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--- wiki:autolit:admin:configure [2023/06/28 00:26]
jthurnham [MA Extraction Modes: Standard vs. Dual]
+++ wiki:autolit:admin:configure [2023/12/06 22:06] (current)
jthurnham [4. Tagging]
@@ Line 4: / Line 4: @@
 ===== Navigate to the Settings Page =====
-{{:wiki:autolit:admin:img1.png?nolink&  }}
+The Settings page is found in the top left of the page, underneath Nest Home and Activity. This link will only appear to the Owner and Admins in the nest; Settings are hidden from Users.
-Administrative functions are split into Nest-level Admin functions and Organization-level Admin functions.
-  * For Organization-level Admin functions, see [[:wiki:autolit:admin:settings:orgs|]].
+===== 1. Add and Manage Admins, Users, and Organizations =====
-  * **Exception: **if you are giving an Organization access to a nest, that is a Nest-level Admin function under the Groups tab under the [[:wiki:autolit:admin:settings:users|Collaborators panel]], not the Manage Organizations page.
-—-
-===== 1. Add and Manage Users =====
+Add or remove User and/or Admin privileges for individuals and access and/or Ownership for Organizations in your specific nest. To learn how to do so for individuals or organizations, see the [[:wiki:autolit:access|Manage Access page]].
-Add or remove User and/or Admin privileges for your specific nest. To learn how to do so for individuals or organizations, see the [[:wiki:autolit:admin:settings:users|Manage Users and Admins page]].
+//Note: Nest-level Admin functions are separate from Organization-level Admin functions.//
+   * For Organization-level Admin functions, see [[:wiki:autolit:admin:settings:orgs|]].
+  * **Exception: **if you are giving an Organization access to or ownership of a nest, that is a Nest-level Admin function; see the [[:wiki:autolit:access|Manage Access page]].
+{{ :undefined:screenshot_2023-12-06_at_15.39.12.png?nolink |}}
-----
 ===== 2. Synthesis =====
@@ Line 22: / Line 23: @@
 From the Synthesis section, you can toggle 'on' or 'off' any Synthesis page:
-  * **Toggle on or off**  Quantitative Synthesis, Qualitative Synthesis, Manuscript, ROB, or PRISMA. If toggled off, that specific subsection will be greyed out in the Synthesis homepage.
+  * **Toggle on or off**  Quantitative Synthesis, Qualitative Synthesis, Dashboard, Manuscript, Critical Appraisal, or PRISMA. If toggled off, that specific subsection will be greyed out in the Synthesis homepage.
 Adjust the privacy/publicity of your Synthesis page to be Public, Protected, or Private:
@@ Line 28: / Line 29: @@
   * **Make a nest protected.**  Toggle this on to make the link to Synthesis undiscoverable and inaccessible to those without the key (or explicitly granted access). You will still be able to share a link with external parties, and the external party will not have to log in to view Synthesis.
   * **Make a nest private.**  Toggle this on for the most protection. Only those explicitly granted access with a NK account will be able to view the Synthesis.
-{{  :wiki:autolit:admin:img2.png?nolink&  }}
+{{  :undefined:synthesis2023.png?nolink&  }}
 ----
@@ Line 52: / Line 53: @@
 **Dual Two-Pass Screening**  combines these functions, meaning each record is screened by two different users and adjudicated at the Abstract step, and then two users must screen at the Full Text step followed by adjudication.
-{{ :undefined:1screen.png?nolink |}}
+{{  :undefined:1screen.png?nolink&  }}
 <WRAP center round important 60%> Toggling between Standard, Two-Pass, and Dual Screening (see image) **can lead to loss of data**, as only the final Inclusion and Exclusion decisions will be saved if you switch between Screening Modes! </WRAP>
@@ Line 58: / Line 59: @@
 ==== Screening Model ====
-**Manual vs. Automatic:**  By default, the Screening Model will be on Manual, meaning that it will only run when a user selects Train Screening Model during the Screening process. Toggling the Screening Model on (see image above) will alter this so that the Model runs as soon as a sufficient number of studies are screened, and this Model will be re-run automatically as more screening occurs. In the image below, if manual the red box will say "Train Screening Model," and if automatic training is on and enough studies are screened, the inclusion probability will be provided-- in this case it is "P(Inclusion): 0.87."
+**Manual vs. Automatic:**  By default, the Screening Model will be on Manual, meaning that it will only run when a user selects Train Screening Model during the Screening process. Toggling the Screening Model on (see image above) will alter this so that the Model runs as soon as a sufficient number of studies are screened, and this Model will be re-run automatically as more screening occurs. In the image below, if manual the red box will say "Train Screening Model," and if automatic training is on and enough studies are screened, the inclusion probability will be provided– in this case it is "P(Inclusion): 0.87."
 **Displayed vs. Hidden:**  By default, the Screening Model will be displayed, meaning that any user will be able to see the probabilities on the Screening panel:
-{{ :undefined:2screen.png?nolink |}}
+{{  :undefined:2screen.png?nolink&  }}
-If you want this probability to be hidden from all users, Admins, and Owners on each individual study, toggle "Hide Probabilities." If hidden, you can still run the model from the Admin page and have the option to turn on Automatic updating. [[wiki:autolit:screening:inclusionpredictionmodel|Learn more about the Screening model here.]]
+If you want this probability to be hidden from all users, Admins, and Owners on each individual study, toggle "Hide Probabilities." If hidden, you can still run the model from the Admin page and have the option to turn on Automatic updating. [[:wiki:autolit:screening:inclusionpredictionmodel|Learn more about the Screening model here.]]
 ==== Import Existing Screening Decisions ====
@@ Line 70: / Line 71: @@
 If there are screening decisions from a previous nest that are relevant to your current nest, you can [[:wiki:autolit:admin:import#import_screening_decisions|import existing screening decisions]] for any record already in your nest by uploading a spreadsheet. To do this, under Screening on the Settings page, selecting "Begin" under Import.
-===== 4. Extraction (previously named Tagging) =====
+===== 4. Tagging =====
-Extraction can be completed in Standard mode, or you can turn on Form-based Mode:
+Tagging, by default, is in Form-based mode or you can turn on Standard mode:
-{{  :wiki:autolit:admin:img4.png?nolink&  }}
+{{  :undefined:screenshot_2023-10-02_at_16.39.21.png?nolink&  }}
-In this mode, you will need to set up Questions in your tag hierarchy that are answered for each study.
+In this mode, your configured tags will be displayed as an open-ended list to be selected from in order to extract data.
+==== Tag Recommendations ====
+Standard tag recommendations are available to all users to assist in the Tagging process. Smart Tag recommendations are only available to enterprise users, but utilize OpenAI GPT 3.5/4 to search Abstracts and Full Texts. Toggling on "Smart (Beta)" will automatically generate recommendations for any included studies with available full texts. This will run in the background.
+You have a limited number of regenerations due to the costliness of each generation. After full text smart recommendations are generated, and for further assistance, you have the option to also generate smart tag recommendations for included abstracts. Learn more about [[:wiki:autolit:tagging:tag_recommendations|Tag Recommendations. ]]
 ==== Import Existing Tags ====
-If there are tags from a previous nest that are relevant to your current nest, you can [[:wiki:autolit:admin:import#import_tags|import existing tags]] for any record already in your nest by uploading a spreadsheet. To do this, under Extraction on the Settings page, selecting “Begin” under Import.
+If there are tags from a previous nest that are relevant to your current nest, you can [[:wiki:autolit:admin:import#import_tags|import existing tags]] for any record already in your nest by uploading a spreadsheet. To do this, under Tagging on the Settings page, selecting “Begin” under Import.
 ----
@@ Line 97: / Line 104: @@
 **Dual MA Extraction**  means that each record will be extracted by two different users and adjudicated by a third. To toggle Dual MA Extraction 'on', select it in the Admin page:
-{{  :wiki:autolit:admin:img6.png?nolink&  }}
+{{  :undefined:settingsdualma.png?nolink&  }}
 {{https://wiki.nested-knowledge.com//home/ubuntu/nkwiki/dokuwiki/lib/plugins/ckgedit/fckeditor/userfiles/image/wiki/autolit/fourteen.png?nolink&}}
@@ Line 109: / Line 116: @@
 ----
-===== 7. Jobs =====
+===== 7. Blinding =====
-The **Jobs**  header in Settings enables you to view all active, completed, and failed Jobs (such as recurring searches, PDF import, etc.) that are running in the background in your nest.
+To avoid bias in your review where multiple reviewers are participating, you may want to consider blinding certain aspects of the process. The Blinding settings allow you turn off or hide features.
-In some cases, such as running searches in Literature Search or Search Exploration, an active job will restrict new activities, such as adding a new search while that Job is active.
+**Blind Adjudication**  allows you hide the reviewer's identity for each decision as to not influence the ultimate decision. For example:
-Click "View Jobs" to view active, completed, and failed Jobs.
+Adjudicate Screening before Blinding:
+{{  :undefined:blind.png?nolink&  }}
+After Blinding:
+{{  :undefined:blind2.png?nolink&  }}
+**Hiding Inclusion Model**  allows you to remove the inclusion probability for each study if turned on, so the reviewer can make a completely independent decision.
+Screening before hiding probabilities:
+{{  :undefined:hide.png?nolink&  }}
+After hiding probabilities:
+{{  :undefined:hide2.png?nolink&  }}
+**Hiding Comments**  removes the Comments tab in the workflow modules (Screening, Tagging, MA Extraction, Critical Appraisal), allowing you to hide any comments made on studies when viewing them. As a result comments can't directly be made as they appear in the queue but can be made and seen when the study is accessed in Study Inspector.
+Right hand side tabs before hiding comments:
+{{  :undefined:comments.png?nolink&  }}
+After hiding comments:
+{{  :undefined:commentsno.png?nolink&  }}
+Hiding Tagging During Screening removes the Tagging tab available as you screen. We offer this capability during screening to be able to apply preliminary tags, but similarly it also exposes users to bias after a previous reviewer has screened and tagged. The before and after mirrors the above Comments removal but for the Tagging tab instead in Screening alone.
 ===== 8. Copying, Renaming, or Deleting a Nest =====
@@ Line 121: / Line 156: @@
 Copying a nest will copy the data and configurations, such as the search terms, references, exclusion reasons, the tagging hierarchy, applied tags, data elements, full-text PDFs, Critical Appraisal systems, the protocol and manuscript, and other configurations. The copied nest is entirely independent of the original nest. Access privileges will not be copied from the old nest and must be configured.
-**Only Owners have the right to delete a nest.** "Delete" can be found next to "Rename"; deleting a nest is irreversible and will completely delete all data related to the project in question!
+**Only Owners have the right to delete a nest.**  "Delete" can be found next to "Rename"; deleting a nest is irreversible and will completely delete all data related to the project in question!
-{{  :wiki:autolit:admin:img8.png?nolink&  }}<WRAP center round alert 60%> \\ Deleting a nest has wide-reaching and irreversible effects, including loss of all nest data. Proceed with caution! \\ </WRAP>
+{{ :undefined:screenshot_2023-12-06_at_15.42.05.png?nolink |}}
+<WRAP center round alert 60%> \\ Deleting a nest has wide-reaching and irreversible effects, including loss of all nest data. Proceed with caution! \\ </WRAP>
 ----
@@ Line 133: / Line 170: @@
 ==== 1. Allocation ====
-Allocation allows you to assign work in specific modules to various members of your team. Learn more about [[wiki:autolit:admin:Allocation|]].
+Allocation allows you to assign work in specific modules to various members of your team. Learn more about [[:wiki:autolit:admin:allocation|]].
 ==== 2. Nest Backups ====
-Nest Backups allow you to manually save up a backup of your nest to capture a version of it at a specific date and time. Learn more about [[wiki:autolit:admin:nestbackups|Nest Backups]].
+Nest Backups allow you to manually save up a backup of your nest to capture a version of it at a specific date and time. Learn more about [[:wiki:autolit:admin:nestbackups|]].

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