Fine-tune documentaiton

[derekrodgers]

Someone should go through analysis as described in our documentation and make sure they can reproduce it without help. If not, we should make it more verbose. We can discuss deficencies and suggested fixes here, then tag PRs that fix the documentation.

[ZhengHe-007]

I'll work on this problem

[ZhengHe-007]

I have encountered a lot of issues on installing packages after running renv::restore() in my r console, for example: Error: Error installing package 'nlme':

• installing source package ‘nlme’ ... package ‘nlme’ successfully unpacked and MD5 sums checked using staged installation ** libs using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ sh: /opt/gfortran/bin/gfortran: No such file or directory using SDK: ‘MacOSX13.3.sdk’ /opt/gfortran/bin/gfortran -arch arm64 -fPIC -Wall -g -O2 -c chol.f -o chol.o make: /opt/gfortran/bin/gfortran: No such file or directory make: *** [chol.o] Error 1 ERROR: compilation failed for package ‘nlme’
• removing ‘/Users/zheng/Downloads/Dynamic33/renv/staging/1/nlme’

  ---

  R was unable to find the gfortran binary. gfortran is required for the compilation of FORTRAN source files. Please check that gfortran is installed and available on the PATH. Please see https://stackoverflow.com/q/35999874 for more information.

Reason(s):

• 'sh: /opt/gfortran/bin/gfortran: No such file or directory'
• 'make: /opt/gfortran/bin/gfortran: No such file or directory' install of package 'nlme' failed [error code 1]

But we already can run the analysis and knit to pdf in the container