Why was Russia defeated in the war with Japan?

The following reasons for the defeat of the Russian Empire in this war can be distinguished:

1) Russia did not underestimate its adversary;

2) The Russian command was indecisive and weak;

3) Transferring troops and weapons to the Far East was a difficult task.

Thus, Japan was able to win this war. A peace treaty was signed between the parties, according to which the winner received the southern part of Sakhalin, as well as other privileges.