DOC: readme

README.rst

@@ -78,8 +78,7 @@ file. For example, the options in the following command line::
 
     funpack \
       --overwrite \
-      --import_all \
-      --log_file log.txt \
+      --write_log \
       --icd10_map_file icd_codes.tsv \
       --category 10 \
       --category 11 \
@@ -89,8 +88,7 @@ file. For example, the options in the following command line::
 Could be stored in a configuration file ``config.txt``::
 
     overwrite
-    import_all
-    log_file       log.txt
+    write_log
     icd10_map_file icd_codes.tsv
     category       10
     category       11
@@ -193,13 +191,14 @@ Output
 ------
 
 
-The main output of FUNPACK is a plain-text tab-delimited[*]_ file which
-contains the input data, after cleaning and processing, potentially with
-some columns removed, and new columns added.
+The main output of FUNPACK is a plain-text file[*]_ which contains the input
+data, after cleaning and processing, potentially with some columns removed,
+and new columns added.
 
 
-If you used the ``--non_numeric_file`` option, the main output file will only
-contain the numeric columns; non-numeric columns will be saved to a separate
+If you used the ``--suppress_non_numerics`` option, the main output file will
+only contain the numeric columns. You can combine this with the
+``--write_non_numerics`` option to save non-numeric columns to a separate
 file.
 
 
@@ -208,7 +207,9 @@ MATLAB, or Excel. It is also possible to pass the output back into
 FUNPACK.
 
 
-.. [*] You can change the delimiter via the ``--tsv_sep`` / ``-ts`` option.
+.. [*] If your output file name ends with ``.csv``, the file will be
+       comma-separated, and if your output file name ends with ``.tsv``, the
+       file will be tab-separated.
 
 
 Loading output into MATLAB
@@ -225,7 +226,7 @@ Loading output into MATLAB
 If you are using MATLAB, you have several options for loading the FUNPACK
 output. The best option is |readtable|_, which will load column names, and
 will handle both non-numeric data and missing values.  Use ``readtable`` like
-so::
+so (assuming that you generated a tab-separated file)::
 
     data = readtable('out.tsv', 'FileType', 'text');
 
@@ -249,10 +250,10 @@ names from the ``table`` object like so::
     colnames        = vertcat(colnames{:});
 
 
-If you have used the ``--description_file`` option, you can load in the
-descriptions for each column as follows::
+If you have used the ``--write_description`` or``--description_file`` options,
+you can load in the descriptions for each column as follows::
 
-    descs = readtable('descriptions.tsv', ...
+    descs = readtable('out_descriptions.tsv', ...
                       'FileType', 'text', ...
                       'Delimiter', '\t',  ...
                       'ReadVariableNames',false);