[Genabel-commits] r1803 - pkg/ProbABEL/src

[L.C. Karssen]

Hi Maksim,

Thank you for fixing bug #5883!

I noticed that the patch wasn't following our coding style guidelines
(see http://genabel.r-forge.r-project.org/codingstyle.html). For example
you had a couple of very long lines and no spaces around operators (i.e.
<<). I've fixed those in r1805.

Regarding the output that print I have a few questions. If I run
ProbABLE now, I get this (partial) output:

Actual number of people in phenofile = 200; using all of these
nphenocols=4
i=3, is_interaction_excluded=0, interaction=1, n_model_terms=2
model=( height ) ~ mu + sex + age
Linear model: ( height ) ~ mu + sex + age + SNP_A1 + sex*SNP_A1

Can you please explain why you print the variables in the line that
starts with "i=3"? Is that just debug output that shouldn't have been
committed?
And about the line starting with "model=": is that also debug output
(the next line prints the same information)?


Thanks for clearing this up,

Lennart.


On 21-08-14 07:57, noreply at r-forge.r-project.org wrote:
> Author: maksim
> Date: 2014-08-21 07:57:37 +0200 (Thu, 21 Aug 2014)
> New Revision: 1803
> 
> Modified:
>    pkg/ProbABEL/src/phedata.cpp
> Log:
> Fixed an issue with --interaction_only when ProbABEL reported wrong model (the same as for --intreaction) while analysis was done correctly for --interaction_only.
> 
> Modified: pkg/ProbABEL/src/phedata.cpp
> ===================================================================
> --- pkg/ProbABEL/src/phedata.cpp	2014-08-15 12:59:56 UTC (rev 1802)
> +++ pkg/ProbABEL/src/phedata.cpp	2014-08-21 05:57:37 UTC (rev 1803)
> @@ -27,6 +27,7 @@
>  #include <fstream>
>  #include <cstdarg>
>  #include <cstdlib>
> +#include <cstring>
>  
>  using std::cout;
>  using std::cerr;
> @@ -66,6 +67,7 @@
>      std::ifstream myfile(fname);
>      char *line = new char[BFS];
>      char *tmp  = new char[BFS];
> +    char *interaction_cov_name  = new char[BFS];
>      noutcomes = noutc;
>      is_interaction_excluded = false;
>  
> @@ -146,6 +148,11 @@
>      model_terms[n_model_terms++] = "mu";
>  #endif
>  
> +
> +
> +
> +
> +
>      if (nphenocols > noutcomes + 1)
>      {
>          infile >> tmp;
> @@ -154,12 +161,18 @@
>          for (int i = (2 + noutcomes); i < nphenocols; i++)
>          {
>              infile >> tmp;
> +            std::cout << "nphenocols="<<nphenocols<<"\n";
> +            std::cout<<"i="<<i<<", is_interaction_excluded="<<is_interaction_excluded<<", interaction="<<interaction<<", n_model_terms="<<n_model_terms<<"\n";
> +            if(n_model_terms == interaction  && is_interaction_excluded)
> +               {
> +               strcpy(interaction_cov_name, tmp);
> +               continue;
> +               }
>  
> -            // if(iscox && ) {if(n_model_terms+1 == interaction-1) {continue;} }
> -            // else      {if(n_model_terms+1 == interaction) {continue;} }
>              model = model + " + ";
>              model = model + tmp;
>              model_terms[n_model_terms++] = tmp;
> +            std::cout << "model="<<model<<"\n";
>          }
>      }
>      model = model + " + SNP_A1";
> @@ -167,29 +180,27 @@
>      {
>          if (iscox)
>          {
> -            model = model + " + " + model_terms[interaction - 1] + "*SNP_A1";
> +           if(!is_interaction_excluded) model = model + " + " + model_terms[interaction - 1] + "*SNP_A1";
> +           else model = model + " + " + interaction_cov_name + "*SNP_A1";
>          }
>          else
>          {
> -            model = model + " + " + model_terms[interaction] + "*SNP_A1";
> +            if(!is_interaction_excluded) model = model + " + " + model_terms[interaction] + "*SNP_A1";
> +            else model = model + " + " + interaction_cov_name + "*SNP_A1";
>          }
>      }
>      model_terms[n_model_terms++] = "SNP_A1";
>  
> -    if (is_interaction_excluded) // exclude covariates from covariate names
> -    {
> -        if (iscox)
> -        {
> -            std::cout << "model is running without "
> -                      << model_terms[interaction - 1] << ", term\n";
> -        }
> -        else
> -        {
> -            std::cout << "model is running without " << model_terms[interaction]
> -                      << ", term\n";
> -        }
> -    }
>  
> +
> +
> +
> +
> +
> +
> +
> +
> +
>  #if LOGISTIC
>      std::cout << "Logistic ";
>  #elif LINEAR
> 
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-- 
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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