Adding stuff about calling multi-software code

90-multi-software.md

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+# Multi-software projects
+
+Many projects will use multiple softwares, along the lines of "use what is appropriate for specific tasks." This may pose particular challenges. I showed that a generic `bash` script can handle running multiple softwares in the right sequence, but some researchers may be more comfortable in a main software package, or may not want to incur the additional complication of relying on `bash`, or worse, restricting reproducibility to a particular platform, for instance by choosing `cmd.exe` (`.bat` files) or Powershell scripts.
+
+## Calling software A from within software B
+
+In order to call external software from within a statistical programming language, it is necessary to know where, on a system, the software can be found. In "Environments", we discussed *search paths*, but in many computing environments, not each piece of software is on that search path.
+
+However, it is possible to explicitly address this. Each software does know where it is installed. In R,
+
+```R
+R.home("bin")
+```
+
+will yield the location of the `R` executable, for instance
+`C:/Program Files/R/R-4.4.0/bin/x64/R`. Note that it will vary by version!
+
+Typing 
+
+```bash
+where python
+```
+
+into a Bash or Zsh terminal (and appropriate commands in Powershell) might yield `C:/Program Files/Python312/python.exe` on a particular windows system. This can then be used, for instance, to call `R` and `python` from a Stata program:
+
+```stata
+global Rterm_path "C:\Program Files\R\R-4.3.1\bin\x64"
+* Set path to python executable here:
+global python_ex "C:\Program Files\Python312\python.exe"
+
+ssc install rsource
+ssc install python
+
+
+python set exec "$python_ex"
+python script "code/run_geo_clean.py"
+
+rsource using "code/figure1.R"
+```
+
+where the Stata packages [`python`](https://ideas.repec.org/c/boc/bocode/s457688.html) and [`rsource`](https://ideas.repec.org/c/boc/bocode/s456847.html) are used.[^pythonstata]
+
+[^pythonstata]: Note that Stata has [integrated Python functionality](https://www.stata.com/manuals/ppystataintegration.pdf) since version 16. The example referenced uses an older Stata package that works for Stata since 2013.

91-big-data.md

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+# Big data and testing
+
+(coming)

92-long-computation.md

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+# Long computations and testing
+
+(coming)

_toc.yml

@@ -23,3 +23,8 @@ parts:
     - file: 71-have-an-undergrad-run-it
     - file: 72-virtual_machines
     - file: 80-docker
+  - caption: More complex setups
+    chapters:
+    - file: 90-multi-software
+    - file: 91-big-data
+    - file: 92-long-computation