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updated install instructions
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agabrown committed Feb 27, 2019
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22 changes: 15 additions & 7 deletions INSTALL.md
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Expand Up @@ -54,9 +54,12 @@ version](./period-luminosity-relation/TutorialPLZ_R.ipynb) of that tutorial.

#### RStan

Follow the instructions
[here](https://github.com/stan-dev/rstan/wiki/Installing-RStan-on-Mac-or-Linux) for the installation
of Rstan. Where the last step is to do from within R (run as root for a system wide installation):
The recommended installation method for RStan (working with RStudio) can be found
[here](https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started).

To install from source follow the instructions
[here](https://github.com/stan-dev/rstan/wiki/Installing-RStan-on-Linux) for the installation of
Rstan. Where the last step is to do from within R (run as root for a system wide installation):

```
> Sys.setenv(MAKEFLAGS = "-j4")
Expand All @@ -65,7 +68,7 @@ of Rstan. Where the last step is to do from within R (run as root for a system w

Note that a `Makevars` file in the ~/.R folder with the following contents is useful for
optimization of the compiled Stan models and supressing of irrelevant warnings (see [RStan install
instructions](https://github.com/stan-dev/rstan/wiki/Installing-RStan-on-Mac-or-Linux)):
instructions](https://github.com/stan-dev/rstan/wiki/Installing-RStan-on-Linux)):

```
CXXFLAGS=-O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -Wno-builtin-macro-redefined
Expand Down Expand Up @@ -129,9 +132,14 @@ version](./period-luminosity-relation/TutorialPLZ_R.ipynb) of that tutorial.

#### RStan

Now follow the instructions
[here](https://github.com/stan-dev/rstan/wiki/Installing-RStan-on-Windows) for the installation of
Rstan. Subsequently make sure that your can run R notebooks by following the
The recommended installation method for RStan (working with RStudio) can be found
[here](https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started).

To install from source follow the instructions
[here](https://github.com/stan-dev/rstan/wiki/Installing-RStan-from-source-on-Windows) for the
installation of Rstan.

Subsequently make sure that your can run R notebooks by following the
[instructions](https://irkernel.github.io/installation/) on
[irkernel.github.io](https://irkernel.github.io). Step 1/2 should be done while running as R as
"administrator".
Expand Down
15 changes: 2 additions & 13 deletions period-luminosity-relation/TutorialPLZ_R.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -57,20 +57,9 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [
{
"data": {
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"text/plain": [
"Plot with title “”"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"outputs": [],
"source": [
"# Define a seed for repeatability\n",
"set.seed(12354)\n",
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