Chapter 2 Single Taxon Starting Points

2.1 Box File Locations

CPR data on individual taxon were delivered through email and stored in the following directory on box.

Box/Adam Kemberling/Box_Projects/continuous_plankton_recorder/

All derived data from these starting files are under this directory. This is not a permanent home, but is the location the cpr_boxpath() refers to in the code:

2.2 Original File Structure

When initially engaging with the CPR data, requests for CPR data on specific taxa were requested and received as individual files. These came in two groups that contain both annual averages and some within-year averages (bi-monthly or quarterly).

Folder	File Name	Description	Temporal Frequency
CPRtimeseries_textX	GOMx.Calanus_finmarchicus.txt	Late stage C. Finmarchicus densities	Quarterly periods
CPRtimeseries_textX	GOMx.Calanus_I-IV.txt	Early-stage C. finmarchicus densities	Quarterly periods
CPRtimeseries_textX	GOMx.Centropages_typicus.txt	Centropages typicus densities	Quarterly periods
CPRtimeseries_textX	GOMx.Chaetognatha_eyecount.txt	Chaetognatha spp. densities	Quarterly periods
CPRtimeseries_textX	GOMx.Euphausiacea_Total.txt	Euphausiacea densities	Quarterly periods
CPRtimeseries_textX	GOMx.Metridia_lucens.txt	Metridia lucens densities	Quarterly periods
CPRtimeseries_textX	GOMx.Oithona_spp..txt	Oithona spp. densities	Quarterly periods
CPRtimeseries_textX	GOMx.Para-Pseudocalanus_spp..txt	Paracalanus & Pseudocalanus densities	Quarterly periods
CPRtimeseries_textX	GOMx.Paraeuchaeta_norvegica.txt	Paraeuchaeta norvegica densities	Quarterly periods
CPRtimeseries_textX	GOMx.Temora_longicornis.txt	Temora longicornis densities	Quarterly periods
CPRtimeseries_textX6	Calanus_finmarchicus.txt	Late stage C. Finmarchicus densities	Bi-monthly periods
CPRtimeseries_textX6	Calanus_I-IV.txt	Early-stage C. finmarchicus densities	Bi-monthly periods
CPRtimeseries_textX6	Centropages_typicus.txt	Centropages typicus densities	Bi-monthly periods
CPRtimeseries_textX6	Chaetognatha_eyecount.txt	Chaetognatha spp. densities	Bi-monthly periods
CPRtimeseries_textX6	Euphausiacea_Total.txt	Euphausiacea densities	Bi-monthly periods
CPRtimeseries_textX6	Metridia_lucens.txt	Metridia lucens densities	Bi-monthly periods
CPRtimeseries_textX6	Oithona_spp..txt	Oithona spp. densities	Bi-monthly periods
CPRtimeseries_textX6	Para-Pseudocalanus_spp..txt	Paracalanus & Pseudocalanus densities	Bi-monthly periods
CPRtimeseries_textX6	Paraeuchaeta_norvegica.txt	Paraeuchaeta norvegica densities	Bi-monthly periods
CPRtimeseries_textX6	Temora_longicornis.txt	Temora longicornis densities	Bi-monthly periods

2.3 Consolidated Taxa Files

These collections of individual taxon abundances are each processed into two additional processed files. One for the yearly densities and the second for quarterly densities. These two intermediate/processed files are:

Folder	File Name	Description
processed_data	cpr_allspecies_long.csv	reshaping of bi-monthly single species taxa
processed_data	cpr_allspecies_long_quarters.csv	reshaping of quarterly single species taxa