Ilya 1/31/2019
pkgTest <- function(x)
{
if (x %in% rownames(installed.packages()) == FALSE) {
install.packages(x, dependencies= TRUE,repos = "http://cran.us.r-project.org")
}
library(x, character.only = TRUE)
}
neededPackages <- c("data.table", "glue", "rlang","tibble", "tidyselect", "dplyr", "ggplot2", "tidyr"
)
#"rstan"
for (package in neededPackages){pkgTest(package)}##
## Attaching package: 'rlang'
## The following object is masked from 'package:data.table':
##
## :=
##
## Attaching package: 'dplyr'
## The following object is masked from 'package:glue':
##
## collapse
## The following objects are masked from 'package:data.table':
##
## between, first, last
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
D = readRDS("Data for Bacillus halotolerans.rds")
#find out field names
names(D)## [1] "bacdive_id" "section" "subsection" "field" "value"
#look at unique fields
unique(D$field)## [1] "species_epithet" "subspecies_epithet"
## [3] "is_type_strain" "domain"
## [5] "phylum" "class"
## [7] "ordo" "family"
## [9] "status_fam" "genus"
## [11] "status_gen" "species"
## [13] "status_spec" "full_scientific_name"
## [15] "ID_reference" "designation"
## [17] "pnu_synonym" "medium_name1"
## [19] "medium_name2" "medium_growth1"
## [21] "medium_growth2" "media_link1"
## [23] "media_link2" "medium_composition1"
## [25] "medium_composition2" "ID_reference1"
## [27] "ID_reference2" "ability1"
## [29] "ability2" "test_type1"
## [31] "test_type2" "temp1"
## [33] "temp2" "temperature_range1"
## [35] "temperature_range2" "pathogenicity_human"
## [37] "pathogenicity_animal" "pathogenicity_plant"
## [39] "biosafety_level" "biosafety_level_comment"
## [41] "DB_sequence" "Sequence_accession_title"
## [43] "seq_acc_num" "sequence_length"
## [45] "NCBI_tax_ID" "NCBI_Gi"
## [47] "text_mined" "history"
## [49] "strain_number" "straininfo_strainnumber1"
## [51] "straininfo_strainnumber2" "straininfo_strainnumber3"
## [53] "straininfo_strainnumber4" "URL1"
## [55] "URL2" "URL3"
## [57] "URL4" "ID_reference3"
## [59] "ID_reference4" NA
## [61] "compound_name" "excreted"
## [63] "DB_sequence1" "DB_sequence2"
## [65] "DB_sequence3" "DB_sequence4"
## [67] "DB_sequence5" "DB_sequence6"
## [69] "DB_sequence7" "DB_sequence8"
## [71] "DB_sequence9" "DB_sequence10"
## [73] "DB_sequence11" "DB_sequence12"
## [75] "DB_sequence13" "DB_sequence14"
## [77] "DB_sequence15" "DB_sequence16"
## [79] "DB_sequence17" "DB_sequence18"
## [81] "DB_sequence19" "DB_sequence20"
## [83] "DB_sequence21" "DB_sequence22"
## [85] "DB_sequence23" "DB_sequence24"
## [87] "DB_sequence25" "DB_sequence26"
## [89] "DB_sequence27" "DB_sequence28"
## [91] "DB_sequence29" "DB_sequence30"
## [93] "DB_sequence31" "DB_sequence32"
## [95] "DB_sequence33" "DB_sequence34"
## [97] "DB_sequence35" "DB_sequence36"
## [99] "DB_sequence37" "DB_sequence38"
## [101] "DB_sequence39" "DB_sequence40"
## [103] "DB_sequence41" "DB_sequence42"
## [105] "DB_sequence43" "DB_sequence44"
## [107] "DB_sequence45" "DB_sequence46"
## [109] "DB_sequence47" "DB_sequence48"
## [111] "DB_sequence49" "DB_sequence50"
## [113] "DB_sequence51" "DB_sequence52"
## [115] "DB_sequence53" "DB_sequence54"
## [117] "DB_sequence55" "DB_sequence56"
## [119] "DB_sequence57" "DB_sequence58"
## [121] "DB_sequence59" "DB_sequence60"
## [123] "DB_sequence61" "DB_sequence62"
## [125] "DB_sequence63" "DB_sequence64"
## [127] "DB_sequence65" "DB_sequence66"
## [129] "DB_sequence67" "DB_sequence68"
## [131] "DB_sequence69" "DB_sequence70"
## [133] "DB_sequence71" "DB_sequence72"
## [135] "DB_sequence73" "DB_sequence74"
## [137] "DB_sequence75" "DB_sequence76"
## [139] "DB_sequence77" "DB_sequence78"
## [141] "DB_sequence79" "DB_sequence80"
## [143] "DB_sequence81" "DB_sequence82"
## [145] "DB_sequence83" "DB_sequence84"
## [147] "Sequence_accession_title1" "Sequence_accession_title2"
## [149] "Sequence_accession_title3" "Sequence_accession_title4"
## [151] "Sequence_accession_title5" "Sequence_accession_title6"
## [153] "Sequence_accession_title7" "Sequence_accession_title8"
## [155] "Sequence_accession_title9" "Sequence_accession_title10"
## [157] "Sequence_accession_title11" "Sequence_accession_title12"
## [159] "Sequence_accession_title13" "Sequence_accession_title14"
## [161] "Sequence_accession_title15" "Sequence_accession_title16"
## [163] "Sequence_accession_title17" "Sequence_accession_title18"
## [165] "Sequence_accession_title19" "Sequence_accession_title20"
## [167] "Sequence_accession_title21" "Sequence_accession_title22"
## [169] "Sequence_accession_title23" "Sequence_accession_title24"
## [171] "Sequence_accession_title25" "Sequence_accession_title26"
## [173] "Sequence_accession_title27" "Sequence_accession_title28"
## [175] "Sequence_accession_title29" "Sequence_accession_title30"
## [177] "Sequence_accession_title31" "Sequence_accession_title32"
## [179] "Sequence_accession_title33" "Sequence_accession_title34"
## [181] "Sequence_accession_title35" "Sequence_accession_title36"
## [183] "Sequence_accession_title37" "Sequence_accession_title38"
## [185] "Sequence_accession_title39" "Sequence_accession_title40"
## [187] "Sequence_accession_title41" "Sequence_accession_title42"
## [189] "Sequence_accession_title43" "Sequence_accession_title44"
## [191] "Sequence_accession_title45" "Sequence_accession_title46"
## [193] "Sequence_accession_title47" "Sequence_accession_title48"
## [195] "Sequence_accession_title49" "Sequence_accession_title50"
## [197] "Sequence_accession_title51" "Sequence_accession_title52"
## [199] "Sequence_accession_title53" "Sequence_accession_title54"
## [201] "Sequence_accession_title55" "Sequence_accession_title56"
## [203] "Sequence_accession_title57" "Sequence_accession_title58"
## [205] "Sequence_accession_title59" "Sequence_accession_title60"
## [207] "Sequence_accession_title61" "Sequence_accession_title62"
## [209] "Sequence_accession_title63" "Sequence_accession_title64"
## [211] "Sequence_accession_title65" "Sequence_accession_title66"
## [213] "Sequence_accession_title67" "Sequence_accession_title68"
## [215] "Sequence_accession_title69" "Sequence_accession_title70"
## [217] "Sequence_accession_title71" "Sequence_accession_title72"
## [219] "Sequence_accession_title73" "Sequence_accession_title74"
## [221] "Sequence_accession_title75" "Sequence_accession_title76"
## [223] "Sequence_accession_title77" "Sequence_accession_title78"
## [225] "Sequence_accession_title79" "Sequence_accession_title80"
## [227] "Sequence_accession_title81" "Sequence_accession_title82"
## [229] "Sequence_accession_title83" "Sequence_accession_title84"
## [231] "seq_acc_num1" "seq_acc_num2"
## [233] "seq_acc_num3" "seq_acc_num4"
## [235] "seq_acc_num5" "seq_acc_num6"
## [237] "seq_acc_num7" "seq_acc_num8"
## [239] "seq_acc_num9" "seq_acc_num10"
## [241] "seq_acc_num11" "seq_acc_num12"
## [243] "seq_acc_num13" "seq_acc_num14"
## [245] "seq_acc_num15" "seq_acc_num16"
## [247] "seq_acc_num17" "seq_acc_num18"
## [249] "seq_acc_num19" "seq_acc_num20"
## [251] "seq_acc_num21" "seq_acc_num22"
## [253] "seq_acc_num23" "seq_acc_num24"
## [255] "seq_acc_num25" "seq_acc_num26"
## [257] "seq_acc_num27" "seq_acc_num28"
## [259] "seq_acc_num29" "seq_acc_num30"
## [261] "seq_acc_num31" "seq_acc_num32"
## [263] "seq_acc_num33" "seq_acc_num34"
## [265] "seq_acc_num35" "seq_acc_num36"
## [267] "seq_acc_num37" "seq_acc_num38"
## [269] "seq_acc_num39" "seq_acc_num40"
## [271] "seq_acc_num41" "seq_acc_num42"
## [273] "seq_acc_num43" "seq_acc_num44"
## [275] "seq_acc_num45" "seq_acc_num46"
## [277] "seq_acc_num47" "seq_acc_num48"
## [279] "seq_acc_num49" "seq_acc_num50"
## [281] "seq_acc_num51" "seq_acc_num52"
## [283] "seq_acc_num53" "seq_acc_num54"
## [285] "seq_acc_num55" "seq_acc_num56"
## [287] "seq_acc_num57" "seq_acc_num58"
## [289] "seq_acc_num59" "seq_acc_num60"
## [291] "seq_acc_num61" "seq_acc_num62"
## [293] "seq_acc_num63" "seq_acc_num64"
## [295] "seq_acc_num65" "seq_acc_num66"
## [297] "seq_acc_num67" "seq_acc_num68"
## [299] "seq_acc_num69" "seq_acc_num70"
## [301] "seq_acc_num71" "seq_acc_num72"
## [303] "seq_acc_num73" "seq_acc_num74"
## [305] "seq_acc_num75" "seq_acc_num76"
## [307] "seq_acc_num77" "seq_acc_num78"
## [309] "seq_acc_num79" "seq_acc_num80"
## [311] "seq_acc_num81" "seq_acc_num82"
## [313] "seq_acc_num83" "seq_acc_num84"
## [315] "sequence_length1" "sequence_length2"
## [317] "sequence_length3" "sequence_length4"
## [319] "sequence_length5" "sequence_length6"
## [321] "sequence_length7" "sequence_length8"
## [323] "sequence_length9" "sequence_length10"
## [325] "sequence_length11" "sequence_length12"
## [327] "sequence_length13" "sequence_length14"
## [329] "sequence_length15" "sequence_length16"
## [331] "sequence_length17" "sequence_length18"
## [333] "sequence_length19" "sequence_length20"
## [335] "sequence_length21" "sequence_length22"
## [337] "sequence_length23" "sequence_length24"
## [339] "sequence_length25" "sequence_length26"
## [341] "sequence_length27" "sequence_length28"
## [343] "sequence_length29" "sequence_length30"
## [345] "sequence_length31" "sequence_length32"
## [347] "sequence_length33" "sequence_length34"
## [349] "sequence_length35" "sequence_length36"
## [351] "sequence_length37" "sequence_length38"
## [353] "sequence_length39" "sequence_length40"
## [355] "sequence_length41" "sequence_length42"
## [357] "sequence_length43" "sequence_length44"
## [359] "sequence_length45" "sequence_length46"
## [361] "sequence_length47" "sequence_length48"
## [363] "sequence_length49" "sequence_length50"
## [365] "sequence_length51" "sequence_length52"
## [367] "sequence_length53" "sequence_length54"
## [369] "sequence_length55" "sequence_length56"
## [371] "sequence_length57" "sequence_length58"
## [373] "sequence_length59" "sequence_length60"
## [375] "sequence_length61" "sequence_length62"
## [377] "sequence_length63" "sequence_length64"
## [379] "sequence_length65" "sequence_length66"
## [381] "sequence_length67" "sequence_length68"
## [383] "sequence_length69" "sequence_length70"
## [385] "sequence_length71" "sequence_length72"
## [387] "sequence_length73" "sequence_length74"
## [389] "sequence_length75" "sequence_length76"
## [391] "sequence_length77" "sequence_length78"
## [393] "sequence_length79" "sequence_length80"
## [395] "sequence_length81" "sequence_length82"
## [397] "sequence_length83" "sequence_length84"
## [399] "NCBI_tax_ID1" "NCBI_tax_ID2"
## [401] "NCBI_tax_ID3" "NCBI_tax_ID4"
## [403] "NCBI_tax_ID5" "NCBI_tax_ID6"
## [405] "NCBI_tax_ID7" "NCBI_tax_ID8"
## [407] "NCBI_tax_ID9" "NCBI_tax_ID10"
## [409] "NCBI_tax_ID11" "NCBI_tax_ID12"
## [411] "NCBI_tax_ID13" "NCBI_tax_ID14"
## [413] "NCBI_tax_ID15" "NCBI_tax_ID16"
## [415] "NCBI_tax_ID17" "NCBI_tax_ID18"
## [417] "NCBI_tax_ID19" "NCBI_tax_ID20"
## [419] "NCBI_tax_ID21" "NCBI_tax_ID22"
## [421] "NCBI_tax_ID23" "NCBI_tax_ID24"
## [423] "NCBI_tax_ID25" "NCBI_tax_ID26"
## [425] "NCBI_tax_ID27" "NCBI_tax_ID28"
## [427] "NCBI_tax_ID29" "NCBI_tax_ID30"
## [429] "NCBI_tax_ID31" "NCBI_tax_ID32"
## [431] "NCBI_tax_ID33" "NCBI_tax_ID34"
## [433] "NCBI_tax_ID35" "NCBI_tax_ID36"
## [435] "NCBI_tax_ID37" "NCBI_tax_ID38"
## [437] "NCBI_tax_ID39" "NCBI_tax_ID40"
## [439] "NCBI_tax_ID41" "NCBI_tax_ID42"
## [441] "NCBI_tax_ID43" "NCBI_tax_ID44"
## [443] "NCBI_tax_ID45" "NCBI_tax_ID46"
## [445] "NCBI_tax_ID47" "NCBI_tax_ID48"
## [447] "NCBI_tax_ID49" "NCBI_tax_ID50"
## [449] "NCBI_tax_ID51" "NCBI_tax_ID52"
## [451] "NCBI_tax_ID53" "NCBI_tax_ID54"
## [453] "NCBI_tax_ID55" "NCBI_tax_ID56"
## [455] "NCBI_tax_ID57" "NCBI_tax_ID58"
## [457] "NCBI_tax_ID59" "NCBI_tax_ID60"
## [459] "NCBI_tax_ID61" "NCBI_tax_ID62"
## [461] "NCBI_tax_ID63" "NCBI_tax_ID64"
## [463] "NCBI_tax_ID65" "NCBI_tax_ID66"
## [465] "NCBI_tax_ID67" "NCBI_tax_ID68"
## [467] "NCBI_tax_ID69" "NCBI_tax_ID70"
## [469] "NCBI_tax_ID71" "NCBI_tax_ID72"
## [471] "NCBI_tax_ID73" "NCBI_tax_ID74"
## [473] "NCBI_tax_ID75" "NCBI_tax_ID76"
## [475] "NCBI_tax_ID77" "NCBI_tax_ID78"
## [477] "NCBI_tax_ID79" "NCBI_tax_ID80"
## [479] "NCBI_tax_ID81" "NCBI_tax_ID82"
## [481] "NCBI_tax_ID83" "NCBI_tax_ID84"
## [483] "NCBI_Gi1" "NCBI_Gi2"
## [485] "NCBI_Gi3" "NCBI_Gi4"
## [487] "NCBI_Gi5" "NCBI_Gi6"
## [489] "NCBI_Gi7" "NCBI_Gi8"
## [491] "NCBI_Gi9" "NCBI_Gi10"
## [493] "NCBI_Gi11" "NCBI_Gi12"
## [495] "NCBI_Gi13" "NCBI_Gi14"
## [497] "NCBI_Gi15" "NCBI_Gi16"
## [499] "NCBI_Gi17" "NCBI_Gi18"
## [501] "NCBI_Gi19" "NCBI_Gi20"
## [503] "NCBI_Gi21" "NCBI_Gi22"
## [505] "NCBI_Gi23" "NCBI_Gi24"
## [507] "NCBI_Gi25" "NCBI_Gi26"
## [509] "NCBI_Gi27" "NCBI_Gi28"
## [511] "NCBI_Gi29" "NCBI_Gi30"
## [513] "NCBI_Gi31" "NCBI_Gi32"
## [515] "NCBI_Gi33" "NCBI_Gi34"
## [517] "NCBI_Gi35" "NCBI_Gi36"
## [519] "NCBI_Gi37" "NCBI_Gi38"
## [521] "NCBI_Gi39" "NCBI_Gi40"
## [523] "NCBI_Gi41" "NCBI_Gi42"
## [525] "NCBI_Gi43" "NCBI_Gi44"
## [527] "NCBI_Gi45" "NCBI_Gi46"
## [529] "NCBI_Gi47" "NCBI_Gi48"
## [531] "NCBI_Gi49" "NCBI_Gi50"
## [533] "NCBI_Gi51" "NCBI_Gi52"
## [535] "NCBI_Gi53" "NCBI_Gi54"
## [537] "NCBI_Gi55" "NCBI_Gi56"
## [539] "NCBI_Gi57" "NCBI_Gi58"
## [541] "NCBI_Gi59" "NCBI_Gi60"
## [543] "NCBI_Gi61" "NCBI_Gi62"
## [545] "NCBI_Gi63" "NCBI_Gi64"
## [547] "NCBI_Gi65" "NCBI_Gi66"
## [549] "NCBI_Gi67" "NCBI_Gi68"
## [551] "NCBI_Gi69" "NCBI_Gi70"
## [553] "NCBI_Gi71" "NCBI_Gi72"
## [555] "NCBI_Gi73" "NCBI_Gi74"
## [557] "NCBI_Gi75" "NCBI_Gi76"
## [559] "NCBI_Gi77" "NCBI_Gi78"
## [561] "NCBI_Gi79" "NCBI_Gi80"
## [563] "NCBI_Gi81" "NCBI_Gi82"
## [565] "NCBI_Gi83" "NCBI_Gi84"
## [567] "ID_reference5" "ID_reference6"
## [569] "ID_reference7" "ID_reference8"
## [571] "ID_reference9" "ID_reference10"
## [573] "ID_reference11" "ID_reference12"
## [575] "ID_reference13" "ID_reference14"
## [577] "ID_reference15" "ID_reference16"
## [579] "ID_reference17" "ID_reference18"
## [581] "ID_reference19" "ID_reference20"
## [583] "ID_reference21" "ID_reference22"
## [585] "ID_reference23" "ID_reference24"
## [587] "ID_reference25" "ID_reference26"
## [589] "ID_reference27" "ID_reference28"
## [591] "ID_reference29" "ID_reference30"
## [593] "ID_reference31" "ID_reference32"
## [595] "ID_reference33" "ID_reference34"
## [597] "ID_reference35" "ID_reference36"
## [599] "ID_reference37" "ID_reference38"
## [601] "ID_reference39" "ID_reference40"
## [603] "ID_reference41" "ID_reference42"
## [605] "ID_reference43" "ID_reference44"
## [607] "ID_reference45" "ID_reference46"
## [609] "ID_reference47" "ID_reference48"
## [611] "ID_reference49" "ID_reference50"
## [613] "ID_reference51" "ID_reference52"
## [615] "ID_reference53" "ID_reference54"
## [617] "ID_reference55" "ID_reference56"
## [619] "ID_reference57" "ID_reference58"
## [621] "ID_reference59" "ID_reference60"
## [623] "ID_reference61" "ID_reference62"
## [625] "ID_reference63" "ID_reference64"
## [627] "ID_reference65" "ID_reference66"
## [629] "ID_reference67" "ID_reference68"
## [631] "ID_reference69" "ID_reference70"
## [633] "ID_reference71" "ID_reference72"
## [635] "ID_reference73" "ID_reference74"
## [637] "ID_reference75" "ID_reference76"
## [639] "ID_reference77" "ID_reference78"
## [641] "ID_reference79" "ID_reference80"
## [643] "ID_reference81" "ID_reference82"
## [645] "ID_reference83" "ID_reference84"
## [647] "text_mined1" "text_mined2"
## [649] "text_mined3" "text_mined4"
## [651] "text_mined5" "text_mined6"
## [653] "text_mined7" "text_mined8"
## [655] "text_mined9" "text_mined10"
## [657] "text_mined11" "text_mined12"
## [659] "text_mined13" "text_mined14"
## [661] "text_mined15" "text_mined16"
## [663] "text_mined17" "text_mined18"
## [665] "text_mined19" "text_mined20"
## [667] "text_mined21" "text_mined22"
## [669] "text_mined23" "text_mined24"
## [671] "text_mined25" "text_mined26"
## [673] "text_mined27" "text_mined28"
## [675] "text_mined29" "text_mined30"
## [677] "text_mined31" "text_mined32"
## [679] "text_mined33" "text_mined34"
## [681] "text_mined35" "text_mined36"
## [683] "text_mined37" "text_mined38"
## [685] "text_mined39" "text_mined40"
## [687] "text_mined41" "text_mined42"
## [689] "text_mined43" "text_mined44"
## [691] "text_mined45" "text_mined46"
## [693] "text_mined47" "text_mined48"
## [695] "text_mined49" "text_mined50"
## [697] "text_mined51" "text_mined52"
## [699] "text_mined53" "text_mined54"
## [701] "text_mined55" "text_mined56"
## [703] "text_mined57" "text_mined58"
## [705] "text_mined59" "text_mined60"
## [707] "text_mined61" "text_mined62"
## [709] "text_mined63" "text_mined64"
## [711] "text_mined65" "text_mined66"
## [713] "text_mined67" "text_mined68"
## [715] "text_mined69" "text_mined70"
## [717] "text_mined71" "text_mined72"
## [719] "text_mined73" "text_mined74"
## [721] "text_mined75" "text_mined76"
## [723] "text_mined77" "text_mined78"
## [725] "text_mined79" "text_mined80"
## [727] "text_mined81" "text_mined82"
## [729] "text_mined83" "text_mined84"
## [731] "GC_content1" "GC_content2"
## [733] "GC_method1" "GC_method2"
## [735] "straininfo_strainnumber5" "straininfo_strainnumber6"
## [737] "straininfo_strainnumber7" "URL5"
## [739] "URL6" "URL7"
## [741] "medium_name" "medium_growth"
## [743] "media_link" "medium_composition"
## [745] "ability" "test_type"
## [747] "temp" "temperature_range"
## [749] "sample_type" "sample_date"
## [751] "geo_loc_name" "country"
## [753] "continent" "latitude"
## [755] "longitude" "enrichment_cult_name"
## [757] "enrichment_cult_composition" "enrichment_cult_duration"
## [759] "enrichment_cult_temp" "isolation_date"
## [761] "procedure_origin" "straininfo_strainnumber"
## [763] "URL"
#look at unique sections
unique(D$section)## [1] "taxonomy_name"
## [2] "culture_growth_condition"
## [3] "application_interaction"
## [4] "molecular_biology"
## [5] "strain_availability"
## [6] "references"
## [7] "morphology_physiology"
## [8] "environment_sampling_isolation_source"
#get just taxonomy name
test = subset(D, section == "taxonomy_name")
#look at unique subsections
unique(test$subsection)## [1] "strains_tax_PNU" "strains" "strains_synonyms_PNU"
#get just strains
test_strains = subset(test, subsection == "strains")
#see what fields are for strain
unique(test_strains$field)## [1] "domain" "phylum" "class"
## [4] "ordo" "family" "genus"
## [7] "species" "species_epithet" "subspecies_epithet"
## [10] "full_scientific_name" "designation" "is_type_strain"
## [13] "ID_reference"
#check is_type_strain
test_strain_type = subset(test_strains, field == "is_type_strain")
table(test_strain_type$bacdive_id,test_strain_type$value)##
## FALSE TRUE
## 100619 0 0
## 100620 0 0
## 100621 0 0
## 11406 1 0
## 11407 0 1
## 11408 1 0
## 135999 1 0
## 138625 1 0
## 139422 1 0
id_1 = subset(D, bacdive_id == "100619")
unique(id_1$value)## [1] "laterosporus"
## [2] NA
## [3] "Bacteria"
## [4] "Firmicutes"
## [5] "Bacilli"
## [6] "Paenibacillaceae"
## [7] "Brevibacillus"
## [8] "gen. nov. (VP) "
## [9] "Brevibacillus laterosporus"
## [10] "comb. nov. (VP)"
## [11] "Brevibacillus laterosporus (Laubach 1916) Shida et al. 1996"
## [12] "20215"
## [13] "STI09656(IMET); 31/73"
## [14] "20216"
## [15] "Bacillus laterosporus"
## [16] "D.Gleim, M.Kracht, N.Weiss et. al.: Prokaryotic Nomenclature Up-to-date - compilation of all names of Bacteria and Archaea, validly published according to the Bacteriological Code since 1. Jan. 1980, and validly published nomenclatural changes since. "
## [17] "Curators of the HKI: Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI). "
#spread
D <- D[,c("bacdive_id",
"field",
"value")]
# D$value[is.na(D$value)] <- -9999#this gets duplicate error, as does replacing with blank
D_uni=distinct(D)#make sure rows are unique
dim(D_uni)## [1] 1120 3
#remove NA values
D_uni = D_uni[!is.na(D_uni$value),]
dim(D_uni)## [1] 1009 3
D_uni = subset(D_uni, field != "ID_reference")
D_uni = subset(D_uni, field != "ID_reference1")
D_uni = subset(D_uni, field != "ID_reference2")
# Spread_1 = spread(D_uni, key = c(bacdive_id, field), value= value)
#this makes columns equal to ID and row equal to field name
# Spread_1 = spread(D_uni, key = bacdive_id, value = value)
Spread_2 = spread(D_uni, key = field, value = value)
write.csv(Spread_2,file = "bacdive_1_species_wide.csv")
#this also works
library(data.table)
# D_cast = dcast(setDT(D), bacdive_id ~ field, value.var = "value")
D_cast = dcast(setDT(D_uni), bacdive_id ~ field, value.var = "value")