Error in lm.fit (x, y, offset = offset, singular.ok = singular.ok, ...) 0 non-na cases

I've already checked other questions about this issue, but since the problem seems very specific, they weren't helpful.

I have a dataframe like this (this is just a quick example, a sample data from dput () is given below):

year species abundance site county
2005 A       2         SH1  Göttingen
2006 A       0         SH1  Göttingen
2007 A       NA        SH1  Göttingen
2008 A       2         SH1  Göttingen
2009 A       NA        SH1  Göttingen
2010 A       2         SH1  Göttingen
2011 A       NA        SH1  Göttingen
2005 B       2         SH1  Göttingen
2006 B       0         SH1  Göttingen
2007 B       NA        SH1  Göttingen
2008 B       2         SH1  Göttingen
2009 B       NA        SH1  Göttingen
2010 B       2         SH1  Göttingen
2011 B       NA        SH1  Göttingen
2005 A       2         SH1  Göttingen
2006 A       0         SH1  Göttingen
2007 A       NA        SH1  Göttingen
2008 A       2         SH1  Göttingen
2009 A       NA        SH1  Göttingen
2010 A       2         SH1  Göttingen
2011 A       NA        SH1  Göttingen
2005 A       2         SH2  Göttingen
2006 A       0         SH2  Göttingen
2007 A       NA        SH2  Göttingen
2008 A       2         SH2  Göttingen
2009 A       NA        SH2  Göttingen
2010 A       2         SH2  Göttingen
2011 A       NA        SH2  Göttingen

      

It contains an abundance of 11 species at several different sites per county (over 1500 locations in counties over $ 400) for each year 2005-2011. for each site in each county each year, all types are counted, so there is either a NA or a number in abundance for each year. The number of sites depends on each county.

I would like to run the following loop to add abundance to multiple columns: it should create a linear model to calculate demographic trends over the years and put the output in an extra row. At the end of the day, I would like to trend for every view on every site over the years:

alldata_lm$slope_abundance_plot <- NA
alldata_lm$p_slope_abundance_plot <- NA

species <- unique(alldata_lm$species)
sites <- unique(alldata_lm$site)

for (i in (1:length(species))) {
  for (k in(1:length(sites))) {        
    print(c(i,k))
    lm1 <-  lm(abundance ~ year, data = alldata_lm[alldata_lm$species == species[i] & alldata_lm$site == sites[k],], na.action=na.omit)
    alldata_lm$slope_abundance_plot[alldata_lm$species == species[i] & alldata_lm$site == sites[k]] <- coefficients(lm1)[2]
    if (nrow(coef(summary(lm1)))>1){ alldata_lm$p_slope_abundance_plot[alldata_lm$species == species[i] & alldata_lm$site == sites[k]] <- coef(summary(lm1))[2,4]}
  }  
}

      

However, when I do this, it returns the following error:

Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 
  alle Fälle NA

      

The same loop works great with a very similar dataframe, the only difference is that the current framework contains a lot more NA.

Removing NA before starting the cycle does not help. I am getting the error whether there is any NA in the abundance column or not. I think the error might happen somewhere else. The year column never contains missing values.

Any help would be appreciated! Thanks to

EXAMPLE DATA

 structure(list(site = structure(c(700L, 700L, 700L, 700L, 700L, 
700L, 700L), .Label = c("bb1", "bb100", "bb101", "bb104", "bb107", 
"bb108", "bb109", "bb11", "bb111", "bb113", "bb115", "bb116", 
"bb117", "bb118", "bb119", "bb120", "bb121", "bb122", "bb123", 
"bb124", "bb125", "bb126", "bb127", "bb129", "bb130", "bb131", 
"bb132", "bb134", "bb135", "bb138", "bb139", "bb14", "bb140", 
"bb143", "bb147", "bb15", "bb150", "bb152", "bb154", "bb155", 
"bb156", "bb157", "bb158", "bb159", "bb163", "bb164", "bb166", 
"bb167", "bb169", "bb170", "bb171", "bb172", "bb173", "bb174", 
"bb175", "bb176", "bb177", "bb178", "bb179", "bb180", "bb181", 
"bb183", "bb186", "bb187", "bb188", "bb19", "bb191", "bb192", 
"bb193", "bb194", "bb197", "bb198", "bb199", "bb20", "bb200", 
"bb201", "bb202", "bb203", "bb204", "bb205", "bb207", "bb208", 
"bb209", "bb21", "bb210", "bb211", "bb212", "bb213", "bb215", 
"bb216", "bb217", "bb218", "bb219", "bb220", "bb221", "bb224", 
"bb225", "bb228", "bb23", "bb230", "bb232", "bb234", "bb237", 
"bb239", "bb242", "bb27", "bb32", "bb35", "bb37", "bb38", "bb39", 
"bb4", "bb40", "bb41", "bb47", "bb49", "bb53", "bb55", "bb58", 
"bb59", "bb6", "bb60", "bb63", "bb65", "bb66", "bb7", "bb70", 
"bb72", "bb73", "bb76", "bb77", "bb79", "bb8", "bb80", "bb81", 
"bb82", "bb84", "bb85", "bb87", "bb89", "bb9", "bb90", "bb91", 
"bb92", "bb93", "bb94", "bb96", "bb97", "bb98", "be14", "be15", 
"be17", "be30", "bw10", "bw100", "bw104", "bw108", "bw111", "bw112", 
"bw12", "bw120", "bw124", "bw126", "bw13", "bw144", "bw146", 
"bw175", "bw183", "bw192", "bw193", "bw198", "bw199", "bw200", 
"bw202", "bw208", "bw210", "bw211", "bw213", "bw215", "bw219", 
"bw225", "bw226", "bw229", "bw236", "bw243", "bw257", "bw262", 
"bw266", "bw268", "bw283", "bw294", "bw3", "bw30", "bw307", "bw326", 
"bw327", "bw338", "bw339", "bw341", "bw35", "bw36", "bw360", 
"bw368", "bw380", "bw381", "bw397", "bw405", "bw42", "bw53", 
"bw58", "bw6", "bw7", "bw84", "bw89", "bw91", "bw92", "bw96", 
"bw97", "by10", "by103", "by109", "by11", "by110", "by111", "by112", 
"by113", "by114", "by115", "by116", "by117", "by118", "by120", 
"by122", "by125", "by126", "by127", "by128", "by129", "by130", 
"by134", "by137", "by14", "by142", "by144", "by146", "by147", 
"by150", "by151", "by152", "by153", "by154", "by155", "by156", 
"by157", "by158", "by159", "by163", "by164", "by166", "by167", 
"by169", "by170", "by171", "by173", "by175", "by176", "by177", 
"by178", "by18", "by180", "by182", "by186", "by187", "by188", 
"by19", "by192", "by193", "by194", "by197", "by200", "by203", 
"by205", "by210", "by212", "by215", "by22", "by222", "by223", 
"by225", "by226", "by229", "by230", "by231", "by233", "by234", 
"by236", "by238", "by239", "by24", "by240", "by241", "by242", 
"by243", "by247", "by248", "by25", "by250", "by251", "by255", 
"by257", "by267", "by268", "by271", "by272", "by274", "by275", 
"by278", "by279", "by28", "by280", "by283", "by284", "by285", 
"by286", "by287", "by289", "by29", "by290", "by291", "by292", 
"by293", "by294", "by295", "by298", "by30", "by303", "by305", 
"by307", "by308", "by310", "by32", "by321", "by322", "by323", 
"by324", "by326", "by331", "by333", "by334", "by337", "by34", 
"by341", "by346", "by347", "by350", "by352", "by356", "by357", 
"by36", "by368", "by37", "by370", "by376", "by378", "by39", "by4", 
"by40", "by41", "by43", "by451", "by452", "by47", "by5", "by52", 
"by53", "by56", "by63", "by64", "by65", "by66", "by67", "by68", 
"by69", "by7", "by72", "by74", "by76", "by79", "by8", "by80", 
"by87", "by88", "by89", "by90", "by91", "by92", "by96", "by97", 
"by98", "hb16", "hb17", "hb18", "hb21", "hb30", "hb5", "hb6", 
"hb7", "hb9", "he100", "he103", "he106", "he107", "he108", "he109", 
"he110", "he111", "he113", "he114", "he115", "he116", "he119", 
"he120", "he122", "he124", "he13", "he130", "he137", "he14", 
"he144", "he145", "he150", "he154", "he18", "he37", "he42", "he46", 
"he47", "he51", "he52", "he66", "he68", "he7", "he70", "he72", 
"he73", "he75", "he82", "he83", "he84", "he85", "he89", "he9", 
"he91", "he93", "he94", "he96", "he97", "hh10", "hh28", "hh29", 
"hh30", "hh41", "hh44", "mv108", "mv109", "mv110", "mv122", "mv124", 
"mv125", "mv126", "mv141", "mv143", "mv15", "mv153", "mv156", 
"mv160", "mv17", "mv24", "mv29", "mv40", "mv41", "mv50", "mv55", 
"mv61", "mv63", "mv76", "mv82", "ni10", "ni100", "ni101", "ni102", 
"ni11", "ni110", "ni111", "ni119", "ni122", "ni125", "ni126", 
"ni13", "ni131", "ni134", "ni135", "ni136", "ni138", "ni14", 
"ni142", "ni146", "ni147", "ni149", "ni15", "ni150", "ni152", 
"ni162", "ni163", "ni166", "ni167", "ni168", "ni169", "ni170", 
"ni171", "ni172", "ni175", "ni182", "ni187", "ni188", "ni189", 
"ni191", "ni192", "ni193", "ni198", "ni2", "ni20", "ni206", "ni215", 
"ni218", "ni225", "ni226", "ni227", "ni231", "ni236", "ni239", 
"ni240", "ni241", "ni242", "ni243", "ni244", "ni246", "ni252", 
"ni257", "ni26", "ni260", "ni263", "ni272", "ni274", "ni282", 
"ni286", "ni290", "ni291", "ni297", "ni298", "ni299", "ni3", 
"ni303", "ni32", "ni34", "ni37", "ni38", "ni39", "ni4", "ni40", 
"ni41", "ni43", "ni45", "ni453", "ni455", "ni46", "ni47", "ni49", 
"ni50", "ni52", "ni55", "ni6", "ni61", "ni63", "ni66", "ni68", 
"ni71", "ni72", "ni73", "ni76", "ni77", "ni85", "ni87", "ni88", 
"ni89", "ni90", "ni91", "ni92", "ni93", "ni95", "ni97", "nw10", 
"nw108", "nw110", "nw112", "nw126", "nw13", "nw130", "nw140", 
"nw142", "nw143", "nw149", "nw154", "nw156", "nw173", "nw182", 
"nw20", "nw25", "nw38", "nw41", "nw5", "nw50", "nw52", "nw53", 
"nw54", "nw55", "nw6", "nw60", "nw63", "nw7", "nw72", "nw73", 
"nw74", "nw84", "nw86", "nw92", "rp101", "rp102", "rp103", "rp106", 
"rp108", "rp109", "rp116", "rp117", "rp120", "rp130", "rp131", 
"rp139", "rp140", "rp143", "rp144", "rp146", "rp21", "rp22", 
"rp23", "rp24", "rp36", "rp4", "rp84", "rp94", "rp99", "sh100", 
"sh101", "sh102", "sh103", "sh106", "sh109", "sh11", "sh111", 
"sh112", "sh117", "sh12", "sh121", "sh123", "sh125", "sh128", 
"sh130", "sh132", "sh14", "sh140", "sh17", "sh18", "sh19", "sh20", 
"sh25", "sh26", "sh27", "sh30", "sh33", "sh34", "sh35", "sh36", 
"sh37", "sh39", "sh42", "sh43", "sh44", "sh45", "sh46", "sh47", 
"sh51", "sh52", "sh54", "sh55", "sh58", "sh59", "sh60", "sh61", 
"sh62", "sh63", "sh65", "sh66", "sh67", "sh69", "sh70", "sh71", 
"sh72", "sh73", "sh74", "sh75", "sh76", "sh78", "sh79", "sh8", 
"sh84", "sh86", "sh88", "sh89", "sh91", "sh93", "sh95", "sh96", 
"sh98", "sh99", "sn104", "sn112", "sn117", "sn120", "sn123", 
"sn131", "sn141", "sn144", "sn145", "sn15", "sn151", "sn158", 
"sn159", "sn16", "sn162", "sn164", "sn165", "sn167", "sn18", 
"sn25", "sn27", "sn28", "sn30", "sn35", "sn40", "sn44", "sn45", 
"sn5", "sn56", "sn69", "sn7", "sn72", "sn74", "sn79", "sn83", 
"sn87", "sn89", "sn9", "sn91", "sn92", "sn93", "sn99", "st1", 
"st100", "st101", "st103", "st105", "st107", "st108", "st109", 
"st11", "st110", "st111", "st112", "st113", "st114", "st115", 
"st116", "st118", "st119", "st120", "st121", "st125", "st126", 
"st127", "st13", "st130", "st134", "st135", "st137", "st139", 
"st140", "st141", "st143", "st144", "st145", "st146", "st147", 
"st148", "st150", "st151", "st153", "st158", "st159", "st160", 
"st162", "st166", "st21", "st24", "st25", "st26", "st27", "st28", 
"st30", "st33", "st34", "st4", "st43", "st47", "st49", "st50", 
"st55", "st56", "st57", "st59", "st60", "st61", "st64", "st69", 
"st70", "st72", "st75", "st77", "st79", "st84", "st87", "st88", 
"st91", "st92", "st97", "st98", "st99", "th100", "th103", "th104", 
"th105", "th112", "th118", "th121", "th123", "th15", "th16", 
"th18", "th19", "th20", "th22", "th26", "th27", "th31", "th32", 
"th36", "th39", "th4", "th40", "th44", "th45", "th49", "th50", 
"th51", "th52", "th55", "th56", "th58", "th59", "th60", "th61", 
"th63", "th64", "th73", "th76", "th8", "th81", "th83", "th85", 
"th91", "th94", "th95", "th96", "th98", "th99"), class = "factor"), 
    year = 2005:2011, species = structure(c(8L, 8L, 8L, 8L, 8L, 
    8L, 8L), .Label = c("common linnet", "common whitethroat", 
    "corn bunting", "eurasian skylark", "northern lapwing", "red-backed shrike", 
    "tree sparrow", "western yellow wagtail", "whinchat", "woodlark", 
    "yellowhammer"), class = "factor"), abundance = c(NA_integer_, 
    NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_, 
    NA_integer_), county = structure(c(48L, 48L, 48L, 48L, 48L, 
    48L, 48L), .Label = c("Aichach-Friedberg, Landkreis", "Alb-Donau-Kreis", 
    "Altmarkkreis Salzwedel", "Alzey-Worms, Landkreis", "Amberg-Sulzbach, Landkreis", 
    "Ammerland, Landkreis", "Anhalt-Bitterfeld, Landkreis", "Ansbach, Landkreis", 
    "Aschaffenburg, Landkreis", "Augsburg, Landkreis", "Aurich, Landkreis", 
    "Böblingen, Landkreis", "Börde, Landkreis", "Bad Dürkheim, Landkreis", 
    "Bad Kissingen, Landkreis", "Bad Kreuznach, Landkreis", "Bad Tölz-Wolfratshausen, Landkreis", 
    "Barnim, Landkreis", "Bautzen, Landkreis", "Bayreuth", "Bayreuth, Landkreis", 
    "Bergstraße, Landkreis", "Berlin", "Biberach, Landkreis", 
    "Bodenseekreis", "Borken, Kreis", "Brandenburg an der Havel, Kreisfreie Stadt", 
    "Breisgau-Hochschwarzwald, Landkreis", "Bremen, Kreisfreie Stadt", 
    "Bremerhaven, Kreisfreie Stadt", "Burgenlandkreis", "Calw, Landkreis", 
    "Celle, Landkreis", "Cham, Landkreis", "Chemnitz, Stadt", 
    "Cloppenburg, Landkreis", "Coburg, Landkreis", "Cottbus, Kreisfreie Stadt", 
    "Cuxhaven, Landkreis", "Dachau, Landkreis", "Dahme-Spreewald, Landkreis", 
    "Darmstadt-Dieburg, Landkreis", "Deggendorf, Landkreis", 
    "Dessau-Roßlau, Kreisfreie Stadt", "Diepholz, Landkreis", 
    "Dillingen a.d.Donau, Landkreis", "Dingolfing-Landau, Landkreis", 
    "Dithmarschen, Landkreis", "Donau-Ries, Landkreis", "Donnersbergkreis", 
    "Dresden, Stadt", "Ebersberg, Landkreis", "Eichsfeld, Kreis", 
    "Eichstätt, Landkreis", "Eisenach, krsfr. Stadt", "Elbe-Elster, Landkreis", 
    "Emmendingen, Landkreis", "Emsland, Landkreis", "Ennepe-Ruhr-Kreis", 
    "Enzkreis", "Erding, Landkreis", "Erfurt, krsfr. Stadt", 
    "Erlangen-Höchstadt, Landkreis", "Erzgebirgskreis", "Esslingen, Landkreis", 
    "Fürstenfeldbruck, Landkreis", "Fürth, Landkreis", "Forchheim, Landkreis", 
    "Frankfurt (Oder), Kreisfreie Stadt", "Frankfurt am Main, Kreisfreie Stadt", 
    "Freising, Landkreis", "Freudenstadt, Landkreis", "Freyung-Grafenau, Landkreis", 
    "Friesland, Landkreis", "Fulda, Landkreis", "Göppingen, Landkreis", 
    "Görlitz, Landkreis", "Göttingen, Landkreis", "Garmisch-Partenkirchen, Landkreis", 
    "Gießen, Landkreis", "Gifhorn, Landkreis", "Goslar, Landkreis", 
    "Gotha, Kreis", "Grafschaft Bentheim, Landkreis", "Greiz, Kreis", 
    "Höxter, Kreis", "Haßberge, Landkreis", "Halle (Saale), Kreisfreie Stadt", 
    "Hamburg", "Hameln-Pyrmont, Landkreis", "Hamm, Kreisfreie Stadt", 
    "Harburg, Landkreis", "Harz, Landkreis", "Havelland, Landkreis", 
    "Heidekreis, Landkreis", "Heidelberg, Kreisfreie Stadt", 
    "Heidenheim, Landkreis", "Heilbronn, Landkreis", "Heinsberg, Kreis", 
    "Hersfeld-Rotenburg, Landkreis", "Herzogtum Lauenburg, Landkreis", 
    "Hildburghausen, Kreis", "Hildesheim, Landkreis", "Hochsauerlandkreis", 
    "Hochtaunuskreis", "Hof, Landkreis", "Holzminden, Landkreis", 
    "Ilm-Kreis", "Ingolstadt", "Jerichower Land, Landkreis", 
    "Köln, Kreisfreie Stadt", "Kaiserslautern, Landkreis", "Karlsruhe, Kreisfreie Stadt", 
    "Karlsruhe, Landkreis", "Kassel, Landkreis", "Kelheim, Landkreis", 
    "Kitzingen, Landkreis", "Kleve, Kreis", "Konstanz, Landkreis", 
    "Kronach, Landkreis", "Kulmbach, Landkreis", "Kusel, Landkreis", 
    "Kyffhäuserkreis", "Lörrach, Landkreis", "Lüchow-Dannenberg, Landkreis", 
    "Lüneburg, Landkreis", "Lahn-Dill-Kreis", "Landkreis Ludwigslust-Parchim", 
    "Landkreis Mecklenburgische Seenplatte", "Landkreis Nordwestmecklenburg", 
    "Landkreis Rostock", "Landkreis Vorpommern-Greifswald", "Landkreis Vorpommern-Rügen", 
    "Landsberg am Lech, Landkreis", "Landshut, Landkreis", "Leer, Landkreis", 
    "Leipzig, Landkreis", "Lichtenfels, Landkreis", "Limburg-Weilburg, Landkreis", 
    "Lippe, Kreis", "Ludwigsburg, Landkreis", "Märkisch-Oderland, Landkreis", 
    "Märkischer Kreis", "Mühldorf a.Inn, Landkreis", "München, Landeshauptstadt", 
    "München, Landkreis", "Main-Spessart, Landkreis", "Main-Tauber-Kreis", 
    "Main-Taunus-Kreis", "Mainz-Bingen, Landkreis", "Mannheim, Universitätsstadt, Kreisfreie Stadt", 
    "Mansfeld-Südharz, Landkreis", "Marburg-Biedenkopf, Landkreis", 
    "Mayen-Koblenz, Landkreis", "Meißen, Landkreis", "Mettmann, Kreis", 
    "Minden-Lübbecke, Kreis", "Mittelsachsen, Landkreis", "Nürnberg", 
    "Nürnberger Land, Landkreis", "Neckar-Odenwald-Kreis", "Neu-Ulm, Landkreis", 
    "Neuburg-Schrobenhausen, Landkreis", "Neumarkt i.d.OPf., Landkreis", 
    "Neustadt a.d.Aisch-Bad Windsheim, Landkreis", "Neustadt a.d.Waldnaab, Landkreis", 
    "Neustadt an der Weinstraße, Kreisfreie Stadt", "Neuwied, Landkreis", 
    "Nienburg (Weser), Landkreis", "Nordfriesland, Landkreis", 
    "Nordhausen, Kreis", "Nordsachsen, Landkreis", "Northeim, Landkreis", 
    "Oberallgäu, Landkreis", "Oberhavel, Landkreis", "Oberspreewald-Lausitz, Landkreis", 
    "Odenwaldkreis", "Oder-Spree, Landkreis", "Offenbach, Landkreis", 
    "Oldenburg, Landkreis", "Olpe, Kreis", "Ortenaukreis", "Osnabrück, Landkreis", 
    "Ostalbkreis", "Ostallgäu, Landkreis", "Osterholz, Landkreis", 
    "Osterode am Harz, Landkreis", "Ostholstein, Landkreis", 
    "Ostprignitz-Ruppin, Landkreis", "Passau, Landkreis", "Peine, Landkreis", 
    "Pfaffenhofen a.d.Ilm, Landkreis", "Pinneberg, Landkreis", 
    "Plön, Landkreis", "Potsdam-Mittelmark, Landkreis", "Potsdam, Kreisfreie Stadt", 
    "Prignitz, Landkreis", "Rastatt, Landkreis", "Ravensburg, Landkreis", 
    "Regen, Landkreis", "Regensburg, Landkreis", "Region Hannover, Landkreis", 
    "Rems-Murr-Kreis", "Rendsburg-Eckernförde, Landkreis", "Reutlingen, Landkreis", 
    "Rhön-Grabfeld, Landkreis", "Rhein-Kreis Neuss", "Rhein-Neckar-Kreis", 
    "Rhein-Sieg-Kreis", "Rheingau-Taunus-Kreis", "Rheinisch-Bergischer Kreis", 
    "Rosenheim, Landkreis", "Rotenburg (Wümme), Landkreis", 
    "Roth, Landkreis", "Rottweil, Landkreis", "Sächsische Schweiz-Osterzgebirge, Landkreis", 
    "Sömmerda, Kreis", "Südliche Weinstraße, Landkreis", "Südwestpfalz, Landkreis", 
    "Saale-Holzland-Kreis", "Saale-Orla-Kreis", "Saalekreis", 
    "Saalfeld-Rudolstadt, Kreis", "Salzlandkreis", "Schaumburg, Landkreis", 
    "Schleswig-Flensburg, Landkreis", "Schmalkalden-Meiningen, Kreis", 
    "Schwabach", "Schwandorf, Landkreis", "Schweinfurt", "Schweinfurt, Landkreis", 
    "Segeberg, Landkreis", "Siegen-Wittgenstein, Kreis", "Sigmaringen, Landkreis", 
    "Soest, Kreis", "Sonneberg, Kreis", "Spree-Neiße, Landkreis", 
    "Stade, Landkreis", "Starnberg, Landkreis", "Steinburg, Landkreis", 
    "Steinfurt, Kreis", "Stendal, Landkreis", "Stormarn, Landkreis", 
    "Straubing-Bogen, Landkreis", "Stuttgart, Landeshauptstadt, Kreisfreie Stadt", 
    "Tübingen, Landkreis", "Teltow-Fläming, Landkreis", "Traunstein, Landkreis", 
    "Uckermark, Landkreis", "Uelzen, Landkreis", "Unstrut-Hainich-Kreis", 
    "Unterallgäu, Landkreis", "Vechta, Landkreis", "Verden, Landkreis", 
    "Viersen, Kreis", "Vogelsbergkreis", "Würzburg, Landkreis", 
    "Waldeck-Frankenberg, Landkreis", "Wartburgkreis", "Weißenburg-Gunzenhausen, Landkreis", 
    "Weilheim-Schongau, Landkreis", "Weimar, krsfr. Stadt", "Weimarer Land, Kreis", 
    "Werra-Meißner-Kreis", "Wesel, Kreis", "Wesermarsch, Landkreis", 
    "Westerwaldkreis", "Wetteraukreis", "Wiesbaden, Landeshauptstadt, Kreisfreie Stadt", 
    "Wittenberg, Landkreis", "Wittmund, Landkreis", "Wolfenbüttel, Landkreis", 
    "Wuppertal, Kreisfreie Stadt", "Zollernalbkreis", "Zwickau, Landkreis"
    ), class = "factor"), slope_abundance_plot = c(NA_real_, 
    NA_real_, NA_real_, NA_real_, NA_real_, NA_real_, NA_real_
    ), p_slope_abundance_plot = c(NA_real_, NA_real_, NA_real_, 
    NA_real_, NA_real_, NA_real_, NA_real_)), .Names = c("site", 
"year", "species", "abundance", "county", "slope_abundance_plot", 
"p_slope_abundance_plot"), row.names = c(61L, 75L, 76L, 91L, 
92L, 93L, 134L), class = "data.frame")

      

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If I print your subset I see the following:

    site year                species abundance                  county slope_abundance_plot p_slope_abundance_plot
61  sh47 2005 western yellow wagtail        NA Dithmarschen, Landkreis                   NA                     NA
75  sh47 2006 western yellow wagtail        NA Dithmarschen, Landkreis                   NA                     NA
76  sh47 2007 western yellow wagtail        NA Dithmarschen, Landkreis                   NA                     NA
91  sh47 2008 western yellow wagtail        NA Dithmarschen, Landkreis                   NA                     NA
92  sh47 2009 western yellow wagtail        NA Dithmarschen, Landkreis                   NA                     NA
93  sh47 2010 western yellow wagtail        NA Dithmarschen, Landkreis                   NA                     NA
134 sh47 2011 western yellow wagtail        NA Dithmarschen, Landkreis                   NA                     NA

      



As you can see, all the abundance values NA

that the error message reported to you. You should use tryCatch

to handle these subsets.

(Btw, the yield is dput

so big that it includes all levels of factors.)

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