growth                 package:CTFS                 R Documentation

_A_n_n_u_a_l _G_r_o_w_t_h _R_a_t_e_s _b_y _C_a_t_e_g_o_r_i_e_s (_U_s_e_r _d_e_f_i_n_e_d _g_r_o_u_p_s)

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

     Computes annual growth rate for all trees or any user defined
     categorization of trees.  Two growth rates can be computed: simple
     change in dbh over time and relative growth rate.  Unrealistically
     high and low values are removed from the summary values.  Growth
     rate in mm dbh per year, relative growth rate in % change in dbh
     per year, standard deviation or 95% confidence limits, and sample
     size are provided.  Two datasets must be used, one for each
     census.

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

     growth(census1, census2, 
             rounddown = FALSE, method = "I", stdev = FALSE, 
             mindbh = 10, err.limit = 4, maxgrow = 75, 
             split1 = NULL, split2 = NULL)

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

 census1: name of census datafile for first census, must be a
          *dataframe*, must be of same length as 'census2'

 census2: name of census datafile for second census, must be a
          *dataframe*, must be of same length as 'census1'

rounddown: logical value in caps.  When TRUE, if either of  census is <
          55, then the 'floor' of the dbh value / 5 is  provided.  When
          FALSE, no change in the dbh is made.

  method: character indicating the type of growth rate to be 
          calculated.  When "I" the annual change in dbh is provided.
          When  "E" the relative growth rate is provided.  see 
          'CTFS.growth' for more details on 'method'.

   stdev: logical value in caps.  When TRUE, the  standard deviation of
          growth is provided.  When FALSE, a 95%  condfidence interval
          is provided.  The confidence limits are not  computed.

  mindbh: minimum DBH in 'census1' for inclusion in computation.

err.limit: number of standard deviations: used for determining  if an
          individual tree growth rate is too high or low for inclusion.

 maxgrow: maximum absolute growth rate, mm per year: used for 
          determining if an individual tree growth rate is too high for
           inclusion.

  split1: a *vector* of categorical values of the same  length as
          'census' which groups trees into classes of  interest for
          which growth values are computed.  This vector can be 
          composed of characters or numbers.

  split2: a second *vector* of categorical values of the same  length
          as 'census' which groups trees into classes of  interest for
          which growth values are computed.  This vector can be 
          composed of characters or numbers.

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

     See 'CTFS.growth' for details on the computation of  growth rates
     and associated functions.

     Any two censuses on a datafile must be used. They do not have to
     be  sequential, only that 'census1' has to be before 'census2'.

     The vectors 'split1' and 'split2' must be of the same length as
     'census1' and 'census2' but can contain     NA. 

     The results of 'growth' can be organized into *dataframes* with
     the use of 'assemble.demography'.

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

     'growth' returns a *list of arrays* with the values of 'split1' as
     the first dimension and the values of 'split2' as the second
     dimension of the array.  The array contains the following named
     components:

     $N0: the number of trees used to compute growth rate

   $rate: the annual mean growth rate in mm per year or % per year,
          type determined by the argument 'method'

   $clim: the 95% confidence limit based on a normal  distribution

$dbhmean: the mean dbh in mm for trees used to compute growth  rate

$meanyrs: mean number of years between census for trees used in  growth
          rate computation.

  $date0: mean date of first census

  $date1: mean date of second census


     If the vector(s) 'split1' and 'split2' are provided by the user,
     then growth rates and associated statistics are computed for each
     value of the vectors.  The vectors are nested so that growth rates
     is computed for each category of 'split2' within each category of
     'split1'

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

     Rick Condit and Pamela Hall

_S_e_e _A_l_s_o:

     'CTFS.growth'

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

     ## Not run: 
     1. Default use of growth()

     growth.all.out <- growth(tst.bci90.full,tst.bci95.full)
     growth.all.out

     2. Create a vector of species names for each tree to compute growth 
     rates for each species.

     bci.spp.vct <- tst.bci90.full$sp
     names(growth.spp.out)
     growth.spp.out$rate

     3.  Create 2 vectors: the first of habitats based on the quad location 
     of each tree and the second of tree species names.

     bci.hab.vct <- sep.quadinfo(tst.bci90.full,bciquad.info,by.col="hab")
     growth.spp.hab.out <- growth(tst.bci90.full,tst.bci95.full,split1=bci.spp.vct,split2=bci.hab.vct)
     growth.spp.hab.out$rate

     ## End(Not run)

