diskUsed | totalDuration | totalInputBytes | totalShuffleRead | totalShuffleWrite | maxMemory |
|---|
Driver Stderr
Driver Stdout
Directory Info


{% extends "layout.html" %} {% block page_title %} Disability and medical conditions {% endblock %} {% block content %} {% include "includes/phase_banner_beta.html" %} {{formData | safe}} Do you have any of the following disabilities or health conditions? Do you have any of the following disabilities or health conditions? severe learning disability diabetes controlled by insulin epilepsy any condition affecting your eyes any condition affecting your field of vision, other than needing to wear glasses or contact lenses total loss of sight in one eye any stroke symptoms lasting longer than one month fits or blackouts any type of brain surgery or severe head injury involving in-patient treatment brain tumour an implanted cardiac pacemaker an implanted cardiac defibrilator (ICD) brain tumour an implanted cardiac pacemaker an implanted cardiac defibrilator (ICD) repeated attacks of sudden disabling giddiness any chronic neurological condition including Multiple Sclerosis, Motor Neurone and Huntington's Disease a serious problem with memory or periods of confusion persistent alcohol problem or dependence persistent drug problem or dependence serious psychiatric illness or mental ill health Parkinson's disease narcolepsy Obstructive Sleep apnoea syndrome yes no {% endblock %}


Festival Guide:
Only the
party leader
for the previous set of participants in the festival may register a score.
Go back.


{% extends "layout.html" %} {% block article_body %} {% markdown %} You work hard to earn money. However, it is your emotional relationship with cash that could determine how hard your money works for you. Your own personal psychological relationship with money influences decisions over how to spend, save or invest it. But are you making the right choices? As our personal finances are usually a very private part of our lives, it can be hard to recognise potentially damaging patterns of behaviour. For example, are you always the person who offers to pay in a restaurant at the end of a meal with friends? Or do you earn a fortune in finance, yet never spend money on new clothes? Perhaps you rate yourself as an investor - but could your frequent trading tip over into a gambling addiction? Or could you be spending beyond your means in order to boost your self esteem?


Get the resolved config object from the local, global and environment config instances.

Get the global config instance.
Get a resolved config property.
The key of the property.
Get the local project config instance.
Gets a resolved config property location.
For example, getLocation('logLevel')
will return:
Location.GLOBAL
if resolved to an environment variable.Location.LOCAL
if resolved to local project config.Location.ENVIRONMENT
if resolved to the global config.The key of the property.
Get a resolved file path or environment variable name of the property.
For example, getPath('logLevel')
will return:
$SFDX_LOG_LEVEL
if resolved to an environment variable../.sfdx/sfdx-config.json
if resolved to the local config.~/.sfdx/sfdx-config.json
if resolved to the global config.undefined
, if not resolved.Note: that the path returned may be the absolute path instead of
relative paths such as ./
and ~/
.
The key of the property.
Get a resolved config property.
Throws SfdxError{ name: 'UnknownConfigKey' } An attempt to get a property that's not supported.
The key of the property.
Initialize this instances async dependencies.
Re-read all property configurations from disk.
Asynchronously constructs and initializes a new instance of a concrete subclass with the optional options
.
An options object providing initialization params to the async constructor.
Aggregate global and local project config files, as well as environment variables for
sfdx-config.json
. The resolution happens in the following bottom-up order:SFDX_LOG_LEVEL
)<workspace-root>/.sfdx/sfdx-config.json
)$HOME/.sfdx/sfdx-config.json
)Use ConfigAggregator.create to instantiate the aggregator.
const aggregator = await ConfigAggregator.create(); console.log(aggregator.getPropertyValue('defaultusername'));


| category | OSS |
|---|---|
| package | OSS_Asterisk |
| copyright | Copyright (c) 2007 - 2012, Open Source Solutions Limited, Dublin, Ireland |
| license | New BSD License |
parseChannelResponse($response) : array
It takes response array it checks if response have data. If it has it tries to parse form this type of array: Array ( [data] => Privilege: Command -- General -- Name: SIP/pcustomer-0000010a Type: SIP UniqueID:<PHONE_NUMBER>.266 LinkedID:<PHONE_NUMBER>.266 ... Indirect Bridge: SIP/ptelco-0000010b -- PBX -- Context: fwd-call Extension: 1201 ... Variables: BRIDGEPVTCALLID=4093270c7dd45f224ffff58f129f3275@<IP_ADDRESS>:5060 BRIDGEPEER=SIP/ptelco-0000010b ... SIPURI=sip:1101@<IP_ADDRESS>:5060
CDR Variables:
level 1: dnid=1201
level 1: calldate=2012-10-18 15:36:07
...
level 1: sequence=337
[Response] => Follows ) To this type of array: Array ( [] => Array ( [Privilege] => Command ) [general] => Array ( [Name] => SIP/pcustomer-0000010a [Type] => SIP [UniqueID] =><PHONE_NUMBER>.266 [LinkedID] =><PHONE_NUMBER>.266 ... [Indirect Bridge] => SIP/ptelco-0000010b ) [pbx] => Array ( [Context] => fwd-call [Extension] => 1201 ... [Variables] => Array ( [BRIDGEPVTCALLID] => 4093270c7dd45f224ffff58f129f3275@<IP_ADDRESS>:5060 [BRIDGEPEER] => SIP/ptelco-0000010b ... [SIPURI] => sip:1101@<IP_ADDRESS>:5060 ) ) [cdr] => Array ( [dnid] => 1201 [calldate] => 2012-10-18 15:36:07 ... [sequence] => 337 ) )
Usage: $presp = $ami->command( "core show channel CHANNEL_NAME" ); $result = OSS_Asterisk_AMI_Parser::parseChannelResponse( $presp );
| var | Response of AMI command |
|---|
array
parseChannelsConciseResponse($response) : array
It takes response array it checks if response have data. If it has it tries to parse form this type of array: Array ( [data] => Privilege: Command SIP/ptelco-00000113!ttelco!!1!Up!AppDial!(Outgoing Line)!1201!cust1!cust1!3!15!SIP/pcustomer-00000112!1350573839.275 SIP/pcustomer-00000112!fwd-call!1201!6!Up!Dial!SIP/ptelco/1201!1101!cust1!cust1!3!15!SIP/ptelco-00000113!1350573837.274
[Response] => Follows
) To this type of array: Array ( [0] => Array ( [0] => SIP/ptelco-00000113 [1] => ttelco [2] => [3] => 1 [4] => Up [5] => AppDial [6] => (Outgoing Line) [7] => 1201 [8] => cust1 [9] => cust1 [10] => 3 [11] => 15 [12] => SIP/pcustomer-00000112 [13] =><PHONE_NUMBER>.275 ) [1] => Array ( [0] => SIP/pcustomer-00000112 ... [13] =><PHONE_NUMBER>.274 ) )
Usage: $resp = $ami->command( "core show channels concise" ); $result = OSS_Asterisk_AMI_Parser::parseChannelsConciseResponse( $resp );
| var | Response of AMI command |
|---|
array
parseSipShowPeerResponse(array $response) : array
This function takes the response array of the form:
Array
(
[data] => "Privilege: Command
* Name : pcustomer
Secret : <Set>
MD5Secret : <Not set>
...
ToHost : customer
Addr->IP : <IP_ADDRESS>:5060
...
Encryption : No"
[Response] => Follows
)
and converts it to an associate array:
Array
(
[Privilege] => Command
[* Name] => pcustomer
[Secret] => <Set>
...
[ToHost] => customer
[Addr->IP] => <IP_ADDRESS>:5060
[Addr] = Array
(
[IP] => <IP_ADDRESS>
[Port] => 5060
)
...
[Encryption] => No
)
Example usage:
$resp = $ami->command( "sip show peer PEER_NAME" );
$result = OSS_Asterisk_AMI_Parser::parsePeerResponse( $resp );
array
Response of AMI command
array


Hi! My name is Miki Collins. I was born and raised in Lakeland, GA. I have been married for 15 years and am the mother of two amazing kids. I am a Mechanical Engineer by trade, graduating from Georgia Tech with a BME in 1999; however, my interests lie in arts and crafts. In my spare time I enjoy painting, scrapbooking, photography, crochet, and helping my kids with their projects.
I also have a sense of adventure and love to travel. In recent years, I have been on multiple trips cruising the Carribean and enjoying learning about the heritage and culture in these areas.
Having worked for the past 20 years in a manufacturing environment in engineering and management roles, I am excited to begin a new venture utilizing my artistic talents in coding and web development.


Team Uporniki Analytics
This is a small analytics app that allows prediction of selected metrics based on historical data using machine learning
Some summary
Wait Time
Last Date:
Next Date:
settings
Talk Time
Last Date:
Next Date:
settings
Handle time
Last Date:
Next Date:
settings


Sara's Page
- Hello....My name is Sara and I live in Kentwood, MI.

- Here are some places to go:
Mom's
page
Dad's
Page
My
Friends & Family (and my photo album)
DD's
Page
Paris
Trip!
Our Visit
to Japan
Our Good Friends
in Japan!
Beanie Babies
Nickelodeon
Star Wars (Cloud City)
Web-Counter
Sign My
Guestbook
View My
Guestbook
- My chat room is below. There are three things you should know. First, this
is a place for me to meet with my on-line friends at pre-arranged times to
chat. If you want to chat, send me an e-mail and we can set up a day and time.
Otherwise, you'll likely be chatting with yourself. Second, the only box you
need to fill in is "user name." Common user names are already taken, so if you
pick something common, the chat room software will reject you and say that a
password is required. You will have good luck if you embed your screen name
(in all caps) in some "gibberish." For example, I might use "hy67rdSARAp98oh"
You don't have use the same "gibberish" each time we chat. You don't even have
to remember the "gibberish" at all. When you've picked your user name, hit the
"ok, connect" button. Third, once you are chatting you can hit the "float"
button and we can chat while surfing other sites, not that you'd ever need to
leave my site!
To visit the CompuServe homepage,
follow this link
Click here to find out more
about Personal Home Pages


--- layout: post title: Missing time slices in beach automated sensor datasets date: '2015-07-30T18:36:56-05:00' author: Open Data Portal Team categories: - Open Data - Data Portal tags: - tech headache - qmqz-2xku - k7hf-8y75 ---
Some hourly updates for the Beach Water Quality - Automated Sensors and Beach Weather Stations - Automated Sensors datasets have been failing since yesterday. The Chicago Park District is aware of the problem and is working to fix it.
Unlike some datasets, the nature of how these datasets are updated means the missing time slices will not be filled in, even after the underlying problem is fixed.


We choose some mothers from anime and took some pictures of them in some scenes they appear.
The challenge is guessing what's the mother and the scene by one some few hints!
If you guess the scene the mother is in take a picture of it and post it here to check if you got it right.
Wins the game who can guess right more scenes and mothers!
If you're seeing this message update your browser: use the lastest version of
Chrome, Edge, Firefox or Safari.
Info and hints:
As the game don't asks for a password or something like this the answers are stored in the browser, then
don't clean the cache, or cookies, or change the browser or the device. If someone do that the resolved scenes
will be shown as not resolved.
All anime in this game can be found and watched legally on Crunchyroll
and some are also on HIDIVE: it's a good idea to check this places.
But the most important thing here is thinking hard! Example: first check in what anime there are mothers,
as an example you will not find any on Gugure! Kokkuri-san.
Small differences in the picture, like the service's logo, don't changes the result, but if the picture
was cropped then it can causa problems. The best way to avoid those problems is taking pictures with the player on full screen. Don't try
to manually crop pictures as it can fail..
Tools and technology used:
WebCrypto, which is a modern technology which allows cryptography in browsers, allowing web pages to protect
certain data, like the game answers.
dHash,
made by Dr. Neal Krawetz, which allows generating a small representation of a big image
in a way small changes in the image don't change this value, and in a simple and fast way.
secrets.js, made by Alexander Stetsyuk,
which implement the Shamir Secret Sharing Scheme, which is used to make the hints work.
If you know what's the scene take a picture of it and submit it here:
You already guessed this scene.
This scene is locked: until it's
unlocked it will not add points in the ranking. But guessing it can unlock new hints.
Important: the subtitles can mess the verification, so
when taking the picture disable the subtitles. In Crunchyroll just press the mouse right button and
select the option that turn those off. In HIDIVE use the button in the bottom right part of the player.
You don't need to save the picture in a file, just open the anime in full screen, press print screen and paste here using Ctrl+V.


Our app is currently available on Google Play! Download now to get started!
Check out what you can do with this app!
Get free cashback,recharges on installing apps!
Complete exclusive offers to earn data recharges!
Invite your friends to Datagenie and earn instantly!
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Welcome!
Howdy! Thanks for stopping by. I'm Murph Strange, and I'm a single dad, programmer, and magician. Basically, I'm a wizard.
I'm a member at freeCodeCamp.org.
Some of my work
Here's some of the weirder things I've made. Hopefully you enjoy them. Check back occasionally, as I am always working on new weird things.
- SmartBoard, a JavaScript powered drawing board and to do list
- Chess, a collaberation with other students at freeCodeCamp
- Professor Insano's Secret Identity
- MUTUS NOMED DETID COCIS
- Math Magic Lock
- Gunslinger - A Puzzle Game
- Coincryption - Another puzzle
- Slot Machine
- Video Poker
- Dice Generator - and Petals Around the Rose game
- Stop Watch
- Timer
- Pomodoro Timer
Where you can find me
I'm not currently for hire, nor interested in opportunities of any kind, yet. I will be available soon.
Back to the top


Johnson Co. Gloves
What we do
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Who we are
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How we work
Maecenas elementum dui quis ornare viverra. Maecenas egestas at mauris ac pulvinar. Mauris ut maximus arcu. Duis ac dolor eu ante vehicula lacinia sit amet feugiat turpis. Vivamus massa tellus, commodo at vulputate nec, semper eget.
Made for you, with care
Our premium glove designers enthusiastically cultivate customized schemas by redefining integrated metacarpus channels in partnership with select importers, streamlining best-of-breed networks to produce aggregated, scaled, value-added handwarming ROI. By harnessing A-list value we integrate peer-to-peer mitt methodologies, competently fashioning compelling sartorial relationships. With Johnson Co.'s next-generation disintermediation of holistic phalangial architectures, this classic leather silhouette with multitone embellishments will have your fists quixotically clenched in quantitized comfort.
Keeping to the mission of unending quality, Johnson Company gloves reaches out to nurture relationships with sourced leather, cotton, nylon, and advanced cloth producers. Select manufacturers and trusted distributors complete the Johnson family, providing streamlined operations for reliable delivery. Get in touch with us to learn more.


The Scratch Team is working hard to fix an issue with the Scratch website
Try reloading the page in a few minutes
Check @Scratch for updates
While the website is being fixed, you can use the Scratch app to make projects offline
While the website is being fixed, you can use the Scratch app to make projects offline


This subpart prescribes policies and procedures for establishing and using basic agreements and basic ordering agreements. (See 13.303 for blanket purchase agreements (BPA’s) and see 35.015(b) for additional coverage of basic agreements with educational institutions and nonprofit organizations.)
(a) Description. A basic agreement is a written instrument of understanding, negotiated between an agency or contracting activity and a contractor, that (1) contains contract clauses applying to future contracts between the parties during its term and (2) contemplates separate future contracts that will incorporate by reference or attachment the required and applicable clauses agreed upon in the basic agreement. A basic agreement is not a contract.
(b) Application. A basic agreement should be used when a substantial number of separate contracts may be awarded to a contractor during a particular period and significant recurring negotiating problems have been experienced with the contractor. Basic agreements may be used with negotiated fixed-price or cost-reimbursement contracts.
(1) Basic agreements shall contain—
(i) Clauses required for negotiated contracts by statute, executive order, and this regulation; and
(ii) Other clauses prescribed in this regulation or agency acquisition regulations that the parties agree to include in each contract as applicable.
(2) Each basic agreement shall provide for discontinuing its future applicability upon 30 days’ written notice by either party.
(3) Each basic agreement shall be reviewed annually before the anniversary of its effective date and revised as necessary to conform to the requirements of this regulation. Basic agreements may need to be revised before the annual review due to mandatory statutory requirements. A basic agreement may be changed only by modifying the agree-ment itself and not by a contract incorporating the agreement.
(4) Discontinuing or modifying a basic agreement shall not affect any prior contract incorporating the basic agreement.
(5) Contracting officers of one agency should obtain and use existing basic agreements of another agency to the maximum practical extent.
(c) Limitations. A basic agreement shall not—
(1) Cite appropriations or obligate funds;
(2) State or imply any agreement by the Government to place future contracts or orders with the contractor; or
(3) Be used in any manner to restrict competition.
(d) Contracts incorporating basic agreements.
(1) Each contract incorporating a basic agreement shall include a scope of work and price, delivery, and other appropriate terms that apply to the particular contract. The basic agreement shall be incorporated into the contract by specific reference (including reference to each amendment) or by attachment.
(2) The contracting officer shall include clauses pertaining to subjects not covered by the basic agreement, but applicable to the contract being negotiated, in the same manner as if there were no basic agreement.
(3) If an existing contract is modified to effect new acquisition, the modification shall incorporate the most recent basic agreement, which shall apply only to work added by the modification, except that this action is not mandatory if the contract or modification includes all clauses required by statute, executive order, and this regulation as of the date of the modification. However, if it is in the Government’s interest and the contractor agrees, the modification may incorporate the most recent basic agreement for application to the entire contract as of the date of the modification.
(a) Description. A basic ordering agreement is a written instrument of understanding, negotiated between an agency, contracting activity, or contracting office and a contractor, that contains (1) terms and clauses applying to future contracts (orders) between the parties during its term, (2) a description, as specific as practicable, of supplies or services to be provided, and (3) methods for pricing, issuing, and delivering future orders under the basic ordering agreement. A basic ordering agreement is not a contract.
(b) Application. A basic ordering agreement may be used to expedite contracting for uncertain requirements for supplies or services when specific items, quantities, and prices are not known at the time the agreement is executed, but a substantial number of requirements for the type of supplies or services covered by the agreement are anticipated to be purchased from the contractor. Under proper circumstances, the use of these procedures can result in economies in ordering parts for equipment support by reducing administrative lead-time, inventory investment, and inventory obsolescence due to design changes.
(c) Limitations. A basic ordering agreement shall not state or imply any agreement by the Government to place future contracts or orders with the contractor or be used in any manner to restrict competition.
(1) Each basic ordering agreement shall—
(i) Describe the method for determining prices to be paid to the contractor for the supplies or services;
(ii) Include delivery terms and conditions or specify how they will be determined;
(iii) List one or more Government activities authorized to issue orders under the agreement;
(iv) Specify the point at which each order becomes a binding contract (e.g., issuance of the order, acceptance of the order in a specified manner, or failure to reject the order within a specified number of days);
(v) Provide that failure to reach agreement on price for any order issued before its price is established (see paragraph (d)(3) of this section) is a dispute under the Disputes clause included in the basic ordering agreement; and
(vi) If fast payment procedures will apply to orders, include the special data required by 13.403.
(2) Each basic ordering agreement shall be reviewed annually before the anniversary of its effective date and revised as necessary to conform to the requirements of this regulation. Basic ordering agreements may need to be revised before the annual review due to mandatory statutory requirements. A basic ordering agreement shall be changed only by modifying the agreement itself and not by individual orders issued under it. Modifying a basic ordering agreement shall not retroactively affect orders previously issued under it.
(d) Orders. A contracting officer representing any Government activity listed in a basic ordering agreement may issue orders for required supplies or services covered by that agreement.
(1) Before issuing an order under a basic ordering agreement, the contracting officer shall—
(i) Obtain competition in accordance with Part 6;
(ii) If the order is being placed after competition, ensure that use of the basic ordering agreement is not prejudicial to other offerors; and
(iii) Sign or obtain any applicable justifications and approvals, and any determination and findings, and comply with other requirements in accordance with 1.602-1(b), as if the order were a contract awarded independently of a basic ordering agreement.
(2) Contracting officers shall—
(i) Issue orders under basic ordering agreements on Optional Form (OF) 347, Order for Supplies or Services, or on any other appropriate contractual instrument;
(ii) Incorporate by reference the provisions of the basic ordering agreement;
(iii) If applicable, cite the authority under 6.302 in each order; and
(iv) Comply with 5.203 when synopsis is required by 5.201.
(3) The contracting officer shall neither make any final commitment nor authorize the contractor to begin work on an order under a basic ordering agreement until prices have been established, unless the order establishes a ceiling price limiting the Government’s obligation and either—
(i) The basic ordering agreement provides adequate procedures for timely pricing of the order early in its performance period; or
(ii) The need for the supplies or services is compelling and unusually urgent (i.e., when the Government would be seriously injured, financially or otherwise, if the requirement is not met sooner than would be possible if prices were established before the work began). The contracting officer shall proceed with pricing as soon as practical. In no event shall an entire order be priced retroactively.


{% include core/head.html %} {% include core/sidebar.html %} {% include components/back_to_top.html %}


--- layout: default --- {% include headertop.html %} {% include headerbottom.html %}
Have the best of both worlds. Construct elegant class hierarchies for maximum code reuse and extensibility, implement their behavior using higher-order functions. Or anything in-between.
Learn MoreScala runs on the JVM, so Java and Scala stacks can be freely mixed for totally seamless integration.
So the type system doesn't feel so static.
Use data-parallel operations on collections, use actors for concurrency and distribution, or futures for asynchronous programming.
Combine the flexibility of Java-style interfaces with the power of classes. Think principled multiple-inheritance.
Think "switch" on steroids. Match against class hierarchies, sequences, and more.
Functions are first-class objects. Compose them with guaranteed type safety. Use them anywhere, pass them to anything.


Man found dead in back of police car after he was arrested in Rockhampton
by Australian Associated PressThe 46-year-old was arrested in the Queensland town for breach of a domestic violence order early on Friday
A man who was arrested by Queensland police has been found dead in the back of a police car while being taken to a watch house.
Police arrested the 46-year-old early on Friday morning over an incident involving a 33-year-old woman in a Rockhampton hotel car park.
“Officers arrested the Rockhampton man for breach of a domestic violence order,” a police statement said.
“Initial investigations indicate the man struggled with police before being restrained and transported to Rockhampton watch house.”
But he was found unresponsive in the back of the police vehicle when it arrived at the watch house around 3.50am and was declared dead at the scene.
The state coroner has been notified and the Crime and Corruption Commission will oversee a Queensland police investigation into the incident.


Links
Moderation Queue
Approved Tweets
Rejected Tweets
Logout
Administration
{% for tweet in tweets %}
{{ tweet.user }}
{{ tweet.text }}
∞
Not Moderated
Approved
Rejected
{% endfor %}


A demonstration of the SVG
Funnel chart. This chart is customised using custom tooltips, a key, the
labels are positioned in the middle of each "segment" and the background bars are set to use a
gradient that goes towards white on the right-hand-side. The font size of the labels has been
increased too.
The tooltips have been customised by using the RGraph.SVG.tooltips.style
object. Any CSS
property that you set on this object will be applied to any subsequent tooltip that's shown.
You
have to use the JavaScript
versions of CSS
property names when setting properties on this object
so hyphens are removed and a capital
letter is added in its place and the occasional properties name is significantly different, for
example (not an exhaustive list!):
| CSS name | JavaScript name |
|---|---|
| background-color | backgroundColor |
| float | cssFloat |
| padding-left | paddingLeft |
| padding-right | paddingRight |
| padding-top | paddingTop |
| padding-bottom | paddingBottom |
| margin-left | marginLeft |
| margin-right | marginRight |
| margin-top | marginTop |
| margin-bottom | marginBottom |
| z-index | zIndex |
There's a full list of CSS properties and the JavaScript versions of their names available here.
When the screen size is smaller, not much changes - the size of the labels and the margins.
   Put this where you want the chart to show up:

This is the code that generates the chart - it should be placed AFTER the
div
tag:


--- layout: post title: "Custom Blogging on a Budget" comments: true subtitle: "Combine free services such as Github and Cloudflare to create a custom, fast and secure blog" date: 2018-10-01 5:45:13 -0700 background: '/img/posts/custom-blog-budget.jpg' ---
I have a love-hate relationship with blogs. As a developer, I use blogs daily when they turn up when searching how to use a feature or fix an error. They are invaluable, and I’m not sure how I would do my job without them. Though when it comes to actually writing my own blog, I tend to lose sight of this same value I could be giving back to others.
Jekyll is an open source static site generator used to transform files (like markdown) into a static html site. It was created back in 2008 by Tom Preston-Werner - the co-founder of Github. As such, it has some great integration with Github that I’ll get into next. My favorite part about Jekyll is the philosophy behind it and the following quote from it’s README file:
Jekyll does what you tell it to do — no more, no less. It doesn't try to outsmart users by making bold assumptions, nor does it burden them with needless complexity and configuration. Put simply, Jekyll gets out of your way and allows you to concentrate on what truly matters: your content.
Jekyll’s installation documentation is top-notch, so I won’t try and duplicate it here. Follow the steps for the environment you want to use and you should be up and running within a few minutes. Here are a few helpful tutorials I used as well:
Once you are up and running, you’ll want to apply a theme to get rid of the default look and feel. There are many free themes to choose from at http://jekyllthemes.org. You can even clone the theme’s git repository and use that as a starting point to get up and running quickly. That is what I wound up doing and it make the configuration process much simpler.
Now that you've got your blog setup, you need a place to host it. Fortunately Github allows you to host a site for free and even includes continuous integration and deployment.
To get started, head over to https://pages.github.com for instructions on setting up github pages to host this blog content. You are basically creating a git repository called username.github.io and adding your files to it. Github is configured to build and serve this project as soon as files are pushed to the repository, and will show up almost instantly on the site.
You’ll likely want to setup a custom domain to use for your blog. I would recommend Cloudflare as a domain registrar as they have a wholesale rate and include whois privacy at no charge. Once you purchase your domain (or if you have one already), you'll need to configure your DNS servers to point to Cloudflare (more on this in the next step). Once the DNS servers are updated, save the changes and allow the changes to propogate. You can always check https://www.whatsmydns.net/ to see the propagation status.
Cloudflare is a great service and with a free account you get access to powerful features like worldwide caching, SSL and DDoS protection. Register for a free Cloudflare account and navigate to the “Add a Site” area. Once you add your site, head over to the “DNS” section to wrap up the Github pages configuration. For this example, I’m going to show www.mydomain.com using a CNAME record. Input “www” as the name and your github pages url as the domain name. Hit the add record button and Cloudflare will now respond to www.domain.com with your github pages site. Navigate to the “Crypto” option and enable SSL with the flexible option. This will allow your users to visit your site under https with a Cloudflare certificate. The great part is you don't have to manage this certificate, and it's free. One more thing you will need to do is head back to your Github account and under the repository settings, set the custom domain field to www.mydomain.com.
People are going to want to comment on your blog, so you’ll want a place for them to do that. Disqus provides a free platform to do this, and is advertisement-free for personal & non-commercial sites. Sign up for a free account and pick a subdomain name to use (mysite.disqus.com). Once you are signed up for an account, you’ll need to copy a block of code into your Jekyll layout file.
I hope this helped to layout plugging multiple services together to create a fast, secure and free blog. Although it requires some setup, if you enjoy that kind of thing it can be a fun experience. Enjoy!


class MyAdsActivity : AppCompatActivity, OnNavigationItemSelectedListener
A screen logged in user ads
Author
Anton Kirichenkov
MyAdsActivity()
A screen logged in user ads |
val id: String
user id |
|
val keyToken: String
token key for SharedPreference |
|
val mail: String
email key for SharedPreference |
|
val name: String
username key for SharedPreference |
|
var token: String?
saved session_id |
fun displayAds(recyclerView: RecyclerView, idUser: Long): Unit
Method for display user ads with recyclerView Adapter. |
|
fun setUsername(nameUser: TextView, userEmail: TextView): Unit
Method for display full user name and email from SharedPreference on nav_header. If user doesn't login, then display "Войти / зарегистрироваться" |


Who are you?.
Not sure where to stay? We've created neighborhood guides for cities all around the world.

See more gorillas
Smokke dope.
Learn more about THC
Trust me.
Learn more about my trusty Schwantz


fitAlgs.basinhopping module¶
- Author
Dominic Hunt
-
class
fitAlgs.basinhopping.
Basinhopping
(method=None, number_start_points=4, allow_boundary_fits=True, boundary_fit_sensitivity=5, **kwargs)[source]¶ Bases:
fitAlgs.fitAlg.FitAlg
The class for fitting data using scipy.optimise.basinhopping
- Parameters
fit_sim (fitAlgs.fitSims.FitSim instance, optional) – An instance of one of the fitting simulation methods. Default
fitAlgs.fitSims.FitSim
fit_measure (string, optional) – The name of the function used to calculate the quality of the fit. The value it returns provides the fitter with its fitting guide. Default
-loge
fit_measure_args (dict, optional) – The parameters used to initialise fit_measure and extra_fit_measures. Default
None
extra_fit_measures (list of strings, optional) – List of fit measures not used to fit the model, but to provide more information. Any arguments needed for these measures should be placed in fit_measure_args. Default
None
bounds (dictionary of tuples of length two with floats, optional) – The boundaries for methods that use bounds. If unbounded methods are specified then the bounds will be ignored. Default is
None
, which translates to boundaries of (0, np.inf) for each parameter.boundary_excess_cost (str or callable returning a function, optional) – The function is used to calculate the penalty for exceeding the boundaries. Default is
boundFunc.scalarBound()
boundary_excess_cost_properties (dict, optional) – The parameters for the boundary_excess_cost function. Default {}
method (string or list of strings, optional) – The name of the fitting method or list of names of fitting methods or name of list of fitting methods. Valid names found in the notes. Default
unconstrained
number_start_points (int, optional) – The number of starting points generated for each parameter. Default 4
allow_boundary_fits (bool, optional) – Defines if fits that reach a boundary should be considered the same way as those that do not. Default is True
boundSensitivity (int, optional) – Defines the smallest number of decimal places difference (so the minimal difference) between a fit value and its related boundaries before a fit value is considered different from a boundary. The default is 5. This is only valid if
allow_boundary_fits
isFalse
-
Name
¶ The name of the fitting method
- Type
string
Notes
unconstrained = [‘Nelder-Mead’,’Powell’,’CG’,’BFGS’] constrained = [‘L-BFGS-B’,’TNC’,’SLSQP’] Custom fitting algorithms are also allowed in theory, but it has yet to be implemented.
For each fitting function a set of different starting parameters will be tried. These are the combinations of all the values of the different parameters. For each starting parameter provided a set of number_start_points starting points will be chosen, surrounding the starting point provided. If the starting point provided is less than one it will be assumed that the values cannot exceed 1, otherwise, unless otherwise told, it will be assumed that they can take any value and will be chosen to be eavenly spaced around the provided value.
See also
fitAlgs.fitAlg.fitAlg
The general fitting method class, from which this one inherits
filtAlgs.fitSims.fitSim
The general fitting class
scipy.optimise.basinhopping
The fitting class this wraps around
-
callback
(x, f, accept)[source]¶ Used for storing the state after each stage of fitter
- Parameters
x (coordinates of the trial minimum) –
f (function value of the trial minimum) –
accept (whether or not that minimum was accepted) –
-
constrained
= ['L-BFGS-B', 'TNC', 'SLSQP']
-
fit
(simulator, model_parameter_names, model_initial_parameters)[source]¶ Runs the model through the fitting algorithms and starting parameters and returns the best one.
- Parameters
simulator (function) – The function used by a fitting algorithm to generate a fit for given model parameters. One example is fitAlgs.fitAlg.fitness
model_parameter_names (list of strings) – The list of initial parameter names
model_initial_parameters (list of floats) – The list of the intial parameters
- Returns
best_fit_parameters (list of floats) – The best fitting parameters
fit_quality (float) – The quality of the fit as defined by the quality function chosen.
testedParams (tuple of two lists and a dictionary) – The two lists are a list containing the parameter values tested, in the order they were tested, and the fit qualities of these parameters. The dictionary contains the coordinates of the trial minimum, the function value of the trial minimum and whether or not that minimum was accepted. Each is stored in a list.
See also
fitAlgs.fitAlg.fitness()
-
unconstrained
= ['Nelder-Mead', 'Powell', 'CG', 'BFGS']


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