mlopez-ibanez / eaf Goto Github PK

R package for plotting the Empirical Attainment Function

Home Page: http://lopez-ibanez.eu/eaftools

Makefile 3.52% R 25.01% C 60.99% Perl 6.90% Python 0.22% TeX 2.91% Shell 0.03% M4 0.41%

multiobjective-optimization r eaf eaf-differences summary-attainment-surfaces hypervolume visualization epsilon inverted-generational-distance

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mbinois geoffreyp rfsilva1

eaf's Issues

Quick doubts on using the library

Hello,
First of all, congratulations for the eaftools library. It is one of the best tools I've seen to visualize the results of multi-objective optimization. I have three quick questions related to its use (I've searched through the documentation, the website, and the source code and did not find it):
1- Is there a way to extract to which percentile each point on the original dataset would belong (the attainment surfaces), after running the eafplot function for maximizing one criteria and minimizing the other one? Example: I've generated a plot with percentiles = c(0, 20, 40, 60, 80, 100) and I can plot the original points in the dataset on the final plot using extra.points. However, it would be very valuable to know to which "percentile class" each point belonged, so I could calculate the % of points in each "percentile class"
2- Is there an example for running the eaf for 3 dimensions?
3- Are there any visualizations planned for the library for optimization in 3 dimensions?
Thanks a lot,
Roberto

Better default reference point for HV calculations

Use the method suggested here: https://dl.acm.org/doi/10.1162/evco_a_00226
to define a default reference point.

Installation problem

Hi,

I wanted to install this package using devtool::install_github("MLopez-Ibanez/eaf") line, but I got the below error:

Downloading GitHub repo MLopez-Ibanez/eaf@master
from URL https://api.github.com/repos/MLopez-Ibanez/eaf/zipball/master
Installing eaf
"C:/PROGRA~1/R/R-35~1.1/bin/x64/R" --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD INSTALL  \
  "C:/Users/Amin/AppData/Local/Temp/Rtmp06uYpP/devtools119026131c0f/MLopez-Ibanez-eaf-ea9b50f"  \
  --library="C:/Users/Amin/Documents/R/win-library/3.5" --install-tests 

* installing *source* package 'eaf' ...
** libs

*** arch - i386
c:/Rtools/mingw_32/bin/gcc  -I"C:/PROGRA~1/R/R-35~1.1/include" -DNDEBUG -DVARIANT=4 -DR_PACKAGE -DDEBUG=1         -O3 -Wall  -std=gnu99 -mtune=generic -c Reaf.c -o Reaf.o
In file included from Rcommon.h:6:0,
                 from Reaf.c:1:
common.h:1:1: error: expected identifier or '(' before '.' token
 ../inst/scripts/mo-tools/common.h
 ^
In file included from Reaf.c:2:0:
eaf.h:1:1: error: expected identifier or '(' before '.' token
 ../inst/scripts/eaf/eaf.h
 ^
Reaf.c: In function 'compute_eaf_C':
Reaf.c:67:5: error: unknown type name 'eaf_t'
     eaf_t **eaf = compute_eaf_helper(DATA, nobj, CUMSIZES, nruns, percentile, nlevels);
     ^
Reaf.c:67:5: warning: implicit declaration of function 'compute_eaf_helper' [-Wimplicit-function-declaration]
Reaf.c:67:19: warning: initialization makes pointer from integer without a cast
     eaf_t **eaf = compute_eaf_helper(DATA, nobj, CUMSIZES, nruns, percentile, nlevels);
                   ^
Reaf.c:69:5: warning: implicit declaration of function 'eaf_totalpoints' [-Wimplicit-function-declaration]
     int totalpoints = eaf_totalpoints (eaf, nlevels);
     ^
Reaf.c:78:29: error: request for member 'size' in something not a structure or union
         int npoints = eaf[k]->size;
                             ^
Reaf.c:80:9: warning: implicit declaration of function 'DEBUG2' [-Wimplicit-function-declaration]
         DEBUG2(
         ^
Reaf.c:81:13: error: expected expression before 'int'
             int totalsize = npoints * nobj;
             ^
Reaf.c:89:53: error: request for member 'data' in something not a structure or union
                 rmat[pos + j * totalpoints] = eaf[k]->data[j + i * nobj];
                                                     ^
Reaf.c:94:9: warning: implicit declaration of function 'eaf_delete' [-Wimplicit-function-declaration]
         eaf_delete (eaf[k]);
         ^
Reaf.c: In function 'compute_eafdiff_C':
Reaf.c:114:5: error: unknown type name 'eaf_t'
     eaf_t **eaf = compute_eaf_helper(DATA, nobj, CUMSIZES, nruns, NULL, nruns);
     ^
Reaf.c:114:19: warning: initialization makes pointer from integer without a cast
     eaf_t **eaf = compute_eaf_helper(DATA, nobj, CUMSIZES, nruns, NULL, nruns);
                   ^
Reaf.c:126:29: error: request for member 'size' in something not a structure or union
         int npoints = eaf[k]->size;
                             ^
Reaf.c:130:13: error: expected expression before 'int'
             int totalsize = npoints * nobj;
             ^
Reaf.c:137:53: error: request for member 'data' in something not a structure or union
                 rmat[pos + j * totalpoints] = eaf[k]->data[j + i * nobj];
                                                     ^
Reaf.c:145:29: error: request for member 'size' in something not a structure or union
         int npoints = eaf[k]->size;
                             ^
Reaf.c:149:13: warning: implicit declaration of function 'attained_left_right' [-Wimplicit-function-declaration]
             attained_left_right (eaf[k]->attained + i * eaf[k]->nruns,
             ^
Reaf.c:149:40: error: request for member 'attained' in something not a structure or union
             attained_left_right (eaf[k]->attained + i * eaf[k]->nruns,
                                        ^
Reaf.c:149:63: error: request for member 'nruns' in something not a structure or union
             attained_left_right (eaf[k]->attained + i * eaf[k]->nruns,
                                                               ^
Reaf.c: In function 'polygon_len':
Reaf.c:165:20: error: 'objective_MIN' undeclared (first use in this function)
     while (*src != objective_MIN)
                    ^
Reaf.c:165:20: note: each undeclared identifier is reported only once for each function it appears in
Reaf.c: In function 'polygon_copy':
Reaf.c:174:20: error: 'objective_MIN' undeclared (first use in this function)
     while (*src != objective_MIN) {
                    ^
Reaf.c: In function 'compute_eafdiff_area_C':
Reaf.c:199:5: error: unknown type name 'eaf_t'
     eaf_t **eaf = compute_eaf_helper(DATA, nobj, CUMSIZES, nruns, NULL, nruns);
     ^
Reaf.c:199:19: warning: initialization makes pointer from integer without a cast
     eaf_t **eaf = compute_eaf_helper(DATA, nobj, CUMSIZES, nruns, NULL, nruns);
                   ^
Reaf.c:201:5: error: unknown type name 'eaf_polygon_t'
     eaf_polygon_t *p = eaf_compute_area (eaf, nruns);
     ^
Reaf.c:201:5: warning: implicit declaration of function 'eaf_compute_area' [-Wimplicit-function-declaration]
Reaf.c:201:24: warning: initialization makes pointer from integer without a cast
     eaf_polygon_t *p = eaf_compute_area (eaf, nruns);
                        ^
Reaf.c:209:5: warning: implicit declaration of function 'vector_int_size' [-Wimplicit-function-declaration]
     int ncol = vector_int_size(&p->col);
     ^
Reaf.c:209:34: error: request for member 'col' in something not a structure or union
     int ncol = vector_int_size(&p->col);
                                  ^
Reaf.c:211:5: error: invalid use of void expression
     DEBUG2(Rprintf ("ncol: %d\n", ncol));
     ^
Reaf.c:218:5: warning: implicit declaration of function 'vector_objective_begin' [-Wimplicit-function-declaration]
     double * p_xy = vector_objective_begin(&p->xy);
     ^
Reaf.c:218:46: error: request for member 'xy' in something not a structure or union
     double * p_xy = vector_objective_begin(&p->xy);
                                              ^
Reaf.c:220:9: warning: implicit declaration of function 'vector_int_at' [-Wimplicit-function-declaration]
         double color = vector_int_at(&p->col, k);
         ^
Reaf.c:220:40: error: request for member 'col' in something not a structure or union
         double color = vector_int_at(&p->col, k);
                                        ^
Reaf.c:224:9: error: invalid use of void expression
         DEBUG2(Rprintf ("color: %d, len = %d\n", color, len));
         ^
Reaf.c:232:9: warning: implicit declaration of function 'vector_int_set' [-Wimplicit-function-declaration]
         vector_int_set(&p->col, k, color);
         ^
Reaf.c:232:26: error: request for member 'col' in something not a structure or union
         vector_int_set(&p->col, k, color);
                          ^
Reaf.c:236:21: error: invalid use of void expression
                     left_len, right_len, left_ncol, right_ncol));
                     ^
Reaf.c:248:37: error: request for member 'xy' in something not a structure or union
     p_xy = vector_objective_begin(&p->xy);
                                     ^
Reaf.c:253:37: error: request for member 'col' in something not a structure or union
         int color = vector_int_at(&p->col, k);
                                     ^
Reaf.c:267:5: warning: implicit declaration of function 'vector_int_dtor' [-Wimplicit-function-declaration]
     vector_int_dtor (&p->col);
     ^
Reaf.c:267:24: error: request for member 'col' in something not a structure or union
     vector_int_dtor (&p->col);
                        ^
Reaf.c:268:5: warning: implicit declaration of function 'vector_objective_dtor' [-Wimplicit-function-declaration]
     vector_objective_dtor (&p->xy);
     ^
Reaf.c:268:30: error: request for member 'xy' in something not a structure or union
     vector_objective_dtor (&p->xy);
                              ^
Reaf.c: In function 'read_data_sets':
Reaf.c:294:5: error: unknown type name 'objective_t'
     objective_t *data = NULL;
     ^
Reaf.c:300:5: warning: implicit declaration of function 'read_objective_t_data' [-Wimplicit-function-declaration]
     read_objective_t_data (filename, &data, &nobj, &cumsizes, &nruns);
     ^
Reaf.c:307:30: warning: passing argument 2 of 'double_transpose' from incompatible pointer type
     double_transpose (rdata, data, ntotal, nobj);
                              ^
In file included from Reaf.c:1:0:
Rcommon.h:104:1: note: expected 'const double *' but argument is of type 'int *'
 double_transpose(double *dst, const double *src,
 ^
Reaf.c:309:15: warning: unused variable 'i' [-Wunused-variable]
     int k, j, i;
               ^
make: *** [Reaf.o] Error 1
ERROR: compilation failed for package 'eaf'
* removing 'C:/Users/Amin/Documents/R/win-library/3.5/eaf'
* restoring previous 'C:/Users/Amin/Documents/R/win-library/3.5/eaf'
In R CMD INSTALL
Installation failed: Command failed (1)

Do you have any idea what is this error for?
Thanks.

ValueError with numpy > 1.16.4 in README Python example

The example in the README of running eaf with Python requires numpy<=1.16.4 (and no later, until rpy2 v3.0.x is released and may fix it). Note that this is referenced in another issue for rpy2 (conda-forge/rpy2-feedstock#28).

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