Error thrown in `estimateD` (incompatibility between package versions)

[dbarneche]

Hello,

Up until yesterday, I was using function estimateD version 2.0.9 of your package, and everything was running fine. However, after updating it, I no longer get the same result, and it keeps throwing an error.

I am attaching a list of sites with frequence incidence data so you can replicate my error. I was hoping you could provide some insight onto why the new version of the package is returning an error:

siteList  <-  list(
'site1'=c(20, 10, 9, 1, 1),
'site2'=c(21, 14, 11, 2, 1, 1, 1),
'site3'=c(2, 2),
'site4'=c(4, 4),
'site5'=c(1, 1),
'site6'=c(1, 1),
'site7'=c(2, 2),
'site8'=c(10, 5, 3, 3, 1, 1, 1, 1),
'site9'=c(4, 3, 3, 1, 1),
'site10'=c(7, 5, 1, 1, 1),
'site11'=c(16, 12, 8, 4, 2, 1),
'site12'=c(9, 9, 7, 1, 1),
'site13'=c(36, 32, 11, 5, 3, 2, 2, 1),
'site14'=c(3, 3),
'site15'=c(6, 2, 2, 1, 1),
'site16'=c(5, 3, 2, 1),
'site17'=c(8, 5, 3, 3, 2),
'site18'=c(5, 5),
'site19'=c(11, 11, 6, 5, 4, 3, 3, 2, 1, 1, 1, 1, 1),
'site20'=c(8, 7, 7, 4, 2, 1, 1, 1, 1, 1),
'site21'=c(5, 5, 5, 2, 1, 1, 1),
'site22'=c(7, 7, 6, 5, 2, 2, 1, 1, 1),
'site23'=c(22, 19, 18, 15, 11),
'site24'=c(10, 10, 5, 5, 4),
'site25'=c(11, 11, 8, 3, 1),
'site26'=c(8, 5, 5, 3, 2),
'site27'=c(17, 13, 13, 7, 6, 1),
'site28'=c(12, 12, 6, 6, 1),
'site29'=c(17, 12, 11, 8, 3, 1),
'site30'=c(8, 8),
'site31'=c(9, 9),
'site32'=c(7, 7),
'site33'=c(8, 8),
'site34'=c(7, 7),
'site35'=c(6, 6),
'site36'=c(5, 5),
'site37'=c(9, 9, 1),
'site38'=c(11, 11),
'site39'=c(6, 6),
'site40'=c(5, 5),
'site41'=c(55, 52, 25, 23, 17, 5, 1),
'site42'=c(34, 30, 4, 1),
'site43'=c(1, 1),
'site44'=c(122, 96, 85, 30, 28, 3, 1, 1),
'site45'=c(77, 74, 42, 30, 24, 22, 13, 4, 2, 1, 1),
'site46'=c(24, 8, 7, 4, 3, 3, 2, 1),
'site47'=c(7, 4, 1, 1, 1),
'site48'=c(2, 1, 1),
'site49'=c(40, 31, 18, 9, 1),
'site50'=c(16, 11, 9, 1),
'site51'=c(9, 6, 4),
'site52'=c(72, 57, 27, 18, 17, 4, 1, 1, 1),
'site53'=c(1, 1),
'site54'=c(1, 1),
'site55'=c(1, 1),
'site56'=c(4, 4, 2, 1, 1, 1, 1),
'site57'=c(5, 4, 2, 1, 1),
'site58'=c(2, 2),
'site59'=c(3, 3),
'site60'=c(3, 1, 1, 1, 1),
'site61'=c(1, 1, 1),
'site62'=c(7, 4, 3, 1, 1, 1),
'site63'=c(1, 1),
'site64'=c(10, 9, 4),
'site65'=c(4, 3, 1),
'site66'=c(1, 1),
'site67'=c(9, 6, 3, 2),
'site68'=c(10, 8, 6, 3),
'site69'=c(6, 3, 3, 3, 1),
'site70'=c(5, 2, 1, 1, 1, 1),
'site71'=c(29, 9, 7, 5, 4, 3, 2, 2, 2, 1),
'site72'=c(4, 4),
'site73'=c(11, 11, 1),
'site74'=c(12, 9, 8),
'site75'=c(4, 3, 1),
'site76'=c(6, 6),
'site77'=c(6, 6),
'site78'=c(12, 12),
'site79'=c(1, 1),
'site80'=c(33, 33),
'site81'=c(2, 2),
'site82'=c(1, 1),
'site83'=c(7, 7),
'site84'=c(4, 3, 1),
'site85'=c(316, 189, 153, 133, 106, 72, 57, 36, 22, 19, 9, 8, 6, 5, 5, 5, 5, 4, 4, 2, 2, 2, 1, 1, 1, 1),
'site86'=c(95, 59, 46, 38, 17, 8, 8, 4, 2, 1, 1, 1),
'site87'=c(69, 62, 36, 19, 18, 14, 10, 4, 1, 1),
'site88'=c(63, 39, 18, 10, 8, 7, 2),
'site89'=c(20, 15, 5, 4, 1),
'site90'=c(50, 42, 25, 24, 7, 5, 3, 2, 1),
'site91'=c(41, 38, 4, 4, 4, 2, 2, 1, 1, 1, 1),
'site92'=c(19, 13, 6, 1),
'site93'=c(47, 47, 1),
'site94'=c(1, 1),
'site95'=c(47, 47),
'site96'=c(138, 111, 50, 7, 3, 2, 1, 1, 1, 1),
'site97'=c(23, 11, 7, 4, 2),
'site98'=c(42, 34, 16),
'site99'=c(4, 4, 2),
'site100'=c(78, 50, 42, 3),
'site101'=c(31, 28, 4, 2, 1),
'site102'=c(26, 21, 7),
'site103'=c(22, 9, 8, 6, 5, 1),
'site104'=c(18, 13, 3, 2),
'site105'=c(4, 3, 1),
'site106'=c(16, 11, 4, 1, 1),
'site107'=c(2, 2),
'site108'=c(8, 4, 4, 1),
'site109'=c(3, 3),
'site110'=c(1, 1),
'site111'=c(8, 3, 3, 1, 1),
'site112'=c(5, 5),
'site113'=c(18, 15, 9),
'site114'=c(8, 5, 4, 1),
'site115'=c(8, 5, 4, 1),
'site116'=c(24, 22, 2, 1),
'site117'=c(17, 9, 9, 4, 1),
'site118'=c(7, 4, 3),
'site119'=c(7, 5, 4),
'site120'=c(53, 31, 11, 6, 5, 5, 3, 3, 1, 1),
'site121'=c(44, 16, 11, 5, 4, 4, 3, 2, 1, 1, 1),
'site122'=c(31, 26, 18, 1),
'site123'=c(23, 16, 12),
'site124'=c(42, 41, 20, 1),
'site125'=c(7, 7, 2),
'site126'=c(36, 31, 24, 4),
'site127'=c(14, 11, 9),
'site128'=c(16, 11, 9, 3),
'site129'=c(38, 31, 16, 1),
'site130'=c(14, 13, 5),
'site131'=c(10, 7, 7),
'site132'=c(33, 30, 12, 1),
'site133'=c(230, 137, 109, 79, 26, 15, 12, 7, 6, 6, 5, 4, 4, 4, 4, 3, 3, 3, 1, 1, 1),
'site134'=c(30, 11, 7, 6, 6, 4, 3, 2, 1),
'site135'=c(28, 24, 7, 1, 1),
'site136'=c(31, 13, 10, 10, 2, 1))

# works fine on iNEXT 2.0.9
library(devtools)
install_version('iNEXT', version = '2.0.9', repos = 'http://cran.us.r-project.org')
library(iNEXT)
estimateD(siteList, 'incidence_freq', base = 'coverage', level = NULL)

# returns error on iNEXT 2.0.12
install.packages('iNEXT')
library(iNEXT)
estimateD(siteList, 'incidence_freq', base = 'coverage', level = NULL, conf = NULL)

Thanks very much for your assistance. Best wishes, D