[SOLVED] How do I save variables from hdf5 file using strings as variable names?

How do I save variables from hdf5 file using strings as variable names?

I have a hdf5 file with multiple variables that I want to automatically store in a list or a matrix.

library(rhdf5)
file = H5Fopen("myfile.h5")
file
HDF5 FILE
        name /
    filename 

                       name       otype  dclass         dim
0  AGB_CO                   H5I_DATASET FLOAT   3          
1  AGB_CUT                  H5I_DATASET FLOAT   17 x 11 x 1
2  AGB_GROWTH               H5I_DATASET FLOAT   17 x 11 x 1
3  AGB_MORT                 H5I_DATASET FLOAT   17 x 11 x 1
4  AGE                      H5I_DATASET FLOAT   1          
5  AREA                     H5I_DATASET FLOAT   1          
6  AREA_SI                  H5I_DATASET FLOAT   1          
7  BALIVE                   H5I_DATASET FLOAT   3          
8  BASAL_AREA_CUT           H5I_DATASET FLOAT   17 x 11 x 1
9  BASAL_AREA_GROWTH        H5I_DATASET FLOAT   17 x 11 x 1
10 BASAL_AREA_MORT          H5I_DATASET FLOAT   17 x 11 x 1

h5info=h5ls("myfile.h5")
names=h5info$name
names
 [1] "AGB_CO"                   "AGB_CUT"                  "AGB_GROWTH"               "AGB_MORT"                
 [5] "AGE"                      "AREA"                     "AREA_SI"                  "BALIVE"                  
 [9] "BASAL_AREA_CUT"           "BASAL_AREA_GROWTH"        "BASAL_AREA_MORT"          "BA_CO"

I can access any variable in the file by typing

file$AGB_CO
[1] 0.04595303 0.02707645 0.03625819

Now I would like to use a loop to save all variables to memory. Something like

for (i in 1:names) {
    vari=paste0("file$",names[i])
    assign(vari,NA)
    *some list or matrix*=as.name(vari)
}

I have tried assign(), eval(), as.name(), none of them works, but I am not able to save them into another variable. However if I type myvar=file$AGB_CO it works. How to implement this?

Solution

There are two solutions I have found. One is to use the above mentioned command h5read("myfile.h5","/"), otherwise the rhdf5 has a specific command h5dump that will take al the content of a file and save it as in a variable while keeping the structure.