fix docs

docs/src/introduction.md

@@ -69,16 +69,18 @@ model = StandardABM(Microbe{1}, space, dt)
 Now, with the `add_agent!` function we will populate the model with microbes of
 the specified type (`Microbe{1}`).
 The only argument we must *always* specify for `add_agent!` is the motility of the microbe, via the `motility` keyword. An overview of the motility interface is given later;
-For now we will just use a Run-Tumble motility with an average run duration of 1 second
-and a constant swimming speed of 20 micron / second.
+For now we will just use a Run-Tumble motility with an average run duration of 1 second and a constant swimming speed of 20 micron / second.
+The third required argument to the call is the distribution of reorientation
+angles, but it is irrelevant in 1-dimensional systems so we can just pass
+an empty array.
 If unspecified, position, direction and speed of the microbe will be assigned randomly;
 all the other fields will be assigned default values from the constructor (unless specified).
 To select a position, it can be passed as the first argument to the `add_agent!` call,
 and any other bacterial parameter can be defined via keyword arguments.
 All of the following are valid calls
 ```
-motility = RunTumble(1.0, [20.0])
-# a Microbe with large radius and low tumble rate
+motility = RunTumble(1.0, [20.0], [])
+# a Microbe with large radius
 add_agent!(model; motility, radius=10.0)
 # a Microbe with custom position and high coefficient of rotational diffusion
 add_agent!((53.2,), model; motility, rotational_diffusivity=0.5)

src/motility.jl

@@ -59,12 +59,13 @@ It is not necessary to indicate impossible transitions; any pair
 transition probability `p=0`.
 
 For example, if we want to define a 3-state motility, composed by a
-slow but long run, a tumble, and a fast but short run, where the two runs
+slow but long run, an instantaneous tumble with some `angle_pdf`,
+and a fast but short run, where the two runs
 can only transition towards the tumble, but the tumble can transition
 with probability 30% towards the slow run and 70% towards the fast run,
 we will call:
 
-    Motility((Run(10.0, 2.0), Tumble(), Run(60.0, 0.5)),
+    Motility((Run(10.0, 2.0), Tumble(0.0, angle_pdf), Run(60.0, 0.5)),
         (1 => 2, 1.0),
         (2 => 1, 0.3), (2 => 3, 0.7),
         (3 => 2, 1.0)