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> library(testthat)
> library(cati)
Loading required package: nlme
Loading required package: ade4
Loading required package: ape
> 
> test_check("cati")
	#################################
	# Community metrics calculation #
	#################################
class: ComIndex
$call: ComIndex(traits = traits.finch, index = "mean(x, na.rm = TRUE)", 
    nullmodels = "regional.ind", ind.plot = ind.plot.finch, sp = sp.finch, 
    nperm = 9, printprogress = FALSE)

###############
$obs: list of observed values
	$mean(x, na.rm = TRUE)

###############
$null: list of null values, number of permutations: 9 
	$mean(x, na.rm = TRUE)_nm ... null model = regional.ind

###############
data used
  data      class  dim    content                                    
1 $traits   matrix 2513,4 traits data                                
2 $ind.plot factor 2513   name of the plot in which the individual is
3 $sp       factor 2513   individuals' groups (e.g. species)         

###############
others
	$namestraits: 4 traits
[1] "WingL"  "BeakH"  "UBeakL" "N.UBkL"

	$sites_richness:
	    DMaj    EspHd FlorChrl  GnovTwr MrchBndl SCruInde 
      50      267      981      258      270      687 

[1] "Observed values"
$`mean(x, na.rm = TRUE)`
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  10.29   10.68   13.43   26.23   28.98   67.79 

[1] "null values"
$`mean(x, na.rm = TRUE)`
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  10.13   10.67   13.40   26.22   28.96   67.98 

	##################
	# T-statistics #
	##################
class: Tstats
$call: Tstats(traits = traits.finch, ind.plot = ind.plot.finch, sp = sp.finch, 
    nperm = 9, printprogress = FALSE)

###############
$Tstats: list of observed and null T-statistics

Observed values
	$T_IP.IC: ratio of within-population variance to total within-community variance
	$T_IC.IR: community-wide variance relative to the total variance in the regional pool
	$T_PC.PR: inter-community variance relative to the total variance in the regional pool

Null values, number of permutations: 9
	$T_IP.IC_nm: distribution of T_IP.IC value under the null model local
	$T_IC.IR_nm: distribution of T_IC.IR value under the null model regional.ind 
	$T_PC.PR_nm: distribution of T_PC.PR value under the null model regional.pop

###############
$variances: list of observed and null variances

###############
data used
  data      class  dim    content                                    
1 $traits   matrix 2513,4 traits data                                
2 $ind.plot factor 2513   name of the plot in which the individual is
3 $sp       factor 2513   individuals' groups (e.g. species)         

###############
others
	$namestraits: 4 traits
[1] "WingL"  "BeakH"  "UBeakL" "N.UBkL"

	$nb.ind_plot:
	ind.plot
    DMaj    EspHd FlorChrl  GnovTwr MrchBndl SCruInde 
      50      267      981      258      270      687 

[1] "Observed values"
$T_IP.IC
     WingL             BeakH             UBeakL            N.UBkL       
 Min.   :0.03435   Min.   :0.01528   Min.   :0.02669   Min.   :0.02385  
 1st Qu.:0.04365   1st Qu.:0.01907   1st Qu.:0.04170   1st Qu.:0.03670  
 Median :0.06448   Median :0.04003   Median :0.05445   Median :0.04035  
 Mean   :0.11608   Mean   :0.10944   Mean   :0.07640   Mean   :0.06147  
 3rd Qu.:0.10115   3rd Qu.:0.05802   3rd Qu.:0.06289   3rd Qu.:0.04939  
 Max.   :0.38311   Max.   :0.48519   Max.   :0.21962   Max.   :0.17637  

$T_IC.IR
     WingL             BeakH             UBeakL           N.UBkL      
 Min.   :0.09246   Min.   :0.06316   Min.   :0.2461   Min.   :0.2569  
 1st Qu.:0.67385   1st Qu.:0.49130   1st Qu.:0.6684   1st Qu.:0.7238  
 Median :1.17073   Median :1.18311   Median :0.9442   Median :0.9800  
 Mean   :1.08518   Mean   :1.12359   Mean   :0.9109   Mean   :0.9677  
 3rd Qu.:1.62569   3rd Qu.:1.62423   3rd Qu.:1.0803   3rd Qu.:1.3144  
 Max.   :1.79158   Max.   :2.28021   Max.   :1.6287   Max.   :1.5250  

$T_PC.PR
     WingL            BeakH             UBeakL           N.UBkL      
 Min.   :0.2261   Min.   :0.08685   Min.   :0.9328   Min.   :0.9356  
 1st Qu.:0.8981   1st Qu.:0.86252   1st Qu.:0.9828   1st Qu.:1.0388  
 Median :1.2233   Median :1.05894   Median :1.1249   Median :1.0992  
 Mean   :1.1303   Mean   :1.23699   Mean   :1.1488   Mean   :1.1955  
 3rd Qu.:1.4737   3rd Qu.:1.32864   3rd Qu.:1.2148   3rd Qu.:1.3513  
 Max.   :1.7622   Max.   :3.00163   Max.   :1.5301   Max.   :1.5852  

[1] "null values"
$T_IP.IC_nm
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.4629  0.9740  0.9985  1.0140  1.0259  2.5871 

$T_IC.IR_nm
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.6501  0.9467  1.0043  0.9999  1.0406  1.6468 

$T_PC.PR_nm
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.     NAs 
 0.0000  0.3407  0.6698  1.0266  1.5345  5.9628      17 

[1] "33 %"
[1] "67 %"
[1] "100 %"
[1] "50 %"
[1] "100 %"
[1] "50 %"
[1] "100 %"
[ FAIL 0 | WARN 600 | SKIP 0 | PASS 80 ]

[ FAIL 0 | WARN 600 | SKIP 0 | PASS 80 ]
> 
> proc.time()
   user  system elapsed 
  19.25    2.20   21.43