drdata                 package:drfit                 R Documentation

_G_e_t _d_o_s_e-_r_e_s_p_o_n_s_e _d_a_t_a _v_i_a _R_O_D_B_C

_D_e_s_c_r_i_p_t_i_o_n:

     Get dose-response data from an adequate ODBC data source

_U_s_a_g_e:

       drdata(substances, experimentator = "%", db = "cytotox", celltype = "IPC-81", 
         enzymetype="AChE", organism="Vibrio fischeri", endpoint="Luminescence", 
         whereClause = "1", ok = "'ok','no fit'")

_A_r_g_u_m_e_n_t_s:

substances: A string or an array of strings with the substance names
          for which dose-response data is to be retrieved.

experimentator: The name of the experimentator whose data is to be
          used. Default is " which means that data from all
          experimentators are retrieved.

      db: The database to be used. Currently, the databases "cytotox",
          "enzymes" and "ecotox" of the UFT Department of Bioorganic
          Chemistry are  supported (default is "cytotox").

celltype: Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and
          U937 are supported.

enzymetype: Currently, only data for AChE, GR and GST are supported.

organism: The organism that was exposed to the chemical. Only important
          if the database "ecotox" is used. Defaults to "Vibrio
          fischeri".

endpoint: The endpoint that should be used for selecting the data. Only
          important if the database "ecotox" is used. Defaults to
          "Luminescence".

whereClause: With this argument, additional conditions for the SQL
          query can be set,  e.g. "plate != 710" (i.e. "Do not retrieve
          data for plate 710"). The default is 1 (in SQL syntax this
          means TRUE).

      ok: With the default value "'ok','no fit'", only data that has
          been checked and set to "ok" or "no fit" in the database is
          retrieved. The argument "no fit" will result in not using the
          data for fitting, but it will be plotted. Another sensible
          argument would be "'ok','no fit','?'", in order to
          additionally retrieve data which has not yet been checked.

_D_e_t_a_i_l_s:

     The function is currently only used for retrieving data from the
     mysql database "cytotox" of the UFT Department of Bioorganic
     Chemistry. Access to this database is limited to UFT staff. 
     Additionally to the installation of the RODBC package, it is
     required to set up a ODBC data source with the name "cytotox",
     using an ODBC driver for mysql, probably myODBC. Then, under Unix,
     you can use iodbc or unixodbc for setting up the respective data
     source with data source name (DSN) "cytotox". For my setting using
     unixodbc, I am using the file '/etc/odbcinst.ini' containing: 

       [MySQL]         
       Description  =  MySQL driver for ODBC
       Driver       =  /usr/local/lib/libmyodbc.so
       Setup        =  /usr/lib/odbc/libodbcmyS.so

     and the file '/etc/odbc.ini' containing:

       [cytotox]       
       Description  =  Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen
       Driver       =  MySQL
       Trace        =  Yes
       TraceFile    =  /tmp/odbc.log
       Database     =  cytotox
       Server       =  eckehaat
       Port         =  3306

_V_a_l_u_e:

    data: A data frame with a factor describing the dose levels, the
          numeric dose levels and a numeric column describing the
          response, as well as the entries for plate, experimentator,
          performed (date of test performance), celltype, unit (of the
          dose/concentration), and for the ok field in the database.

_A_u_t_h_o_r(_s):

     Johannes Ranke  jranke@uni-bremen.de  <URL:
     http://www.uft.uni-bremen.de/chemie/ranke>

_E_x_a_m_p_l_e_s:

     # Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81
     # cells
     ## Not run: drdata(c("TBT","ZnPT2"))

