merge README into README.md

README.md

@@ -1,2 +1,92 @@
 # TS-lookup
-This is the code from Goes et al. (2018) to infer salinity for temperature profiles
+
+- This is the code from Goes et al. (2018) to infer salinity for temperature profiles.
+- This matlab package is to calculate the salinity from temperature profiles.
+
+## REFERENCE
+
+Goes, M., J. Christophersen, S. Dong, G. Goni, and M.O. Baringer, 2018: An Updated Estimate of Salinity for the Atlantic Ocean Sector Using Temperature–Salinity Relationships. J. Atmos. Oceanic Technol., 35, 1771–1784, <https://doi.org/10.1175/JTECH-D-18-0029.1>
+
+
+## INSTALLATION
+
+run: `csh install.sh`
+
+## TEST
+
+run in matlab: `example.m`
+
+## Notes 
+
+- Now it works for the whole globe between `70S-65N`.
+- **NEEDS FOLDER WOA13 TO WORK**
+
+## Contents of this package
+
+- `Calc_sal_Thacker_Goes_EmDr_Stom_svd_globe.m` : Calculate the salinity from the T profiles.
+- inputs:
+
+```
+        TT - temperature
+        PP - pressure
+        lat - latitude
+        lon - longitude
+        timet - time
+        pad - use padding or not (1 and 0)
+        Pout - vector os interpolated depths if wanted
+        mehod - choose between Thacker [default], goes, annual, svd
+```
+
+- outputs:
+
+```
+         y2 - salinity (Now it is NaN free - linearly interpolated)
+         y3 - smoothed version of y2
+         TT - temperature profiles (can be interpolated is Pout provided)
+         PP - new depth profile
+```
+
+- `example.m` : runs one example using `data_example.mat` and produces the following figures.
+
+```
+   TS_orig_reconstruct_map_%g_scatter_SA.eps
+   TS_orig_reconstruct_SA.eps
+   TS_orig_reconstruct_scatter_SA.eps
+```
+
+## Fitted parameters for each region in the globe
+
+```
+fit_sigma_cora_argo_extended_fitlm_MD_thackergoes_noyear.mat
+fit_sigma_cora_argo_extended_fitlm_NA_thackergoes_noyear.mat
+fit_sigma_cora_argo_extended_fitlm_NOP_thackergoes_noyear.mat
+fit_sigma_cora_argo_extended_fitlm_NO_thackergoes_noyear.mat
+fit_sigma_cora_argo_extended_fitlm_NP_thackergoes_noyear.mat
+fit_sigma_cora_argo_extended_fitlm_SA_thackergoes_noyear.mat
+fit_sigma_cora_argo_extended_fitlm_SOI_thackergoes_noyear.mat
+fit_sigma_cora_argo_extended_fitlm_SOP_thackergoes_noyear.mat
+fit_sigma_cora_argo_extended_fitlm_SO_thackergoes_noyear.mat
+fit_sigma_cora_argo_extended_fitlm_SP_thackergoes_noyear.mat
+fit_sigma_cora_argo_extended_fitlm_TA_thackergoes_noyear.mat
+fit_sigma_cora_argo_extended_fitlm_TI_thackergoes_noyear.mat
+fit_sigma_cora_argo_extended_fitlm_TP_thackergoes_noyear.mat
+fit_sigma_cora_argo_extended_fitlm_FC_thackergoes_noyear_ryanonly.mat
+```
+
+## And using the Svd method
+
+```
+fit_sigma_cora_argo_extended_svd_MD.mat
+fit_sigma_cora_argo_extended_svd_NA.mat
+fit_sigma_cora_argo_extended_svd_NO.mat
+fit_sigma_cora_argo_extended_svd_NOP.mat
+fit_sigma_cora_argo_extended_svd_NP.mat
+fit_sigma_cora_argo_extended_svd_SA.mat
+fit_sigma_cora_argo_extended_svd_SOI.mat
+fit_sigma_cora_argo_extended_svd_SO.mat
+fit_sigma_cora_argo_extended_svd_SOP.mat
+fit_sigma_cora_argo_extended_svd_SP.mat
+fit_sigma_cora_argo_extended_svd_TA.mat
+fit_sigma_cora_argo_extended_svd_TI.mat
+fit_sigma_cora_argo_extended_svd_FC_ryanonly.mat
+```