RemoveNACases.RdFunction to remove the table rows for which all measurements of interest are non-available (NA). A particular list of measurement names can be explicitly provided or selected by a common initial pattern. The default setting removes the rows with no log-ratio available.
RemoveNACases(data, measureNames = NULL, prefix = logPrefix)A dataframe with the input measurements.
A vector of characters with the list of measurements
to be considered for missing values. If NULL (default), all measurements
starting by prefix are considered.
A character string with the initial pattern to select the
list of measurements. The default is given by the internal variable
logPrefix. It is in effect only when measureNames = NULL.
A dataframe with the same columns as the input dataframe but removing the rows with missing values for all measurements in the list.
## Read an example dataset:
dataFile <- system.file("extdata", "dataValenzuelaLamas2008.csv.gz",
package = "zoolog")
dataExample <- utils::read.csv2(dataFile,
na.strings = "",
encoding = "UTF-8")
## We can observe the first lines (excluding some columns for visibility):
head(dataExample)[, -c(6:20,32:64)]
#> Site N.inv UE Especie Os GL Bp Dp SD DD Bd Dd BT
#> 1 ALP 4918 10364 bota 1 fal 54.0 31.3 30.6 28.1 26.3 27.5 20.0 NA
#> 2 ALP 4919 10364 bota 1 fal 54.5 27.9 31.8 26.0 22.8 25.3 19.5 NA
#> 3 ALP 3453 10410 ovar 1fal ant 27.1 9.9 12.3 17.9 9.0 9.0 NA NA
#> 4 ALP 3455 10410 ovar 1fal ant 27.6 9.6 12.2 7.6 8.9 8.3 NA NA
#> 5 ALP 4245 7036 cahi hum NA 128.3 NA 12.9 NA 27.4 26.6 23.6
#> 6 ALP 4674 10227 cahi hum NA NA NA NA NA 26.0 25.7 22.3
#> GLc BFd Dl
#> 1 NA NA NA
#> 2 NA NA NA
#> 3 NA NA NA
#> 4 NA NA NA
#> 5 NA NA NA
#> 6 NA NA NA
## Remove the cases not including any measurement present in the reference.
refMeasureNames <- unique(reference$Combi$Measure)
refMeasureNames
#> [1] GL GLc
#> [3] Bp Dp
#> [5] SD Bd
#> [7] BT HTC
#> [9] Dd BFp
#> [11] BFd GLl
#> [13] GLpe SLC
#> [15] GLP LG
#> [17] BG DPA
#> [19] BPC WCM
#> [21] LA DC
#> [23] Dl GB
#> [25] L H
#> [27] SDO LAR
#> [29] SH GLm
#> [31] LeP GL
#> [33] DEM DVM
#> [35] DEL DVL
#> [37] WCL Dm
#> [39] 1 2
#> [41] 3 9
#> [43] 10 24
#> [45] 34 38
#> [47] 40 41
#> [49] 43 45
#> [51] 48 50
#> [53] GLC Ll
#> [55] DFd GH
#> [57] DS GLT
#> [59] SBT SDT
#> [61] GBT GDT
#> [63] HS LFo
#> [65] SB GLF
#> [67] BFcr BFcd
#> [69] Breadth of caudal channel LCDe
#> [71] Breadth of cranial channel LAPa
#> [73] SBV BPtr
#> [75] BPacd PL
#> [77] HFcr DHA
#> [79] Breadth of acetabulum LS
#> [81] Depth Distal depth, flat against posterior
#> [83] Maximum lateral depth
#> 83 Levels: BFd BFp BT Bd Bp Dd Dp GL GLc GLl GLpe HTC SD BG BPC DC DPA ... SBV
dataExamplePruned <- RemoveNACases(dataExample,
measureNames = refMeasureNames)
## The first lines of the output data frame show at least one available
## measurement value in the selected list:
head(dataExamplePruned)[, -c(6:20,32:64)]
#> Site N.inv UE Especie Os GL Bp Dp SD DD Bd Dd BT
#> 1 ALP 4918 10364 bota 1 fal 54.0 31.3 30.6 28.1 26.3 27.5 20.0 NA
#> 2 ALP 4919 10364 bota 1 fal 54.5 27.9 31.8 26.0 22.8 25.3 19.5 NA
#> 3 ALP 3453 10410 ovar 1fal ant 27.1 9.9 12.3 17.9 9.0 9.0 NA NA
#> 4 ALP 3455 10410 ovar 1fal ant 27.6 9.6 12.2 7.6 8.9 8.3 NA NA
#> 5 ALP 4245 7036 cahi hum NA 128.3 NA 12.9 NA 27.4 26.6 23.6
#> 6 ALP 4674 10227 cahi hum NA NA NA NA NA 26.0 25.7 22.3
#> GLc BFd Dl
#> 1 NA NA NA
#> 2 NA NA NA
#> 3 NA NA NA
#> 4 NA NA NA
#> 5 NA NA NA
#> 6 NA NA NA
## If we compute first the log-ratios
dataExampleWithLogs <- LogRatios(dataExample)
#> Warning: Reference for Sus scrofa used for cases of Sus domesticus.
#> Reference for Sus scrofa used for cases of Sus.
#> Reference for Oryctolagus cuniculus used for cases of Oryctolagus.
#> Reference for Canis lupus used for cases of Canis.
#> Reference for Ovis aries used for cases of Ovis.
#> Set useGenusIfUnambiguous to FALSE if this behaviour is not desired.
#> Warning: Data includes some cases recorded as
#> * Equus (which is a Genus)
#> for which the reference for Equus asinus or Equus caballus could be used.
#> * Caprini (which is a Tribe)
#> for which the reference for Ovis aries or Capra hircus could be used.
#> Set joinCategories as appropriate if you want to use any of them.
## the cases not including any log-ratio can be removed with the
## default logPrefix
dataExampleWithLogsPruned <- RemoveNACases(dataExampleWithLogs)
head(dataExampleWithLogsPruned)[, -c(6:20,32:64)]
#> Site N.inv UE Especie Os GL Bp Dp SD DD Bd Dd BT
#> 1 ALP 3453 10410 ovar 1fal ant 27.1 9.9 12.3 17.9 9.0 9.0 NA NA
#> 2 ALP 3455 10410 ovar 1fal ant 27.6 9.6 12.2 7.6 8.9 8.3 NA NA
#> 3 ALP 4245 7036 cahi hum NA 128.3 NA 12.9 NA 27.4 26.6 23.6
#> 4 ALP 4674 10227 cahi hum NA NA NA NA NA 26.0 25.7 22.3
#> 5 ALP 4085 10253 cahi hum NA NA NA NA NA 27.9 27.3 23.2
#> 6 TFC 24 407 ceel mc 262.7 41.3 30.8 25.0 21.2 41.1 27.1 NA
#> GLc BFd Dl logGL logBp logDp logSD logBd logDd
#> 1 NA NA NA NA -0.07991177 -0.07265930 0.2629585 -0.08911977 NA
#> 2 NA NA NA NA -0.09327573 -0.07620458 -0.1090810 -0.12428419 NA
#> 3 NA NA NA NA 0.40167955 NA -0.2116296 -0.15130497 -0.06787875
#> 4 NA NA NA NA NA NA NA -0.17408218 -0.08282727
#> 5 NA NA NA NA NA NA NA -0.14345133 -0.05659774
#> 6 NA NA NA NA NA NA NA -0.03354115 NA
#> logBT logGLc logBFd logDl logGB logSLC logGLP logBG logLG logDPA logBPC logLA
#> 1 NA NA NA NA NA NA NA NA NA NA NA NA
#> 2 NA NA NA NA NA NA NA NA NA NA NA NA
#> 3 NA NA NA NA NA NA NA NA NA NA NA NA
#> 4 NA NA NA NA NA NA NA NA NA NA NA NA
#> 5 NA NA NA NA NA NA NA NA NA NA NA NA
#> 6 NA NA NA NA NA NA NA NA NA NA NA NA
#> logLAR logSH logSB logL logH
#> 1 NA NA NA NA NA
#> 2 NA NA NA NA NA
#> 3 NA NA NA NA NA
#> 4 NA NA NA NA NA
#> 5 NA NA NA NA NA
#> 6 NA NA NA NA NA