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General reorganization and cleanup - hardware, install steps, flashing, background reading #1537

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update or remove most remaining broken links, with the exception of a…
… few that are already noted in the text as not working (e.g. hot button app link) and images in the deprecated pi setup page
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Kim Scott committed Feb 26, 2020
commit 147033eab953e580ccc020e5232b96de0c31bb31
2 changes: 1 addition & 1 deletion docs/docs/Build Your Rig/step-2-wifi-dependencies.md
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@@ -311,7 +311,7 @@ Once your setup script finishes, **make sure to [watch the pump loop logs](<../B

**NOTE**: If you are using RFM69HCW as RF module:

If you have connected your RFM69HCW module as described in [Soldering RFM69HCW](<../Gear Up/edison#soldering>), while running interactive setup use following option:
If you have connected your RFM69HCW module as described in [Soldering RFM69HCW](<../Gear Up/pi-based-rigs#soldering>), while running interactive setup use following option:
```
3) RFM69HCW (DIY: SPI)
```
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@@ -48,7 +48,7 @@ The second method involves installing an application called xDripAPS onto your r

**EASIEST:** For either Android or iPhone G4/G5 users, you can plug the CGM receiver directly into your rig via USB. This will pull BGs into the rig directly from the receiver and be used for looping. If you are a G4 user, this should also bring RAW BG data into the rig during sensor restarts or ??? times (although multiple users with pediatric model G4 receivers have reported inability to obtain raw data. This seems to be related to a firmware difference between adult and pediatric G4 receivers). The rig will loop using RAW BGs so long as the BG value is under 150 mg/dl. A few notes about how to make the direct-receiver configuration work:

* Explorer boards built prior to late January of 2017 are not always working well/automatically with a CGM receiver plugged in. These boards can be identified by looking to see if they say "2016" on the board's label tag, as shown in the photo below. The boards can be fixed to use a CGM receiver by making a single trace cut, but doing so will disable the board's the ability to re-flash your Edison. Please make sure you have a second Explorer board or another base block or breakout board that you can use to re-flash the Edison if needed before considering this modification. For more details, see [this issue](https://github.com/EnhancedRadioDevices/915MHzEdisonExplorer/issues/14), and if you decide to make the cut, see [this document for details on how to cut the copper trace from pin 61 of the 70 pin connector](https://github.com/EnhancedRadioDevices/915MHzEdisonExplorer/wiki#usb-otg-flakiness). Cut in two places and dig out the copper between. Cut by poking a razor point in. Avoid the narrow trace above the one being cut.
* Explorer boards built prior to late January of 2017 are not always working well/automatically with a CGM receiver plugged in. These boards can be identified by looking to see if they say "2016" on the board's label tag, as shown in the photo below. The boards can be fixed to use a CGM receiver by making a single trace cut, but doing so will disable the board's the ability to re-flash your Edison. Please make sure you have a second Explorer board or another base block or breakout board that you can use to re-flash the Edison if needed before considering this modification. For more details, see [this issue](https://github.com/EnhancedRadioDevices/915MHzEdisonExplorer/issues/14), and if you decide to make the cut, see [this document for details on how to cut the copper trace from pin 61 of the 70 pin connector](https://github.com/EnhancedRadioDevices/915MHzEdisonExplorer/wiki#usb-otg-issue-on-beta-board). Cut in two places and dig out the copper between. Cut by poking a razor point in. Avoid the narrow trace above the one being cut.

* Explorer Boards that shipped at or after the end of February 2017/first week of March 2017 should enable users to simply plug in the CGM receiver to the OTG port, and a USB battery into the UART port, in order to run offline and pull BGs from the receiver. Those boards will have a label of v1.2 2017.

2 changes: 1 addition & 1 deletion docs/docs/Customize-Iterate/useful-mobile-apps.md
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@@ -123,7 +123,7 @@ If you want to run a particular command, just click on the command & confirm whi

#### SimpleSSH file navigation

Perhaps a more slightly advanced-user (or curious-user) feature of SimpleSSH is the ability to use the file/directory navigator. The navigator (accessed using the magnifying glass icon in Hosts page) will allow you to peruse the various directories and files used by your rig and openaps. If you wanted to see your oref0 code, it is stored in the `root/src/oref0` folder. Or if you wanted to see your loop directory, you could navigate to your `root/myopenaps` folder. This can be particularly useful if you are getting troubleshooting help and someone asks "What does your pumphistory.json show?"...you could easily navigate to that file and copy the contents of it. (Note: For further reading about the file structure of your loop and rig, see [here](<../Troubleshooting/general_linux_troubleshooting#directories-on-your-rig>) For example, here's the navigation chain to find your pumphistory.json:
Perhaps a more slightly advanced-user (or curious-user) feature of SimpleSSH is the ability to use the file/directory navigator. The navigator (accessed using the magnifying glass icon in Hosts page) will allow you to peruse the various directories and files used by your rig and openaps. If you wanted to see your oref0 code, it is stored in the `root/src/oref0` folder. Or if you wanted to see your loop directory, you could navigate to your `root/myopenaps` folder. This can be particularly useful if you are getting troubleshooting help and someone asks "What does your pumphistory.json show?"...you could easily navigate to that file and copy the contents of it. (Note: For further reading about the file structure of your loop and rig, see [here](<../Troubleshooting/General_linux_troubleshooting#directories-on-your-rig>) For example, here's the navigation chain to find your pumphistory.json:

![SimpleSSH navigation example](../Images/navigate.png)

6 changes: 3 additions & 3 deletions docs/docs/Gear Up/pi-based-rigs.md
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@@ -132,7 +132,7 @@ Here's a rough-and-ready budget version of a rig put together: contents of a 200
### Summary of what you need:
* Raspberry Pi Zero
* RFM69HCW
* [microSD Card](<../Gear Up/edison-explorer-board#sd-card>)
* [microSD Card](<#sd-card>)
* Bread board
* Jumper wires
* Soldering iron
@@ -188,7 +188,7 @@ Summary of what you need for a Pi/Bonnet rig:
There is be a Pi+Bonnet rig as an option for closing the loop with OpenAPS. This hardware is available from Adafruit, and is called the [Adafruit RFM69HCW Transceiver Radio Bonnet - 868 or 915 MHz - RadioFruit](https://www.adafruit.com/product/4072). As of October 2019, this hardware is supported via automated setup via `oref0-setup.sh`.

#### PI
You also need a Raspberry Pi. Many users are opting for the "Raspberry Pi Zero WH" - with headers - so you don't have to solder, and can simply add the HAT onto the Pi. See this [PiZeroWH from Adafruit](https://www.adafruit.com/product/3708), or [from other sellers around the world](https://www.raspberrypi.org/products/#buy-now-modal)
You also need a Raspberry Pi. Many users are opting for the "Raspberry Pi Zero WH" - with headers - so you don't have to solder, and can simply add the HAT onto the Pi. See this [PiZeroWH from Adafruit](https://www.adafruit.com/product/3708), or [from other sellers around the world](https://www.raspberrypi.org/products/)

As an alternative, you can also use the bonnet with a Raspberry Pi 2/3/4.

@@ -331,7 +331,7 @@ Here's a rough-and-ready budget version of a rig put together: contents of a 200
### Summary of what you need:
* Raspberry Pi Zero
* RFM69HCW
* [microSD Card]((<../Gear Up/pi-based-rigs#sd-card))
* [microSD Card]((<../Gear Up/pi-based-rigs#sd-card>))
* Bread board
* Jumper wires
* Soldering iron
2 changes: 1 addition & 1 deletion docs/docs/Gear Up/rig-options.md
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@@ -6,7 +6,7 @@ You have several options for hardware:

2. The other option is a Raspberry Pi-based setup, with the new Explorer HAT. This rig setup makes it easier to see information when offline because it has an onboard screen for displaying readouts. [Go here for hardware required and setup instructions for Pi/HAT setups](<../Gear Up/pi-based-rigs>). There is also an experimental alternative to an Explorer HAT, RFM69HCW, which can serve as the radio on a Pi-based rig, but will not have the screen, and requires you to solder.

3. Yet another option is a Raspberry Pi-based setup, with an Adafruit RFM69HCW Bonnet. This rig setup makes it easier to see information when offline because it has a small onboard screen for displaying readouts, but it does not come with charging hardware for a battery like the Explorer HAT or Explorer Board. You will need to build your own charging circuit or use a USB power block if you want to make this rig portable. However, this makes an excellent stationary or backup rig! [See here for the list of hardware required for Pi/Bonnet setups](<../Gear Up/pi-based-rigs#hardware-information-for-pi-based-setups-with-the-adafruit-rfm69hcw-bonnet>).
3. Yet another option is a Raspberry Pi-based setup, with an Adafruit RFM69HCW Bonnet. This rig setup makes it easier to see information when offline because it has a small onboard screen for displaying readouts, but it does not come with charging hardware for a battery like the Explorer HAT or Explorer Board. You will need to build your own charging circuit or use a USB power block if you want to make this rig portable. However, this makes an excellent stationary or backup rig! [See here for the list of hardware required for Pi/Bonnet setups](<../Gear Up/pi-based-rigs#hardware-information-for-pi-based-setups-with-the-adafruit-rhm69hcw-bonnet>).

4. (Not recommended, but supported) There is an experimental alternative to prefabricated hardware on the Raspberry Pi (Explorer HAT or Adafruit Bonnet), which can serve as the radio on a Pi-based rig, but will not have the screen and requires you to solder. [See here for the list of hardware required for more details on a setup with RFM69HCW breakout board](<../Gear Up/pi-based-rigs#hardware-information-for-pi-based-setups-with-rfm69hcw-experimental>).

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@@ -33,7 +33,7 @@ There are three key assumptions the OpenAPS algorithm makes about how insulin ac

100 = (4 \* 60 \* (75 / 180))

> **NOTE:** The insulin action assumptions described here are set to change with the release of [oref0, version 0.6.0](https://github.com/openaps/oref0/tree/0.6.0-dev). The new assumptions will use exponential functions for the insulin action curves and will allow some user flexibility to use pre-set parameters for different classes of fast-acting insulins (Humalog, Novolog, and Apidra vs. Fiasp, for example). For a discussion of the alternate specifications of insulin action curves, see [oref0 Issue #544](https://github.com/openaps/oref0/issues/544). When oref0, version 0.6.0 is released and the current assumptions are no longer recommended, this documentation will be updated.
> **NOTE:** The insulin action assumptions described here are set to change with the release of [oref0, version 0.6.0](https://github.com/openaps/oref0/releases/tag/v0.6.0). The new assumptions will use exponential functions for the insulin action curves and will allow some user flexibility to use pre-set parameters for different classes of fast-acting insulins (Humalog, Novolog, and Apidra vs. Fiasp, for example). For a discussion of the alternate specifications of insulin action curves, see [oref0 Issue #544](https://github.com/openaps/oref0/issues/544). When oref0, version 0.6.0 is released and the current assumptions are no longer recommended, this documentation will be updated.


## What The Insulin Activity Assumptions Look Like
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