networkspikes             package:sjemea             R Documentation

_C_o_m_p_u_t_e _n_e_t_w_o_r_k _s_p_i_k_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Compute the network spikes in an MEA recording, by averaging over
     all the electrodes in the array.

_U_s_a_g_e:

     s$ns <- compute.ns(s, ns.T=0.003, ns.N=10,sur=100)
     show.ns(ns, ...)

_A_r_g_u_m_e_n_t_s:

       s: MEA data structure

    ns.T: Bin width (in msec) for counting spikes.

    ns.N: Threshold number of active electrodes required to make
          network spike

     sur: How many bins either side of peak to retain when computing
          the mean network spike

      ns: A network spike data structure, returned by 'compute.ns'

     ...: Other plot arguments to pass to 'show.ns'

_D_e_t_a_i_l_s:

     To see the mean network spikes after they have computed, just look
     at the mean object.

     If you wish to see the individual network spikes, try show.ns(ns,
     ...) where the remaining args are passed to the plot function.

_V_a_l_u_e:

     A list with the following elements: 

  counts: vector giving the number of active electrodes in each bin;
          this can be very long!

    ns.N: The value of ns.N used.

    ns.T: the value of ns.T used.

    mean: The profile of the mean network spike (this is a time series
          object)

measures: If N network spikes were found, this is a matrix with N rows,
          one per network spike.

   brief: A short vector summarizing the network spikes.

_A_u_t_h_o_r(_s):

_R_e_f_e_r_e_n_c_e_s:

     Eytan and Marom (2006) J Neuroscience.

_S_e_e _A_l_s_o:

_E_x_a_m_p_l_e_s:

     data.file <- system.file("examples", "TC89_DIV15_A.nexTimestamps",
                              package = "sjemea")
     s <- sanger.read.spikes( data.file, beg=400, end=700)
     s$ns <- compute.ns(s, ns.T=0.003, ns.N=10,sur=100)
     plot(s$ns)
     plot(s$ns, xlim=c(450, 500))

     plot(s$ns$mean)                         #show mean NS.
     summary(s$ns)
     s$ns$brief

