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When forward and reverse reads agree, their events are in the same place and span the same length, we will take forward read event as representative. If both strands cover event in question, but one strand has no indel, amplicanConsensus will change behavior according to the strict parameter. To successfully run our analysis it is mandatory to have a configuration file. Take a look at our example:. You can find example config file path by running:. You can still use amplican like normal.
To run amplican with default options, along with generation of all posible reports you can use amplicanPipeline function. We have already attached results of the default amplican analysis look at other vignettes of the example dataset, but take a look below at how you can do that yourself. You will understand it is worth waiting when reports will be ready. Here you can find. Rmd files that are our reports for example dataset. We already crafted. Open one of the reports with your favourite browser now. Rmd file and knit it again. This way you have all the power over plotting.
First step of our analysis is to filter out reads that are not complying with our default restrictions:. This table is also summarized in one of the reports. As you can see for our example dataset we have two barcodes, to which correspond 21 and 20 reads. Each of the barcodes has unique reads, which means forward and reverse reads are compacted when they are identical.
There is 8 and 9 unique reads for each barcode. Normally you will probably see only half of your reads being assigned to the barcodes. Reads are assigned when for forward read we can find forward primer and for reverse read we can find reverse primer. Primers have to be perfectly matched. With this option specified only one of the reads forward or reverse have to have primer perfectly matched. It should provide you additional look at raw numbers which we use for various plots in reports.
Take a look at example extension:. File RunParameters. Other than that this file has no purpose. In example dataset there is one unassigned read. Take a look at the alignment events file which contains all the insertions, deletions, cuts and mutations. This file can be used in various ways. Examples you can find in.
Rmd files we prepare using amplicanReport. Abuse is not negated by the age of the offender. The focus might be more appropriate as date violence; at the least, Linda should be informed that she committed battery against Bobby.
While Mary is, hopefully, providing help to Linda in dealing with her anger and lack of self-control, reporting should also be done. Mary should be taking a close look at the relationship between year-old Linda and year-old Bobby.
If Mary learns that this relationship is sexual, she must report it since Linda is I would make a strong effort to find a group working with adolescents with anger issues; sometimes young clients respond best when they know others have similar issues. Comment to No.
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Physical injury inflicted on a minor, by other than accidental means, by any person, is abuse. The fact that Linda is also a minor is immaterial in this situation. If Linda and Bobby were having sexual relations, a mandatory report would need to be made on this aspect as well, due to the disparate ages of 12 and LMFT Mark reviewed his standard informed consent with both Susie and her parents, including a section on confidentiality which briefly mentioned reasons for a breach of confidentiality, including "harm to self. After the third session, Susie admitted to LMFT Mark that she was sexually active with a few different people in her high school, and that she smoked pot on weekends.
LMFT Mark again determined not to breach confidentiality. After the seventh session, Susie told LMFT Mark that she had been drinking heavily, and had started blacking out at parties, waking up in strange beds clearly having had sexual intercourse.
It is wise to establish the limits of confidentiality in the beginning of treatment and inform the parents that if the therapist speaks to them, it is unlikely the teenager will confide in the therapist. Unfortunately, there are many grey areas in common adolescent behaviors. Certainly having multiple sexual partners is risky behavior — emotionally as well as health-wise STDs.
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In addition to addressing this issue clinically, I would want to know if condoms are being used, and if she is aware of the sexual history of her partners. I would bring up the question of self-endangerment and whether her parents need to know, but I would not break confidentiality unless I felt the client was risking consequences such as acquiring the HIV virus through highly risky behavior, and was unwilling to change her behavior.
Then I would explain to the client why we needed to inform her parents. In terms of the cutting, this meets the threshold of self-harm in my opinion. Though she may not be cutting near arteries but how much does she know about anatomy?
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Therefore, the parents must be involved in the treatment. Comment to Vignette No. All patients, minors included, have a general right of confidentiality in their mental health treatment. It is rarely obvious or clear cut, and likely varies from therapist to therapist. Generally speaking, the therapist must exercise the reasonable degree of skill, knowledge and care that would ordinarily be exercised by other therapists. In cases where there is a risk of self-harm to a client, one of the issues is whether or not the therapist was aware of facts from which he or she could reasonably conclude that the client was likely to self-inflict harm in the absence of preventative measures.
Also, consultation with a colleague is often beneficial when working with complex, and high risk clients, because it reflects that the therapist is prudent and thorough in his or her treatment of the particular client.
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