Commit f544cc52 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

DOC: readme

parent 3525939e
......@@ -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);
......
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