README polish

Author: gregorgorjanc

README.md

@@ -27,7 +27,74 @@ The key files you should study are:
 You can install and test this package by running:
 
 ```
+# Install from GitHub
 remotes::install_github("HighlanderLab/RcppTskitTestLinking")
+
+# Load the package
 library(RcppTskitTestLinking)
-?ts_num_individuals2
+
+# Check the help page for one implemented function
+?ts_num_individuals_ptr2
+```
+
+Now run the example from the help page.
+Below we mark it up to explain what is what.
+
 ```
+# Find an example tree sequence file in RcppTskit package
+> ts_file <- system.file("examples", "test.trees", package = "RcppTskit")
+> ts_file
+[1] "/Users/ggorjanc/Library/R/arm64/4.5/library/RcppTskit/examples/test.trees"
+
+# Load tree sequence into R workspace
+> ts <- RcppTskit::ts_load(ts_file)
+
+# Check summary of the tree sequence
+> ts
+Object of class 'TreeSequence'
+$ts
+         property            value
+1     num_samples              160
+2 sequence_length            10000
+3       num_trees               26
+4      time_units      generations
+5        min_time                0
+6        max_time 7.47028168974859
+7    has_metadata            FALSE
+
+$tables
+        table number has_metadata
+1 provenances      2           NA
+2 populations      1         TRUE
+3  migrations      0        FALSE
+4 individuals     80        FALSE
+5       nodes    344        FALSE
+6       edges    414        FALSE
+7       sites   2376        FALSE
+8   mutations   2700        FALSE
+
+# Note that we have 80 individuals in ts
+
+# We can obtain the same number by running
+> ts$num_individuals()
+[1] 80
+
+# This demo package implemented the same function
+# that is available in RcppTskit, but since we here
+# focus just on C++ code, we have to work with the
+# pointer object (externalptr) `ts$pointer` and
+# not with the tree sequence object (TreeSequence) `ts`
+> ts_num_individuals_ptr2(ts$pointer)
+[1] 80
+```
+
+## Wrap up
+
+Hopefully this demo package shows you sufficiently well on how
+to leverage `RcppTskit` for your package.
+
+If we develop any methods that should work on
+the tree sequence object (`TreeSequence`),
+then the methods could go into `RcppTskit::TreeSequence` or
+new packages could inherit from this class and add their
+methods.