README.md

BDTREScheck

A package for doing checks on the Tree Swallow databases. Will print a list with the results (problematic lines) of the different checks executed.

Installation

To install, do:


# install and load devtools to be able to install packages from GitHub with install_github
install.packages("devtools")
library(devtools)

# install package
install_github("frousseu/BDTREScheck")
library(BDTREScheck)
?checkBD

Column Names Required

adults: ferme, nichoir, id, annee, nnich, idcouvee, heure, jjulien, prefixe, suffixe, idadult, condition, sexe_morpho, age_morpho, sexe_gen, locus_sexe_gen, couleur, age_exact, laile1, laile2, masse, tarse1, tarse2, trougauche, troudroite, pararectrice, plaqueincu, Cause_recapt, commentaire, observateur

chicks: ferme, nichoir, id, annee, nnich, idcouvee, heure, jjulien, prefixe, suffixe, idois, sexe_gen, locus_sexe_gen, condition, numero_oisillon, jour_suivi, envol, masse, 9primaires1, 9primaires2, tarse1, tarse2, commentaires, manipulateur

broods: idcouvee, id, ferme, nichoir, annee, codesp, nnich, noeufs, noisnes, noisenvol, noismort, dispa_ois, dispa_oeufs, abandon, pred_pot, dponte, dincub, declomin, declomax, denvomin, denvomax, dabanmin, dabanmax, idF1, idM1, idF2, idF3, idM2, idM3, Commentaires

How To Use

Run checks:


library(BDTREScheck)

x<-checkBD(
  dsn="//argus.dinf.fsci.usherbrooke.ca/DBio_Rech_Data/Projet_Hirondelle/1_Donnees/11_Principales",
  year=2015,
  adultsNew=NULL,
  broodsNew=NULL,
  chicksNew=NULL,
  adultsOld="Adultes_2004-2015.xlsx",
  broodsOld="Couvee_2004-2015.xlsx",
  chicksOld="Oisillons_2004-2015.xlsx",
  sheet=1
)

Display results:


x
x[4]

Show the list of checks:


checkShow(html=FALSE)

TODO

Current List Of Checks (updated 2018-02-05)

ID Checks 1 "GENERAL: Remove rows with NA id's in broodsNew" 2 "GENERAL: Remove rows with NA id's in adultsNew" 3 "GENERAL: Remove rows with NA id's in chicksNew" 4 "GENERAL: Are column names in adult consistent?" 5 "GENERAL: Are column names in chicksNew consistent?" 6 "GENERAL: Are column names in broodsNew consistent?" 7 "GENERAL: Are column names consistant across old and new databases" 8 "ADULTS: Wrong ferme id observed" 9 "NESTLINGS: Wrong ferme id observed" 10 "BROODS: Wrong ferme id observed" 11 "ADULTS: Wrong nichoir id observed" 12 "NESTLINGS: Wrong nichoir id observed" 13 "BROODS: Wrong nichoir id observed" 14 "ADULTS: id column doesn't correspond to ferme + nichoir id" 15 "NESTLINGS: id column doesn't correspond to ferme + nichoir id" 16 "BROODS: id column doesn't correspond to ferme + nichoir id" 17 "ADULTS: idcouv doesn't correspond to ferme + nichoir + annee + nnich column" 18 "NESTLINGS: idcouv doesn't correspond to ferme + nichoir + annee + nnich column" 19 "BROODS: idcouv doesn't correspond to ferme + nichoir + annee + nnich column" 20 "ADULTS: Wrong prefixe name observed (is it a new prefixe?)" 21 "ADULTS: Wrong suffixe name observed (too short/long)" 22 "ADULTS: idadult doesn't correspond to prefixe + suffixe" 23 "ADULTS: idadult doesn't correspond to id + year + LETTER" 24 "NESTLINGS: Wrong prefixe name observed (is it a new prefixe?)" 25 "NESTLINGS: Wrong suffixe name observed (too short/long)" 26 "NESTLINGS: idois doesn't correspond to prefixe + suffixe" 27 "NESTLINGS: idois doesn't correspond to idcouvee + numero_oisillon" 28 "ADULTS: Show all unique values in columns for which the number of possible values is restricted" 29 "BROODS: Show all unique values in columns for which the number of possible values is restricted" 30 "NESTLINGS: Show all unique values in columns for which the number of possible values is restricted" 31 "ADULTS/BROODS: Females assigned to an idcouv in adults db but no female is assigned to this idcouv in broods db (check capture dates)" 32 "ADULTS/BROODS: Females assigned to an idcouv in adults db but not referenced in broods db (idF2 or idF3)" 33 "ADULTS/BROODS: Females captured at a nestbox but not assigned to an idcouv in adults db (check nnich)" 34 "ADULTS/BROODS: Females captured at a nestbox but assigned to a wrong idcouv in adults db (check nnich)" 35 "ADULTS/BROODS: Males assigned to an idcouv in adults db but no male is assigned to this idcouv in broods db (check capture dates or morpho/gen sex identity)" 36 "ADULTS/BROODS: Males assigned to an idcouv in adults db but not referenced in broods db (idM2 or idM3)" 37 "ADULTS/BROODS: Males captured at a nestbox but not assigned to an idcouv in adults db (check nnich)" 38 "ADULTS/BROODS: Males captured at a nestbox but assigned to a wrong idcouv in adults db (check nnich)" 39 "BROODS: Female referenced as second female when only one female captured (change to idF1 - some exceptions possible)" 40 "BROODS: Male referenced as second males when only one male captured (change to idM1)" 41 "BROODS: Two males captured in the same nestbox but not properly reported (idM2 and idM3, not idM1)" 42 "BROODS: Males (idM1) assigned to brood with no nestlings (not coherent)" 43 "ADULTS: Sex/age incoherencies (few exceptions when condition !=0)" 44 "ADULTS: Some colors not in the list of possible values?" 45 "ADULTS: Brown females (>50%) not assigned to SY?" 46 "ADULTS: Individual with a couleur assigned, but without morpho_age (no check for condition != 0)" 47 "ADULTS: Dead individual with a couleur assigned, but without morpho_age (probably nothing to do)" 48 "ADULTS: Capture time outside 06:00 and 20:40 (max)" 49 "NESTLINGS: Capture time outside 06:00 and 20:40 (max)" 50 "ADULTS: Wrong sexe_gen/locus_sexe_gen association (both NA or with values)" 51 "ADULTS: Check for adults with changing sexe_morph (within the current breeding season ONLY)" 52 "ADULTS: Check for adults with changing sexe_morph (across seasons - MUST be concordant (see Donnees_Codes.docx))" 53 "ADULTS: Check for adults with changing sexe_gen (within the current breeding season ONLY)" 54 "ADULTS: Check for adults with changing sexe_gen (across seasons)" 55 "ADULTS: Check for adults with changing locus_sexe_gen (within the current breeding season ONLY)" 56 "ADULTS: Check for adults with changing locus_sexe_gen (across seasons)" 57 "ADULTS: Missing one wing measurement" 58 "ADULTS: Missing one tarsus measurement" 59 "ADULTS: Wing measurement outside the range of likely values (105-128 mm)" 60 "ADULTS: Wing measurement 1 and 2 too far apart (>1 mm)" 61 "ADULTS: Weight measurements outside the range of likely values (15-30g)" 62 "ADULTS: Tarsus measurements outside the range of likely values (10-14 mm)" 63 "ADULTS: tarsus measurement 1 and 2 too far apart (>0.1 mm)" 64 "ADULTS: Wrong condition status" 65 "ADULTS: Wrong plaqueincu status" 66 "ADULTS: Male with brood patch (plaqueincu)" 67 "ADULTS: Wrong Cause_capture status" 68 "ADULTS: Visits are not all 2 days apart for the following farms (maybe caused by presence of NAs)" 69 "NESTLINGS: Visits are not all 2 days apart for the following farms (maybe caused by presence of NAs)" 70 "ADULTS: Check for duplicates using all columns" 71 "BROODS: Check for duplicates using all columns" 72 "CHICKS: Check for duplicates using all columns" 73 "ADULTS: Check for adults with more than one entry for a single date (probably duplicated lines - remove one)" 74 "NESTLINGS: Check for chicks with more than one entry for a single date (probably duplicated lines - remove one)" 75 "NESTLINGS: Check for chicks with more than one entry for a single age" 76 "ADULTS: Check for adults found at more than one farm (maybe not an error)" 77 "NESTLINGS: Check for nestlings found at more than one nestbox" 78 "NESTLINGS/BROODS: Capture date of young is later than the minimal abandonment date if nest was abandoned" 79 "NESTLINGS/BROODS: Capture date of young is before the laying date" 80 "NESTLINGS/BROODS: jjulien of young that doesn't correspond to declomax + jour_suivi" 81 "NESTLINGS: Wrong sexe_gen/locus_sexe_gen association (both NA or with values)" 82 "NESTLINGS: Check for individuals with changing sexe_gen" 83 "NESTLINGS: Check for individuals with changing locus_sexe_gen" 84 "NESTLINGS: Wrong chick conditions (4 possible values; vivant, disparu, mort or disparuj16)" 85 "NESTLINGS: Dead or disappeared nestlings without a 0 for flight code (few exceptions possibles, see comments)" 86 "NESTLINGS: Nestling with disparuj16 condition but without a 1 for flight code" 87 "NESTLINGS: Make sure that living nestlings with a 0 flight code are eventually dead or disappeared" 88 "NESTLINGS: Make sure that no nestling comes back to life" 89 "NESTLINGS: Check that numero_oisillon are from 1 to nb of nestlings" 90 "NESTLINGS: Nestlings which were followed for 12 days or more should have a band number as id and otherwise they should have a farm/brood id (maybe an exception, comments [Oisillon non bagué car trop petit à J12])" 91 "NESTLINGS: Chicks for which there is a band number but it does not correspond to the id of the chick" 92 "NESTLINGS: Missing one wing measurement" 93 "NESTLINGS: Missing one tarsus measurement" 94 "NESTLINGS: 9primaires larger than expected (65 mm, no age consideration)" 95 "NESTLINGS: 9primaires outside the range of likely values at 6-day-old (0 - 10 mm)" 96 "NESTLINGS: 9primaires outside the range of likely values at 12-day-old (5 - 45 mm)" 97 "NESTLINGS: 9primaires outside the range of likely values at 16-day-old (15 - 65 mm)" 98 "NESTLINGS: 9primaires 1 and 2 too far apart (>0.1 mm)" 99 "NESTLINGS: Weight measurements larger than expected (27 g, no age consideration)" 100 "NESTLINGS: Weight measurements outside the range of likely value at 2-days-old (1-8 g)" 101 "NESTLINGS: Weight measurements outside the range of likely value at 6-days-old (2-20 g)" 102 "NESTLINGS: Weight measurements outside the range of likely value at 12-days-old (10-27 g)" 103 "NESTLINGS: Weight measurements outside the range of likely value at 16-days-old (12-27 g)" 104 "NESTLINGS: Tarsus measurements outside the range of likely values (10-14 mm)" 105 "NESTLINGS: Tarsus measurement 1 and 2 too far apart (>0.1 mm)" 106 "NESTLINGS/BROODS: Broods that are in chicks db but not in broods db" 107 "NESTLINGS/BROODS: TRES broods with at least one nestling that are in broods db but not in chicks db" 108 "ADULTS/NESTLINGS: Check for individuals with changing sexe_gen across db" 109 "ADULTS: Check for either missing or wrong age_exact column for individuals hatched in our study system" 110 "BROODS: Check for duplicates in idcouvee" 111 "BROODS: Check for duplicates in id/nnich (change nnich)" 112 "BROODS: Check for missing id (add lines for them)" 113 "BROODS: Wrong codesp (some other species were exceptionnally ringed)" 114 "BROODS: checks if the nnich number is good assuming only one line per brood" 115 "BROODS: Wrong abandon / pred_pot" 116 "BROODS: Wrong chronology in events within a brood" 117 "BROODS: Broods with more nestlings than eggs" 118 "BROODS: More/less nestlings than nestling status (noines != noisenvol + noismort + dispa_ois)" 119 "BROODS: Too much eggs/nestlings within the same brood (8 and more; few exception possible, see comments)" 120 "BROODS: Event dates outside the range of possible values (JJ 95-220)" 121 "BROODS: No fledging or abandon date for TRES broods (exception possibles, see comments" 122 "BROODS: Missing 1 value in declo (min or max)" 123 "BROODS: Missing 1 value in denvo for TRES (min or max)" 124 "BROODS: Wrong denvomin for other species (should be NA)" 125 "BROODS: Missing 1 value in daban (min or max)" 126 "BROODS: Very long time elapse between laying date and incubation initiation (> 2 weeks; 2 different broods?)" 127 "BROODS: Very short time elapse between laying date and incubation initiation (< 5 days)" 128 "BROODS: Very long time elapse between laying date and hatching date (> 4 weeks; 2 different broods?)" 129 "BROODS: Very short time elapse between laying date and hatching date (< 10 days)" 130 "BROODS: Very long time elapse between incubation initiation and hatching date (> 2 weeks; 2 different broods?)" 131 "BROODS: Very short time elapse between incubation initiation and hatching date (< 1 week)" 132 "BROODS: Too long time elapse between minimum and maximum hatching date (> 1 day)" 133 "BROODS: Too long time elapse between minimum and maximum abandon date (> 1 day) when nestlings >=1" 134 "BROODS: Too long time elapse between minimum and maximum fledging date (> 1 week)" 135 "BROODS: Too short time elapse between minimum and maximum fledging date (< 1 day; exception possible, see comments)" 136 "NESTLINGS/BROODS: Inconsistency in the number of nestlings between databases (NESTLINGS: Nois, Nenvol, Ndead, Ndispa - MAYBE some nestlings with num_ois = NA)"

frousseu/BDTREScheck documentation built on May 7, 2018, 10:51 p.m.