predict.gam with new factor levels - r

I'm running a hurdle type analysis on species distribution data which involves two fitting steps. The first step is to model (m1) presence/absence data using all data with family=quasibinomial. The second step (m2) is to use positive presence only data with family=Gamma. This works wonderfully until I try to predict using the second model (m2) on the full dataset I receive an error due to new factor levels. I understand why I am receiving this error; there are factor levels that appear in the full dataset that are not present in the reduce (presence only) dataset. My question is how do I work around this error so that I can get predictions using the second model on the full set?
I am using mgcv.
Edit: Updated with additional code and data.
# Step1 - GAM using full dataset for presence/absense
grays<-structure(list(Grid_ID = structure(c(39L, 51L, 52L, 67L), .Label = c("1",
"1,000", "1,001", "1,008", "1,009", "1,010", "1,011", "1,012",
"1,013", "1,014", "1,015", "1,016", "1,022", "1,023", "1,024",
"1,025", "1,026", "1,027", "1,028", "1,029", "1,034", "1,035",
"1,036", "1,037", "1,039", "1,040", "1,045", "1,046", "1,047",
"1,048", "1,053", "1,054", "1,055", "10", "100", "101", "103",
"104", "105", "106", "107", "108", "109", "11", "110", "118",
"119", "12", "122", "125", "126", "127", "128", "129", "13",
"130", "131", "132", "133", "14", "141", "142", "15", "150",
"151", "152", "153", "154", "155", "156", "157", "158", "159",
"160", "161", "162", "163", "167", "168", "169", "173", "174",
"175", "176", "177", "178", "179", "180", "181", "182", "183",
"184", "185", "188", "189", "190", "196", "197", "198", "199",
"2", "20", "200", "201", "202", "203", "204", "205", "206", "207",
"209", "210", "211", "219", "22", "220", "221", "222", "223",
"224", "225", "226", "227", "228", "229", "23", "230", "231",
"233", "234", "235", "236", "237", "24", "246", "247", "248",
"249", "25", "250", "252", "253", "254", "255", "256", "257",
"258", "259", "26", "260", "261", "267", "268", "269", "27",
"270", "271", "272", "273", "274", "275", "276", "277", "278",
"279", "28", "280", "281", "286", "287", "288", "289", "29",
"290", "291", "292", "293", "294", "295", "296", "297", "298",
"299", "3", "300", "301", "302", "303", "305", "306", "307",
"308", "309", "310", "311", "312", "313", "314", "315", "316",
"317", "318", "319", "320", "321", "326", "327", "328", "329",
"330", "331", "332", "333", "334", "335", "336", "337", "339",
"340", "341", "343", "344", "345", "346", "347", "348", "349",
"350", "351", "352", "355", "356", "357", "36", "360", "361",
"362", "363", "364", "365", "366", "367", "368", "369", "37",
"372", "373", "374", "38", "380", "381", "382", "383", "384",
"385", "386", "39", "391", "392", "397", "398", "399", "4", "40",
"400", "401", "402", "408", "409", "41", "410", "412", "413",
"414", "415", "416", "417", "42", "423", "424", "425", "426",
"43", "430", "431", "432", "433", "434", "44", "441", "442",
"443", "444", "447", "448", "449", "45", "450", "451", "458",
"459", "46", "460", "461", "462", "463", "464", "465", "466",
"470", "471", "472", "473", "474", "475", "476", "484", "485",
"486", "487", "488", "489", "490", "491", "492", "496", "497",
"498", "499", "5", "500", "501", "513", "514", "515", "516",
"517", "518", "523", "524", "525", "526", "527", "528", "529",
"54", "541", "542", "543", "544", "545", "55", "550", "551",
"552", "553", "554", "56", "569", "57", "570", "571", "572",
"573", "574", "578", "579", "580", "581", "582", "599", "60",
"600", "601", "602", "603", "604", "605", "606", "607", "608",
"609", "61", "610", "62", "626", "627", "628", "629", "63", "632",
"633", "634", "635", "636", "637", "638", "639", "64", "653",
"654", "655", "656", "657", "658", "659", "660", "663", "664",
"665", "666", "667", "668", "669", "670", "671", "672", "673",
"687", "688", "689", "690", "691", "692", "693", "696", "697",
"698", "699", "7", "700", "701", "702", "703", "704", "705",
"716", "717", "718", "720", "721", "722", "723", "724", "725",
"726", "727", "728", "739", "74", "740", "741", "746", "747",
"748", "749", "75", "750", "751", "752", "753", "754", "764",
"765", "768", "769", "77", "770", "771", "772", "773", "78",
"782", "783", "784", "788", "789", "79", "790", "798", "799",
"8", "80", "800", "801", "804", "805", "81", "812", "813", "814",
"815", "816", "819", "82", "820", "821", "827", "828", "829",
"83", "830", "831", "833", "834", "835", "836", "84", "842",
"843", "844", "845", "846", "849", "85", "850", "851", "852",
"853", "854", "860", "861", "862", "863", "864", "869", "870",
"871", "872", "873", "874", "88", "881", "882", "883", "884",
"885", "886", "89", "890", "891", "892", "893", "894", "9", "902",
"903", "904", "905", "906", "908", "909", "910", "911", "912",
"922", "923", "924", "925", "926", "927", "928", "929", "930",
"940", "941", "942", "943", "944", "945", "946", "947", "948",
"957", "958", "959", "96", "960", "961", "962", "963", "964",
"965", "966", "97", "976", "977", "978", "979", "980", "981",
"982", "983", "984", "992", "993", "994", "995", "996", "997",
"998", "999"), class = "factor"), Grid_Lat = c(56.85582097, 56.90062505,
56.90024495, 56.94461032), Grid_Long = c(153.4783612, 153.4777153,
153.3954873, 153.3124098), Er_Pres = c(0L, 0L, 0L, 0L), Er_Count = c(0L,
0L, 0L, 0L), Er_Count_Density = c(0, 0, 0, 0), Month = structure(c(8L,
8L, 8L, 8L), .Label = c("1", "2", "3", "4", "5", "6", "7", "8",
"9", "10", "11"), class = "factor"), Year = structure(c(1L, 1L,
1L, 1L), .Label = c("1997", "1998", "1999", "2000", "2001", "2002",
"2003", "2004", "2005", "2006", "2007", "2008", "2009", "2010",
"2011", "2012", "2013"), class = "factor"), chl = c(0.53747,
0.53747, 0.53747, 0.581741), SST = c(13.4171, 13.4171, 13.4171,
13.4025002), Bathymetry = c(76.11354065, 92.14147949, 90.60312653,
71.55316162), Grid_Area = c(25, 25, 25, 25), DFS = c(6.807817092,
4.233185446, 9.199096676, 5.153224038), Slope = c(0.13670446,
0.38316911, 0.08646853, 0.20038579), DOY = c(244L, 244L, 244L,
244L)), .Names = c("Grid_ID", "Grid_Lat", "Grid_Long", "Er_Pres",
"Er_Count", "Er_Count_Density", "Month", "Year", "chl", "SST",
"Bathymetry", "Grid_Area", "DFS", "Slope", "DOY"), row.names = c(NA,
4L), class = "data.frame")
m1<-gam(Er_Pres~ s(Grid_Lat,Grid_Long,k=10,bs='tp')+Month+Year+s(SST,k=5,bs='tp'),family=quasibinomial(link='logit'),data=grays,gamma=1.4,offset(Grid_Area))
#step 2 - reduce dataset and run second GAM for positive abundance only.
grays2<-subset(grays,Er_Pres>0)
m2<-gam(Er_Count~ Year +s(Grid_Lat,Grid_Long,k=10,bs='tp') + s(SST,k=5,bs='tp') + s(sqrt(DFS),k=5,bs='tp') + Month +log10(chl),family=Gamma(link='log'),data=grays2,Gamma=1.4,offset(Grid_Area))
Running the second model gives me the follow error:
Error in predict.gam(m2, newdata = full, type = "response") :
1997, 1998, 2006, 2007 not in original fit


This is an old post, so I suspect you have found a solution by now, but if not consider this:
If you only want to account for data within the same year being more similar than data across year, but you are not necessarily interested in the effect of particular years (say the difference between 2007 and 1998) then you could specify year as a random effect.
I believe there are several ways to do this, but in mgcv, you can specify:
s(Year, bs="re")

Related

Creating raster from dataframe creates an error

I am running a random forest comparing PC_Countto multiple variables
rf_h_count_km <- randomForest (
formula = PC_count ~NLCD+Pop_Focal+NLUD+Population+Urban+Slope+NLCD21_f+NLCD22_f+NLCD23_f+NLCD24_f+Density+PC,
data = training,
method = 'rf',
tuneGrid = tuneGrid,
ntree = 100,
nodesize = 5,
importance = TRUE,
trControl = ctrl,
metric = "ROC"
)
The random forest ran successfully, but now I am trying to convert the output into a prediction raster. Seeing that the predictor variable is otained from a dataframe and the independent variables from a raster stack I have not found a way to do it directly
#predict the response variable with training data
l<-raster::predict(rf_h_count_km, type="response", data=testing, index=2, na.rm=TRUE, progress="window", overwrite=TRUE)
I converted the output array into datframe format
x<-as.data.frame(l)
names(x) <- c("try")
Secondly, I created an empty raster with the dimensions needed
r = raster(ncols=225, nrows=176, xmn=-1788075, xmx=-1584465, ymn=1481625, ymx=1717755, res=1000)
Thirdly, I tried adding the values from the dataframe to the raster. However, this produces an error
> raster::values(r)<-x$try
Error in setValues(x, value) :
length(values) is not equal to ncell(x), or to 1
Is there any way that I could add these values into the raster without producing the error?
Below is a segment of the 1-column dataframe
> dput(head(x,500))
structure(list(try = c(1.25482243953606, 1.29704685733086, 1.59604755116753,
1.27323310015838, 1.65523336838096, 1.16055734781969, 1.91659455992709,
1.52214228365861, 1.39167234672577, 1.39345512204005, 1.14707832355435,
1.38027338524104, 1.43416846811582, 1.19860901400402, 1.36468712553493,
1.39169436843932, 1.331203829109, 1.92116276432308, 1.76695170198865,
1.29033362603409, 1.49713229698021, 1.43769464696184, 1.68270039388572,
1.44802123045305, 1.48484344231137, 1.5923432415293, 1.89790742744141,
1.32407450302128, 1.41150242816569, 1.56883137580953, 1.39132737542988,
1.34693405858518, 1.70515171668636, 1.787306308579, 1.53811871225996,
1.54649976632651, 1.37557485902264, 1.42460519475178, 1.84602421808187,
1.46107494748112, 1.48574351291447, 1.55515920286892, 1.47435149169411,
2.06774644973887, 1.67011263561363, 1.53676870286262, 1.51437261683124,
1.65344434977873, 1.52521033303975, 1.33428311000463, 1.86538942543929,
1.1728691498302, 1.17687652159234, 1.80537815643604, 1.49692701357964,
1.00050456141199, 1.47365424021922, 1.47114102470081, 1.39277787775097,
0.865697705973826, 1.50096649740468, 1.13385260841033, 1.65271338239792,
1.46884690867827, 1.481906677787, 1.14199273373277, 1.68774387988497,
1.51872838325436, 1.38328649616044, 1.67114602131701, 1.54848407844392,
1.3996624303754, 1.71789148484286, 1.33823346156167, 1.25566170818395,
1.55020641523366, 1.17128373170123, 1.26915332769989, 1.66256952986062,
1.50038471501031, 1.30659761867545, 1.38389413400123, 1.59603869890816,
1.28059405159913, 1.49876041289129, 1.45692568883059, 1.82472848165875,
1.23544716197641, 1.30844258992342, 1.62576923439109, 1.26939004412273,
1.58507687431416, 1.31481901026701, 1.4575809162353, 1.53809208050283,
1.16766113344713, 1.56314563435862, 1.55411214306813, 1.78357145366888,
1.4329858089636, 1.43396598308919, 1.39465154299149, 1.48451992338695,
1.24684337200367, 1.96110469737173, 1.16625138690017, 0.775810330702323,
1.00045993259336, 1.37686548806939, 1.62733354682162, 1.68759141765908,
1.628166880637, 1.94206520355245, 1.61238598818564, 1.96885931093973,
1.34625059573652, 1.31831686519609, 1.53290631646635, 1.57775601413376,
1.58363330493889, 1.89319841817133, 0.782837422055985, 1.64643379323501,
1.66712161497969, 1.29699891021702, 1.47429558125218, 1.68691877809511,
1.74608775523785, 1.9991622606389, 1.56607510448966, 1.6309907225318,
1.46078033728118, 1.17142033440308, 1.40255145198544, 1.33112985551097,
1.15166500669548, 1.80419274569205, 1.62729203127811, 1.83685487185426,
1.58635321656375, 1.82779066393067, 1.34477410566094, 1.49887518851983,
1.50264666884424, 1.30559742049033, 1.70529841717443, 1.36461045525143,
1.35656649147087, 1.37880956124176, 1.32825774615472, 1.4743468228756,
1.68848953739118, 1.5714969472275, 1.28051735582015, 1.70382287292112,
1.48697666114366, 1.52509854662891, 2.00215110778257, 1.51573583601317,
1.52652734904295, 1.83725972310248, 1.43565914024433, 1.65558396263679,
1.28093702179809, 1.34220737362985, 1.45510583039298, 1.34188715043272,
1.59560616172484, 1.18911884147528, 1.76384130089723, 1.14960238421033,
1.36430236202792, 1.62519404962719, 1.41158597502356, 0.797289908270849,
1.15520086855207, 1.42517561255296, 1.00047571138336, 1.31365223086707,
1.4129217354065, 1.29535822063539, 1.67078827797151, 1.54029946373479,
1.84666725485803, 1.31394353069208, 1.30563028604674, 1.81450886504348,
1.19491662297257, 1.27229869878179, 1.28963013410991, 1.43762367763379,
1.16928002123748, 0.76442403537918, 1.28823684878266, 1.74785996977029,
1.64959703066888, 1.5509430052318, 1.45843245579434, 1.63183302686946,
1.59733661443473, 0.760843648977963, 1.36684005161429, 1.84519682070654,
1.50049023315098, 1.7050215606835, 1.62763853632365, 1.56200633371077,
1.51191419294519, 1.6116950079444, 1.76167964082101, 1.6283596872148,
1.60698192017333, 1.66810316469347, 1.16126887133296, 1.38968215164831,
1.48455441438511, 0.660013152279427, 1.53085391999465, 1.82842047029258,
1.1661862475647, 1.00044570589583, 1.70599622205831, 1.38431550482051,
1.50410961983431, 1.61241963890188, 1.68592745635435, 1.36708568021482,
1.49941207893968, 1.48543479320907, 1.35809437513195, 1.55296348681227,
1.59819516191763, 1.48481302388378, 1.4061746887853, 1.36929246790332,
1.39266730855954, 1.46027138849061, 1.53273782134419, 1.16136716380526,
1.56032756345299, 1.76303556273634, 1.30009474488364, 0.713431047919119,
1.27230670052624, 1.74416452489221, 1.61122408130062, 1.89634699686347,
1.47106580278593, 1.28149781048158, 1.55039187691515, 1.70574909049325,
1.30713212157724, 1.52846086526416, 1.67346330500358, 1.43438661455238,
1.18645458508454, 1.63936712727192, 1.41112353469103, 1.2761061429259,
1.27580024677754, 1.3072009173607, 0.76482905669465, 1.48493548485036,
1.62951834284185, 1.26147044940371, 1.51789060097793, 1.41333216708036,
1.33639249077728, 1.45542697933075, 1.43760708672506, 1.71199034891044,
1.26027699097399, 1.32370075969687, 1.14957580510731, 1.42015421688412,
1.80770319259332, 1.56027185359019, 1.26335891477022, 1.14435742981936,
1.21496018704641, 1.1581564288297, 1.53379063258365, 1.51294803803159,
1.30732487742837, 1.43717349783508, 1.43486086288793, 1.50187858120187,
1.15120725634633, 1.35400674186641, 1.55364027339135, 1.94536872847578,
1.710630763992, 1.71391827834412, 1.00050653319808, 1.30922140163975,
1.66640189638562, 1.70458770847952, 1.41382683700093, 1.54886023547989,
1.62626167586269, 1.91473409741524, 1.63101761509542, 1.67304098596854,
1.43182019801906, 1.14567627381978, 1.35238386442408, 1.64751122114616,
1.34873996399922, 1.37023850292472, 1.53564601207952, 1.57505619181632,
1.36708995300055, 1.56941164647469, 1.16925475135763, 0.842871188459787,
1.3812699305909, 1.41386414196727, 1.16059409444905, 1.76201853912225,
1.44222009921562, 1.64997144444006, 1.38376159924388, 1.61003199654573,
1.57499790571938, 1.15201686470987, 1.76676689613511, 1.8096908759832,
1.20486311868743, 1.68728039392101, 1.42500419002418, 1.44665607038376,
1.58123291895195, 1.14005656747451, 1.48678222431433, 1.44661082228836,
1.61171967442807, 1.30729777317031, 1.42286763782785, 1.40553596608522,
1.55064563919909, 1.70051648043645, 1.69303294109564, 1.5515686820675,
1.49226483353159, 1.43554567483609, 1.30857962097702, 1.41632801810122,
1.66756491810872, 1.44526232593268, 1.48719674319771, 1.42309996893368,
1.6580257935528, 1.5829194496966, 1.64235861450852, 1.44895677424997,
1.61443646370592, 1.68792404047021, 1.56680875163758, 1.63772239523653,
1.38406187171508, 1.18445033651953, 1.80761413246068, 1.52670027322229,
1.13013642070425, 1.56261574480113, 1.6888386513478, 1.00051404040559,
1.53839461415883, 1.58065043297887, 1.45576137913913, 1.49989463209582,
1.28055237635367, 1.50010654014454, 1.42137860072691, 1.56511565854225,
1.70639749591321, 1.41508801317881, 1.73233307347998, 1.13841982707047,
1.4400662466764, 1.80565275760731, 0.77520490363639, 1.61527499647451,
1.32672943129696, 1.76607190217432, 1.27583861087918, 1.73820202046061,
1.51335423345056, 1.30921314993083, 1.89626987520185, 1.4473406270278,
1.35322135964277, 2.01512208326191, 1.50393203460877, 1.68770896622325,
0.805436684457629, 1.37740579297073, 1.76790174733803, 1.6562649800791,
1.34223556479203, 1.15246311383752, 1.68485931618636, 1.40568909806569,
0.784724015738059, 1.49886040116948, 1.8272016947891, 1.76469931390133,
1.26688645784432, 1.72643807856103, 1.43467491769798, 1.26459859241559,
1.68797176508759, 1.46051637830131, 1.49869552936372, 1.14441765225327,
1.57745957616188, 1.28307917058032, 1.74574595151118, 1.35334508600179,
1.59272719674702, 1.19935222312585, 1.35880915261704, 1.15239419992794,
1.4044441578425, 1.39219305326424, 1.44629956051605, 2.01162723040148,
1.4711194451495, 1.62984928328262, 1.29120536667572, 1.7437705740116,
1.32490447606648, 1.73704376707315, 1.60847808850637, 1.38597284699774,
1.59628605075663, 1.43444007060914, 1.3244765426713, 1.36864321432182,
1.60706449020901, 1.14400820678228, 1.28098051291041, 1.59293724647213,
1.20693559821733, 0.762694890744079, 1.00051265006564, 1.15238864138768,
1.94340119252715, 1.18820627573647, 1.36578984019797, 1.78610658908017,
1.6139282437022, 1.56664750472243, 1.28225859203438, 1.351183496751,
1.74883140168085, 1.98997982109868, 1.36718566083602, 1.81044434104092,
1.27607390816209, 1.45917517513078, 1.46192984151842, 1.72610404482554,
1.6265388077098, 1.55430788004514, 1.44485886502457, 1.73699539353876,
1.48594712331721, 1.42357556702341, 1.32457308337899, 1.55064010993579,
1.42291188618139, 1.64818926255211, 1.13841846135019, 1.95209192401635,
1.66937085634394, 1.55376682098252, 1.624705399401, 1.30640121517372,
1.28092432425333, 1.42589541938036, 1.41146701872041, 1.14830789689793,
1.3160788417034, 1.58225727505092, 1.16056978361285, 1.4883577330535,
1.41232141834121, 1.52493787348832, 1.62487746013324, 1.43269182322572,
1.55049696656887, 1.53525920970974, 1.31609276967797, 1.68663626612582,
1.46992801989381, 1.51568282463528, 1.56295971478745, 1.43171059023851,
1.48486531481598)), row.names = c("4", "5", "8", "9", "10", "13",
"15", "16", "17", "18", "19", "20", "21", "22", "23", "26", "27",
"28", "29", "31", "34", "35", "37", "39", "40", "41", "42", "43",
"44", "45", "46", "47", "48", "49", "50", "51", "54", "55", "56",
"57", "59", "60", "61", "62", "63", "64", "66", "67", "68", "71",
"72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82",
"83", "84", "85", "86", "87", "88", "89", "90", "92", "93", "94",
"95", "96", "97", "98", "99", "100", "102", "103", "104", "105",
"106", "107", "108", "109", "111", "112", "113", "114", "115",
"117", "118", "119", "120", "121", "123", "124", "125", "126",
"127", "128", "130", "131", "132", "133", "134", "135", "136",
"137", "138", "139", "141", "143", "144", "145", "147", "148",
"150", "152", "153", "154", "156", "158", "159", "162", "163",
"165", "168", "169", "172", "174", "175", "176", "177", "178",
"179", "180", "182", "183", "184", "185", "186", "187", "188",
"190", "191", "194", "196", "197", "198", "199", "202", "204",
"205", "206", "208", "209", "211", "212", "213", "214", "215",
"216", "217", "218", "219", "220", "221", "223", "224", "227",
"228", "229", "230", "231", "232", "233", "236", "238", "239",
"240", "241", "242", "243", "244", "245", "248", "251", "254",
"255", "257", "258", "259", "260", "262", "263", "264", "265",
"266", "268", "270", "271", "272", "273", "274", "276", "278",
"279", "280", "281", "282", "283", "284", "285", "286", "287",
"288", "289", "290", "292", "293", "295", "296", "297", "300",
"301", "304", "307", "309", "310", "312", "314", "315", "316",
"317", "318", "319", "320", "321", "322", "323", "324", "325",
"326", "327", "328", "330", "331", "332", "333", "334", "336",
"339", "340", "345", "346", "349", "350", "351", "352", "353",
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"366", "367", "368", "369", "370", "371", "372", "373", "376",
"377", "378", "380", "381", "382", "383", "384", "385", "386",
"391", "392", "395", "396", "398", "399", "400", "403", "404",
"405", "406", "407", "408", "409", "410", "411", "413", "414",
"415", "417", "418", "419", "420", "421", "422", "424", "426",
"427", "428", "429", "430", "431", "433", "434", "435", "436",
"437", "441", "442", "443", "446", "447", "449", "450", "451",
"453", "454", "457", "458", "459", "460", "463", "465", "466",
"467", "468", "469", "470", "471", "472", "473", "475", "476",
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"500", "502", "503", "506", "508", "509", "510", "511", "512",
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"579", "580", "581", "582", "583", "584", "585", "586", "588",
"589", "591", "592", "593", "596", "598", "599", "601", "602",
"604", "606", "608", "609", "610", "611", "614", "615", "616",
"617", "618", "619", "620", "621", "623", "626", "627", "628",
"629", "630", "632", "633", "634", "635", "636", "637", "638",
"639", "640", "641", "642", "644", "645", "646", "647", "649",
"650", "651", "653", "654", "655", "656", "657", "658", "659",
"660", "662", "663", "664"), class = "data.frame")

Here is how you can do that with terra (the replacement for raster)
library(terra)
logo <- rast(system.file("ex/logo.tif", package="terra"))
names(logo) <- c("red", "green", "blue")
p <- matrix(c(48, 48, 48, 53, 50, 46, 54, 70, 84, 85, 74, 84, 95, 85,
66, 42, 26, 4, 19, 17, 7, 14, 26, 29, 39, 45, 51, 56, 46, 38, 31,
22, 34, 60, 70, 73, 63, 46, 43, 28), ncol=2)
a <- matrix(c(22, 33, 64, 85, 92, 94, 59, 27, 30, 64, 60, 33, 31, 9,
99, 67, 15, 5, 4, 30, 8, 37, 42, 27, 19, 69, 60, 73, 3, 5, 21,
37, 52, 70, 74, 9, 13, 4, 17, 47), ncol=2)
xy <- rbind(cbind(1, p), cbind(0, a))
e <- extract(logo, xy[,2:3])
v <- data.frame(cbind(pa=xy[,1], e[,-1]))
library(randomForest)
rfm <- randomForest(formula=pa~., data=v)
p <- predict(logo, rfm)
I copied this from the help file ?terra::predict. The same example for raster is available in raster::predict.
Note that the first argument to predict should be a SpatRaster (or a Raster* for the raster package). What you do:
l <- raster::predict(rf_h_count_km,...)
is wrong because that just gives you the predictions for the model training data, as you do not provide the raster data to predict to.
((and raster::predict is a generic function that will select the appropriate implementation based on the first argument. In this case it will just go to randomForest::predict))
Unless you trained your model with all your raster data, in which case you could use something like
rfma <- randomForest(formula=red~., data=as.data.frame(logo))
r <- rast(logo, nlyr=1)
values(r) <- predict(rfma)

Lower Bound of a Curve

I have a curve likes the following:
As can be seen, there are two upper bound and lower bound curves on the above (see the following image for the approx visualization!):
I have tried to find the lower bound by the following code:
lower_bound = rbind()
for(i in 2:(length(data[,1])-1))
{
if(data[i,2] < data[i+1,2] && data[i,2] < data[i-1,2])
{
lower_bound = rbind2(lower_bound, c(data[i,1], data[i,2]))
}
}
But, the problem is there are some local minima in the middle, so the result is not what I've expected (as follow).
Hence the question is how can I find the lower bound of such a curve in R? Is there any known algorithm to find the lower bound?
About the minimal reproducible example, I've included 500 of data (to make sense) in the following:
structure(c(3.54246575342466, 5.75616438356164, 6.54246575342466,
9.73424657534247, 7.75616438356164, 9.75616438356164, 1.41917808219178,
2.75342465753425, 3.16986301369863, 2.27123287671233, 3.74520547945205,
5.74520547945205, 4.29315068493151, 3.37260273972603, 8.37534246575343,
3.33698630136986, 5.04657534246575, 6.92328767123288, 1.33972602739726,
6.34246575342466, 26.358904109589, 2.34794520547945, 4.35068493150685,
7.35342465753425, 27.3671232876712, 1.15068493150685, 2.14794520547945,
4.15342465753425, 6.15342465753425, 9.15616438356164, 19.1616438356164,
29.1698630136986, 2.58904109589041, 4.5972602739726, 9.6, 29.613698630137,
3.10684931506849, 8.11780821917808, 3.35068493150685, 8.37260273972603,
5.11506849315068, 28.1315068493151, 5.36986301369863, 28.386301369863,
4.87945205479452, 4.46027397260274, 5.35616438356164, 25.3698630136986,
25.8684931506849, 5.85479452054795, 1.85205479452055, 4.37260273972603,
6.37260273972603, 9.37534246575343, 19.3835616438356, 29.3890410958904,
18.3808219178082, 1.36986301369863, 8.37534246575343, 3.37260273972603,
5.85479452054795, 28.3890410958904, 2.87671232876712, 4.87945205479452,
7.37808219178082, 8.17260273972603, 28.186301369863, 4.29315068493151,
6.96164383561644, 26.3479452054795, 7.96438356164384, 1.53972602739726,
1.58630136986301, 5.04657534246575, 16.6356164383562, 18.4684931506849,
25.0602739726027, 15.6493150684932, 24.8547945205479, 25.3506849315068,
26.1068493150685, 16.0547945205479, 2.16712328767123, 19.2657534246575,
20.6849315068493, 1.04383561643836, 3.04383561643836, 23.0575342465753,
3.29315068493151, 4.13150684931507, 2.04383561643836, 22.0575342465753,
22.8904109589041, 2.87671232876712, 5.54246575342466, 25.5561643835616,
1.04931506849315, 6.05205479452055, 26.0657534246575, 2.09041095890411,
7.09315068493151, 27.1068493150685, 2.09041095890411, 4.09315068493151,
6.09315068493151, 9.0958904109589, 19.1013698630137, 29.1095890410959,
1.83287671232877, 1.42739726027397, 3.43013698630137, 9.3041095890411,
2.72328767123288, 8.58082191780822, 2.8958904109589, 4.92054794520548,
9.92328767123288, 6.92054794520548, 19.9315068493151, 29.9369863013699,
20.9315068493151, 2.25205479452055, 22.2657534246575, 3.40821917808219,
23.4219178082192, 8.21095890410959, 3.20821917808219, 5.20821917808219,
18.8027397260274, 19.8054794520548, 21.7232876712329, 2.25205479452055,
22.8054794520548, 24.4301369863014, 4.41643835616438, 25.2684931506849,
5.25479452054795, 6.33698630136986, 26.3506849315068, 2.87671232876712,
4.29315068493151, 2.78630136986301, 1.2958904109589, 1.75890410958904,
2.29041095890411, 7.2958904109589, 3.44657534246575, 4.5041095890411,
9.73424657534247, 8.21643835616438, 6.29315068493151, 7.50684931506849,
3.75616438356164, 7.96438356164384, 9.96438356164384, 29.9780821917808,
17.3452054794521, 26.8547945205479, 5.5041095890411, 7.17260273972603,
6.13150684931507, 3.62739726027397, 5.79452054794521, 7.7972602739726,
5.75616438356164, 3.09041095890411, 8.0958904109589, 9.63013698630137,
4.93424657534247, 6.93424657534247, 9.93698630136986, 19.9452054794521,
6.42191780821918, 8.96438356164384, 28.9780821917808, 15.7643835616438,
18.7205479452055, 1.20547945205479, 4.16986301369863, 24.1835616438356,
25.2520547945205, 26.3095890410959, 9.61917808219178, 12.3424657534247,
14.2986301369863, 23.7698630136986, 3.71232876712329, 8.71506849315069,
3.58082191780822, 1.25205479452055, 5.96164383561644, 3.46027397260274,
8.46301369863014, 7.88219178082192, 5.54246575342466, 6.46027397260274,
4.79452054794521, 3.20821917808219, 15.5506849315068, 9.5972602739726,
20.6, 2.09041095890411, 1.87671232876712, 22.2191780821918, 5.67397260273973,
25.7260273972603, 26.9753424657534, 7.2958904109589, 27.5205479452055,
8.17260273972603, 28.3095890410959, 29.2246575342466, 3.87945205479452,
9.13424657534247, 5.84109589041096, 3.96164383561644, 4.54246575342466,
9.92602739726027, 29.9397260273973, 16.1397260273973, 16.1780821917808,
16.1397260273973, 18.7643835616438, 18.7643835616438, 20.2191780821918,
20.6383561643836, 20.8904109589041, 1.16712328767123, 21.2657534246575,
1.33424657534247, 2.04383561643836, 2.20547945205479, 4.75616438356164,
2.92054794520548, 23.2219178082192, 4.09315068493151, 4.24931506849315,
5.13150684931507, 5.96164383561644, 6.20821917808219, 27.3917808219178,
29.2246575342466, 9.75890410958904, 8.75890410958904, 28.2712328767123,
8.42465753424658, 28.4383561643836, 2.37260273972603, 4.37534246575343,
4.75616438356164, 1.67123287671233, 3.96164383561644, 2.37260273972603,
5.04657534246575, 2.25205479452055, 5.62739726027397, 4.29315068493151,
1.29041095890411, 3.5041095890411, 5.5041095890411, 5.09315068493151,
3.83561643835616, 8.46301369863014, 3.42191780821918, 1.33424657534247,
4.5041095890411, 4.79452054794521, 6.37534246575343, 7.21095890410959,
9.37808219178082, 29.3534246575342, 3.54246575342466, 28.6904109589041,
8.2958904109589, 8.54246575342466, 4.62739726027397, 12.4082191780822,
19.4712328767123, 20.972602739726, 3.67397260273973, 4.42191780821918,
4.46027397260274, 25.3890410958904, 5.87945205479452, 25.8931506849315,
2.20547945205479, 27.2246575342466, 7.88219178082192, 1.43561643835616,
2.43561643835616, 4.46027397260274, 6.46027397260274, 9.46301369863014,
19.4712328767123, 29.4767123287671, 2.45753424657534, 9.63013698630137,
7.88219178082192, 23.641095890411, 5.13150684931507, 6.46027397260274,
9.7972602739726, 29.8109589041096, 3.21095890410959, 8.21643835616438,
4.92328767123288, 3.25479452054795, 2.62465753424658, 3.71232876712329,
5.75616438356164, 25.7698630136986, 6.20821917808219, 1.20547945205479,
4.96164383561644, 2.09041095890411, 4.13150684931507, 2.45753424657534,
27.4767123287671, 7.46301369863014, 3.2, 18.2164383561644, 1.1972602739726,
5.20821917808219, 8.21095890410959, 28.2246575342466, 19.972602739726,
7.50684931506849, 9.92602739726027, 3.75616438356164, 1.38904109589041,
3.39178082191781, 19.4082191780822, 2.04383561643836, 24.0602739726027,
5.75616438356164, 26.4356164383562, 6.42191780821918, 28.0630136986301,
8.21095890410959, 18.2164383561644, 6.37534246575343, 3.96164383561644,
6.87945205479452, 7.75890410958904, 5.54246575342466, 7.75890410958904,
2.19452054794521, 27.213698630137, 29.227397260274, 8.2, 5.87945205479452,
1.12876712328767, 3.12876712328767, 7.54520547945206, 2.74246575342466,
4.74520547945205, 6.74520547945205, 9.74794520547945, 29.7616438356164,
3.58904109589041, 8.53150684931507, 18.5369863013699, 28.5452054794521,
4.96164383561644, 19.3479452054795, 1.04657534246575, 21.386301369863,
3.96164383561644, 5.42191780821918, 3.62739726027397, 7.13150684931507,
2.54246575342466, 27.5616438356164, 18.0547945205479, 4.16986301369863,
9.25753424657534, 4.76986301369863, 15.2164383561644, 6.37534246575343,
8.17808219178082, 3.73424657534247, 1.26849315068493, 6.27123287671233,
6.2986301369863, 19.3945205479452, 17.1397260273973, 1.20547945205479,
6.20821917808219, 3.37534246575342, 5.25479452054795, 4.75616438356164,
6.54246575342466, 3.16986301369863, 2.04383561643836, 4.25479452054795,
1.04383561643836, 7.71506849315069, 5.09315068493151, 4.42191780821918,
6.71232876712329, 3.04383561643836, 1.67945205479452, 3.30958904109589,
3.96164383561644, 2.92054794520548, 7.92602739726027, 27.9397260273973,
2.83835616438356, 7.46301369863014, 8.21095890410959, 7.23835616438356,
27.2520547945205, 2.53972602739726, 6.58904109589041, 9.96438356164384,
29.9780821917808, 16.4301369863014, 18.3671232876712, 19.2657534246575,
20.386301369863, 2.37534246575342, 6.46027397260274, 26.4739726027397,
6.62739726027397, 4.75616438356164, 6.71232876712329, 28.8958904109589,
15.5123287671233, 14.8465753424658, 14.8465753424658, 2.0027397260274,
3.20821917808219, 3.71232876712329, 1.6958904109589, 2.07671232876712,
7.75616438356164, 2.88493150684931, 4.29315068493151, 1.84931506849315,
8.8958904109589, 1.12328767123288, 5.38630136986301, 5.12602739726027,
8.25205479452055, 3.24931506849315, 1.38904109589041, 5.89315068493151,
6.60821917808219, 1.5013698630137, 3.46027397260274, 6.5041095890411,
7.75890410958904, 6.54246575342466, 9.37808219178082, 3.96164383561644,
5.04657534246575, 7.04657534246575, 8.13424657534247, 6.13150684931507,
9.37808219178082, 7.96438356164384, 11.0493150684932, 12.213698630137,
2.12876712328767, 6.67397260273973, 4.46027397260274, 24.4739726027397,
3.75616438356164, 8.75890410958904, 18.7643835616438, 8.46301369863014,
5.13150684931507, 9.88219178082192, 9.33150684931507, 5.96164383561644,
7.25753424657534, 5.62739726027397, 7.50684931506849, 4.84109589041096,
3.46027397260274, 3.92054794520548, 18.5095890410959, 7.13150684931507,
8.59178082191781, 3.42191780821918, 6.75616438356164, 4.75616438356164,
2.95890410958904, 3.96164383561644, 20.4328767123288, 1.41917808219178,
21.4328767123288, 22.1041095890411, 2.09041095890411, 23.2219178082192,
3.20821917808219, 3.75616438356164, 24.7698630136986, 25.4739726027397,
4.46027397260274, 2.75970346198464, 3.45063169924232, 3.64711503029937,
4.21614538082358, 4.46897200885451, 4.78330432863798, 2.44945159376164,
3.0246987676982, 3.18637219409113, 2.82704067767991, 3.39633877759394,
4.01211492772477, 3.58227507536714, 3.26211339894416, 4.58021400951056,
3.24894671597498, 3.81640051029768, 4.29811641034397, 2.41235239871336,
4.16381972504066, 4.82320604897032, 2.85924829032196, 3.60102245001335,
4.38947242891732, 4.83225858506487, 2.32276057802484, 2.77466777269801,
3.53613679638981, 4.11732178923756, 4.70239811454869, 5.02684596680901,
4.89394362719873, 2.95858956427959, 3.67972641713649, 4.76329504168897,
4.91952178329268, 3.16243766754998, 4.53553009720828, 3.25401782240246,
4.57975033696973, 3.83648225102819, 4.85066377882221, 3.90946630290976,
4.85924427553214, 3.7665702648057, 3.63632959242775, 3.90561093988307,
4.82873462476434, 4.25993172383506, 3.47661513525158, 2.08147939877802,
3.04373161945452, 3.60670989847648, 4.16882946922235, 4.45461902145002,
4.34162315280691, 4.48802758727908, 1.86206866940942, 4.01581962612883,
2.69771901556242, 3.47661513525158, 4.29494911958988, 2.50903075277185,
3.20217588142397, 3.83011128813872, 3.980829920259, 4.28800748360142,
3.58227507536714, 4.30653857989399, 4.82319396445967, 4.50784277427558,
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2.6364550425402, 2.83579574924565, 4.27355104887647, 4.26316357649486,
3.07193520904601), .Dim = c(500L, 2L), .Dimnames = list(c("1",
"2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13",
"14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24",
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"461", "462", "463", "464", "465", "466", "467", "468", "469",
"470", "471", "472", "473", "474", "475", "476", "477", "478",
"479", "480", "481", "482", "483", "484", "485", "486", "487",
"488", "489", "490", "491", "492", "493", "494", "495", "496",
"497", "498", "499", "500"), NULL))

For a relatively simple implementation, you can try as follows:
Consider a running slice of the data, with a constant width. The width must be larger than the largest gap.
Construct the upper and lower hull of the points, using the Monotone Chain algorithm (there is no need to sort, your points are already by increasing abscissa). https://en.wikibooks.org/wiki/Algorithm_Implementation/Geometry/Convex_hull/Monotone_chain
For the middle abscissa in the slice, estimate the two ordinates on the convex hull (by identifying the hull edges at that particular absicssa). By sweeping, this will create the desired curves. At both ends of the range, use all abscissas in the first and last half-slices.
There will be a small downward bias where the curvature is high and/or the window is large, but nobody's perfect.
The total running time will be proportional to the product of the number of points and the window width. But I guess that an incremental version can do better.

There is a linear programming approach to this, and you might find R packages that will do linear programming for you.
Find a space of smooth curves such as splines, where a smooth curve is a linear combination of basis functions.
Now solve the linear program to minimize the sum, taken over all points, of the value at that point minus the value from a linear combination of basis functions at that point, subject to the constraint that the linear combination of basis functions must be no larger than the value at that point.

Anova loop in R

Im currently making a lot of ANOVA's in R and my code looks like this:
My data looks like this:
structure(list(Vial_nr = c(151L, 151L, 151L, 162L), Concentration = structure(c(1L,
1L, 1L, 1L), .Label = c("a", "b", "c", "d", "e", "x", "y"), class = "factor"),
Line = structure(c(1L, 1L, 1L, 1L), .Label = c("20", "23",
"40", "73"), class = "factor"), Sex = structure(c(1L, 1L,
1L, 1L), .Label = c("f", "m"), class = "factor"), Fly = structure(c(1L,
2L, 3L, 1L), .Label = c("1", "2", "3"), class = "factor"),
Temp = structure(c(1L, 1L, 1L, 1L), .Label = c("23", "29"
), class = "factor"), X0.5_sec = c(51.84, 41.28, 8.64, 28.8
), X1_sec = c(41.76, 8.64, 10.56, 42.72), X1.5_sec = c(42.72,
17.28, 10.08, 57.12), X2_sec = c(51.36, 29.76, 19.68, 71.52
), X2.5_sec = c(52.8, 44.64, 39.36, 69.12), X3_sec = c(55.68,
52.8, 58.08, 82.56), Vial = structure(c(138L, 138L, 138L,
149L), .Label = c("1", "2", "3", "4", "5", "6", "7", "8",
"9", "10", "11", "12", "13", "14", "15", "16", "17", "18",
"19", "20", "21", "22", "23", "24", "25", "26", "27", "28",
"29", "30", "31", "32", "33", "34", "35", "36", "37", "38",
"40", "41", "42", "43", "47", "49", "50", "56", "57", "59",
"61", "62", "63", "64", "66", "67", "68", "69", "70", "71",
"72", "73", "74", "75", "76", "77", "78", "79", "80", "81",
"82", "83", "84", "85", "86", "87", "88", "89", "90", "91",
"92", "93", "94", "95", "96", "97", "98", "99", "100", "101",
"102", "103", "104", "105", "106", "107", "108", "109", "110",
"111", "112", "113", "114", "115", "116", "117", "118", "119",
"120", "121", "122", "123", "124", "125", "126", "127", "128",
"129", "130", "131", "132", "133", "134", "135", "136", "137",
"138", "139", "140", "141", "142", "143", "144", "145", "146",
"147", "148", "149", "150", "151", "152", "153", "154", "155",
"156", "157", "158", "159", "160", "161", "162", "163", "164",
"165", "166", "167", "168", "169", "170", "171", "172", "173",
"174", "175", "176", "177", "178", "179", "180", "181", "182",
"183", "184", "185", "186", "187", "188", "189", "190", "191",
"192", "193", "194", "195", "196", "197", "198", "199", "200",
"201", "202", "203", "204", "205", "206", "207", "208", "209",
"210", "211", "212", "213", "214", "215", "216", "217", "218",
"219", "220", "221", "222", "223", "224", "225", "226", "227",
"228", "229", "230", "231", "232", "233", "234", "235", "236",
"237", "238", "239", "240", "241", "242", "243", "244", "245",
"246", "247", "248", "249", "250", "251", "252", "253", "254",
"255", "256", "257", "258", "259", "260", "261", "262", "263",
"264", "265", "266", "267", "268", "269", "270", "271", "273",
"274", "275", "276", "277", "278", "279", "280", "461", "462",
"463", "464", "465", "466", "467", "468", "469", "470", "471",
"472", "473", "474", "475", "476", "477", "478", "479", "480",
"481", "482", "483", "484", "485", "486", "487", "488", "489",
"490", "491", "492", "493", "494", "495", "496", "497", "498",
"499", "500", "501", "502", "503", "504", "505", "506", "507",
"508", "509", "510", "511", "512", "513", "514", "515", "516",
"517", "518", "519", "520", "521", "522", "523", "524", "525",
"526", "527", "528", "529", "530", "531", "532", "533", "534",
"535", "536", "537", "538", "539", "540", "541", "542", "543",
"544", "545", "546", "547", "548", "549", "550"), class = "factor")), .Names = c("Vial_nr",
"Concentration", "Line", "Sex", "Fly", "Temp", "X0.5_sec", "X1_sec",
"X1.5_sec", "X2_sec", "X2.5_sec", "X3_sec", "Vial"), row.names = 4:7, class = "data.frame")
dat <- read.table("Complete RING.txt", header =TRUE)
str(dat)
dat$Vial <- as.factor(dat$Vial)
dat$Line <- as.factor(dat$Line)
dat$Fly <- as.factor(dat$Fly)
dat$Temp <- as.factor(dat$Temp)
str(dat)
Line20af <- subset(dat, Line=="20" & Concentration=="a" & Sex=="f")
Line20bf <- subset(dat, Line=="20" & Concentration=="b" & Sex=="f")
Line20cf <- subset(dat, Line=="20" & Concentration=="c" & Sex=="f")
Line20df <- subset(dat, Line=="20" & Concentration=="d" & Sex=="f")
Line20ef <- subset(dat, Line=="20" & Concentration=="e" & Sex=="f")
Line20xf <- subset(dat, Line=="20" & Concentration=="x" & Sex=="f")
Line20yf <- subset(dat, Line=="20" & Concentration=="y" & Sex=="f")
out20 <- matrix(ncol=6, nrow=7)
colnames(out20) <- colnames(Line20af)[7:12]
rownames(out20) <- paste0("Concentration", 1:7)
for(i in 1:6){
tmp <- data.frame(Line20af[,6+i],Line20af$Temp)
colnames(tmp)<-c("y","c")
fit1=lm(y~c,data=tmp)
fit2=lm(y~1,data=tmp)
out20[1,i]<-anova(fit1,fit2)$"Pr(>F)"[2]
tmp <- data.frame(Line20bf[,6+i],Line20bf$Temp)
colnames(tmp)<-c("y","c")
fit1=lm(y~c,data=tmp)
fit2=lm(y~1,data=tmp)
out20[2,i]<-anova(fit1,fit2)$"Pr(>F)"[2]
tmp <- data.frame(Line20cf[,6+i],Line20cf$Temp)
colnames(tmp)<-c("y","c")
fit1=lm(y~c,data=tmp)
fit2=lm(y~1,data=tmp)
out20[3,i]<-anova(fit1,fit2)$"Pr(>F)"[2]
tmp <- data.frame(Line20df[,6+i],Line20df$Temp)
colnames(tmp)<-c("y","c")
fit1=lm(y~c,data=tmp)
fit2=lm(y~1,data=tmp)
out20[4,i]<-anova(fit1,fit2)$"Pr(>F)"[2]
tmp <- data.frame(Line20ef[,6+i],Line20ef$Temp)
colnames(tmp)<-c("y","c")
fit1=lm(y~c,data=tmp)
fit2=lm(y~1,data=tmp)
out20[5,i]<-anova(fit1,fit2)$"Pr(>F)"[2]
tmp <- data.frame(Line20xf[,6+i],Line20xf$Temp)
colnames(tmp)<-c("y","c")
fit1=lm(y~c,data=tmp)
fit2=lm(y~1,data=tmp)
out20[6,i]<-anova(fit1,fit2)$"Pr(>F)"[2]
tmp <- data.frame(Line20yf[,6+i],Line20yf$Temp)
colnames(tmp)<-c("y","c")
fit1=lm(y~c,data=tmp)
fit2=lm(y~1,data=tmp)
out20[7,i]<-anova(fit1,fit2)$"Pr(>F)"[2]
}
xtable(out20)
But doing this a lot of times just copy paste seems really dumb, i have tried to make temp data fields so i dont get to many datasets, however that doesn't yield any results. I have also tried to make a for loop using unique() on Concentration to make create the new datasets but then R doesn't print any results. Is there a way to optimize this piece of script to streamline my workflow and not overflow my workspace?
EDIT: added dput of data snip

Not sure what this error refers to, in beanplot

When I attempt to create a Beanplot for some data I get the following error
library(beanplot)
beanplot(error ~ rates, data = result[result$stream=="Speelyai", ],
col=c("orange", "black", "white", "red"), border ="pink",
what=c(0,1,1,1), maxstripline=.20)
Error in bw.SJ(x, method = "dpi") : sample is too sparse to find TD
Here is an attempt at using dput to provide a reproducible example
dput(head(result, 20))
structure(list(stream = c("Brooks", "Siouxon", "Speelyai", "Brooks",
"Siouxon", "Speelyai", "Brooks", "Siouxon", "Speelyai", "Brooks",
"Siouxon", "Speelyai", "Brooks", "Siouxon", "Speelyai", "Brooks",
"Siouxon", "Speelyai", "Brooks", "Siouxon"), n = c(3, 3, 3, 4,
4, 4, 5, 5, 5, 6, 6, 6, 7, 7, 7, 8, 8, 8, 9, 9), rates = c(3,
3, 3, 7.5, 7.5, 7.5, 10, 10, 10, 13, 13, 13, 15, 15, 15, 17,
17, 17, 19.5, 19.5), means = c(0.962915209069, 0.583192916943,
0.619923506082, 0.972270732503, 0.586503057099, 0.6118633820775,
0.9637475111, 0.580441970844, 0.5959238270885, 0.948657459436,
0.5846854247605, 0.559714620214, 0.954776205607, 0.582733153046333,
0.588721324855, 0.927079783491, 0.589401183924667, 0.584910716913,
0.9468615412695, 0.578929242163667), column = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L), .Label = c("1", "2", "3", "4", "5", "6", "7", "8",
"9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19",
"20", "21", "22", "23", "24", "25", "26", "27", "28", "29", "30",
"31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41",
"42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52",
"53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63",
"64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74",
"75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85",
"86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96",
"97", "98", "99", "100", "101", "102", "103", "104", "105", "106",
"107", "108", "109", "110", "111", "112", "113", "114", "115",
"116", "117", "118", "119", "120", "121", "122", "123", "124",
"125", "126", "127", "128", "129", "130", "131", "132", "133",
"134", "135", "136", "137", "138", "139", "140", "141", "142",
"143", "144", "145", "146", "147", "148", "149", "150", "151",
"152", "153", "154", "155", "156", "157", "158", "159", "160",
"161", "162", "163", "164", "165", "166", "167", "168", "169",
"170", "171", "172", "173", "174", "175", "176", "177", "178",
"179", "180", "181", "182", "183", "184", "185", "186", "187",
"188", "189", "190", "191", "192", "193", "194", "195", "196",
"197", "198", "199", "200", "201", "202", "203", "204", "205",
"206", "207", "208", "209", "210", "211", "212", "213", "214",
"215", "216", "217", "218", "219", "220", "221", "222", "223",
"224", "225", "226", "227", "228", "229", "230", "231", "232",
"233", "234", "235", "236", "237", "238", "239", "240", "241",
"242", "243", "244", "245", "246", "247", "248", "249", "250",
"251", "252", "253", "254", "255", "256", "257", "258", "259",
"260", "261", "262", "263", "264", "265", "266", "267", "268",
"269", "270", "271", "272", "273", "274", "275", "276", "277",
"278", "279", "280", "281", "282", "283", "284", "285", "286",
"287", "288", "289", "290", "291", "292", "293", "294", "295",
"296", "297", "298", "299", "300", "301", "302", "303", "304",
"305", "306", "307", "308", "309", "310", "311", "312", "313",
"314", "315", "316", "317", "318", "319", "320", "321", "322",
"323", "324", "325", "326", "327", "328", "329", "330", "331",
"332", "333", "334", "335", "336", "337", "338", "339", "340",
"341", "342", "343", "344", "345", "346", "347", "348", "349",
"350", "351", "352", "353", "354", "355", "356", "357", "358",
"359", "360", "361", "362", "363", "364", "365", "366", "367",
"368", "369", "370", "371", "372", "373", "374", "375", "376",
"377", "378", "379", "380", "381", "382", "383", "384", "385",
"386", "387", "388", "389", "390", "391", "392", "393", "394",
"395", "396", "397", "398", "399", "400", "401", "402", "403",
"404", "405", "406", "407", "408", "409", "410", "411", "412",
"413", "414", "415", "416", "417", "418", "419", "420", "421",
"422", "423", "424", "425", "426", "427", "428", "429", "430",
"431", "432", "433", "434", "435", "436", "437", "438", "439",
"440", "441", "442", "443", "444", "445", "446", "447", "448",
"449", "450", "451", "452", "453", "454", "455", "456", "457",
"458", "459", "460", "461", "462", "463", "464", "465", "466",
"467", "468", "469", "470", "471", "472", "473", "474", "475",
"476", "477", "478", "479", "480", "481", "482", "483", "484",
"485", "486", "487", "488", "489", "490", "491", "492", "493",
"494", "495", "496", "497", "498", "499", "500", "501", "502",
"503", "504", "505", "506", "507", "508", "509", "510", "511",
"512", "513", "514", "515", "516", "517", "518", "519", "520",
"521", "522", "523", "524", "525", "526", "527", "528", "529",
"530", "531", "532", "533", "534", "535", "536", "537", "538",
"539", "540", "541", "542", "543", "544", "545", "546", "547",
"548", "549", "550", "551", "552", "553", "554", "555", "556",
"557", "558", "559", "560", "561", "562", "563", "564", "565",
"566", "567", "568", "569", "570", "571", "572", "573", "574",
"575", "576", "577", "578", "579", "580", "581", "582", "583",
"584", "585", "586", "587", "588", "589", "590", "591", "592",
"593", "594", "595", "596", "597", "598", "599", "600", "601",
"602", "603", "604", "605", "606", "607", "608", "609", "610",
"611", "612", "613", "614", "615", "616", "617", "618", "619",
"620", "621", "622", "623", "624", "625", "626", "627", "628",
"629", "630", "631", "632", "633", "634", "635", "636", "637",
"638", "639", "640", "641", "642", "643", "644", "645", "646",
"647", "648", "649", "650", "651", "652", "653", "654", "655",
"656", "657", "658", "659", "660", "661", "662", "663", "664",
"665", "666", "667", "668", "669", "670", "671", "672", "673",
"674", "675", "676", "677", "678", "679", "680", "681", "682",
"683", "684", "685", "686", "687", "688", "689", "690", "691",
"692", "693", "694", "695", "696", "697", "698", "699", "700",
"701", "702", "703", "704", "705", "706", "707", "708", "709",
"710", "711", "712", "713", "714", "715", "716", "717", "718",
"719", "720", "721", "722", "723", "724", "725", "726", "727",
"728", "729", "730", "731", "732", "733", "734", "735", "736",
"737", "738", "739", "740", "741", "742", "743", "744", "745",
"746", "747", "748", "749", "750", "751", "752", "753", "754",
"755", "756", "757", "758", "759", "760", "761", "762", "763",
"764", "765", "766", "767", "768", "769", "770", "771", "772",
"773", "774", "775", "776", "777", "778", "779", "780", "781",
"782", "783", "784", "785", "786", "787", "788", "789", "790",
"791", "792", "793", "794", "795", "796", "797", "798", "799",
"800", "801", "802", "803", "804", "805", "806", "807", "808",
"809", "810", "811", "812", "813", "814", "815", "816", "817",
"818", "819", "820", "821", "822", "823", "824", "825", "826",
"827", "828", "829", "830", "831", "832", "833", "834", "835",
"836", "837", "838", "839", "840", "841", "842", "843", "844",
"845", "846", "847", "848", "849", "850", "851", "852", "853",
"854", "855", "856", "857", "858", "859", "860", "861", "862",
"863", "864", "865", "866", "867", "868", "869", "870", "871",
"872", "873", "874", "875", "876", "877", "878", "879", "880",
"881", "882", "883", "884", "885", "886", "887", "888", "889",
"890", "891", "892", "893", "894", "895", "896", "897", "898",
"899", "900", "901", "902", "903", "904", "905", "906", "907",
"908", "909", "910", "911", "912", "913", "914", "915", "916",
"917", "918", "919", "920", "921", "922", "923", "924", "925",
"926", "927", "928", "929", "930", "931", "932", "933", "934",
"935", "936", "937", "938", "939", "940", "941", "942", "943",
"944", "945", "946", "947", "948", "949", "950", "951", "952",
"953", "954", "955", "956", "957", "958", "959", "960", "961",
"962", "963", "964", "965", "966", "967", "968", "969", "970",
"971", "972", "973", "974", "975", "976", "977", "978", "979",
"980", "981", "982", "983", "984", "985", "986", "987", "988",
"989", "990", "991", "992", "993", "994", "995", "996", "997",
"998", "999", "1000"), class = "factor"), value = c(0.427070064,
0.905037358, 0.085540211, 1.43338843, 0.50574543, 0.3225239615,
0.889842105, 0.475018001, 0.150794906, 1.324221046, 0.3947968405,
0.370059413, 1.763186222, 0.794329673, 0.366688618666667, 0.288093907,
0.599490175666667, 1.31257167275, 1.147111171, 0.587266637333333
), truevalue = c(0.944062036, 0.585852702, 0.583984402, 0.944062036,
0.585852702, 0.583984402, 0.944062036, 0.585852702, 0.583984402,
0.944062036, 0.585852702, 0.583984402, 0.944062036, 0.585852702,
0.583984402, 0.944062036, 0.585852702, 0.583984402, 0.944062036,
0.585852702), error = c(-0.516991972, 0.319184656, -0.498444191,
0.489326394, -0.0801072719999999, -0.2614604405, -0.054219931,
-0.110834701, -0.433189496, 0.38015901, -0.1910558615, -0.213924989,
0.819124186, 0.208476971, -0.217295783333333, -0.655968129, 0.0136374736666667,
0.72858727075, 0.203049135, 0.00141393533333334)), .Names = c("stream",
"n", "rates", "means", "column", "value", "truevalue", "error"
), row.names = c(NA, 20L), class = "data.frame")

Error: only defined on a data frame with all numeric variables with ddply on large dataset

I'm trying to calculate sums and means on a very large dataset (~22000 records) for several parameters (e.g. Er_Count, Mn_Count) by month, year , Survey ID and Grid ID. I tried this code initially to get overall sums:
dlply(Effort_All,c("Er_Count","Mn_Count","Bp_Count"),sum)
And received the following error:
Error: only defined on a data frame with all numeric variables
Since I cannot even get overall sums, I am unable to get statistics by the specific variables either. Do I need to split the data in some manner?
I have included a sample dataset of 25 records below.
structure(list(Grid_ID = structure(c(527L, 92L, 331L, 395L, 934L,
93L), .Label = c("1", "1,000", "1,001", "1,002", "1,003", "1,004",
"1,005", "1,006", "1,007", "1,008", "1,009", "1,010", "1,011",
"1,012", "1,013", "1,014", "1,015", "1,016", "1,017", "1,018",
"1,019", "1,020", "1,021", "1,022", "1,023", "1,024", "1,025",
"1,026", "1,027", "1,028", "1,029", "1,030", "1,031", "1,032",
"1,033", "1,034", "1,035", "1,036", "1,037", "1,038", "1,039",
"1,040", "1,041", "1,042", "1,043", "1,044", "1,045", "1,046",
"1,047", "1,048", "1,049", "1,050", "1,051", "1,052", "1,053",
"1,054", "1,055", "1,056", "1,057", "1,058", "1,059", "1,060",
"1,061", "10", "100", "101", "102", "103", "104", "105", "106",
"107", "108", "109", "11", "110", "111", "112", "113", "114",
"115", "116", "117", "118", "119", "12", "120", "121", "122",
"123", "124", "125", "126", "127", "128", "129", "13", "130",
"131", "132", "133", "134", "135", "136", "137", "138", "139",
"14", "140", "141", "142", "143", "144", "145", "146", "147",
"148", "149", "15", "150", "151", "152", "153", "154", "155",
"156", "157", "158", "159", "16", "160", "161", "162", "163",
"164", "165", "166", "167", "168", "169", "17", "170", "171",
"172", "173", "174", "175", "176", "177", "178", "179", "18",
"180", "181", "182", "183", "184", "185", "186", "187", "188",
"189", "19", "190", "191", "192", "193", "194", "195", "196",
"197", "198", "199", "2", "20", "200", "201", "202", "203", "204",
"205", "206", "207", "208", "209", "21", "210", "211", "212",
"213", "214", "215", "216", "217", "218", "219", "22", "220",
"221", "222", "223", "224", "225", "226", "227", "228", "229",
"23", "230", "231", "232", "233", "234", "235", "236", "237",
"238", "239", "24", "240", "241", "242", "243", "244", "245",
"246", "247", "248", "249", "25", "250", "251", "252", "253",
"254", "255", "256", "257", "258", "259", "26", "260", "261",
"262", "263", "264", "265", "266", "267", "268", "269", "27",
"270", "271", "272", "273", "274", "275", "276", "277", "278",
"279", "28", "280", "281", "282", "283", "284", "285", "286",
"287", "288", "289", "29", "290", "291", "292", "293", "294",
"295", "296", "297", "298", "299", "3", "30", "300", "301", "302",
"303", "304", "305", "306", "307", "308", "309", "31", "310",
"311", "312", "313", "314", "315", "316", "317", "318", "319",
"32", "320", "321", "322", "323", "324", "325", "326", "327",
"328", "329", "33", "330", "331", "332", "333", "334", "335",
"336", "337", "338", "339", "34", "340", "341", "342", "343",
"344", "345", "346", "347", "348", "349", "35", "350", "351",
"352", "353", "354", "355", "356", "357", "358", "359", "36",
"360", "361", "362", "363", "364", "365", "366", "367", "368",
"369", "37", "370", "371", "372", "373", "374", "375", "376",
"377", "378", "379", "38", "380", "381", "382", "383", "384",
"385", "386", "387", "388", "389", "39", "390", "391", "392",
"393", "394", "395", "396", "397", "398", "399", "4", "40", "400",
"401", "402", "403", "404", "405", "406", "407", "408", "409",
"41", "410", "411", "412", "413", "414", "415", "416", "417",
"418", "419", "42", "420", "421", "422", "423", "424", "425",
"426", "427", "428", "429", "43", "430", "431", "432", "433",
"434", "435", "436", "437", "438", "439", "44", "440", "441",
"442", "443", "444", "445", "446", "447", "448", "449", "45",
"450", "451", "452", "453", "454", "455", "456", "457", "458",
"459", "46", "460", "461", "462", "463", "464", "465", "466",
"467", "468", "469", "47", "470", "471", "472", "473", "474",
"475", "476", "477", "478", "479", "48", "480", "481", "482",
"483", "484", "485", "486", "487", "488", "489", "49", "490",
"491", "492", "493", "494", "495", "496", "497", "498", "499",
"5", "50", "500", "501", "502", "503", "504", "505", "506", "507",
"508", "509", "51", "510", "511", "512", "513", "514", "515",
"516", "517", "518", "519", "52", "520", "521", "522", "523",
"524", "525", "526", "527", "528", "529", "53", "530", "531",
"532", "533", "534", "535", "536", "537", "538", "539", "54",
"540", "541", "542", "543", "544", "545", "546", "547", "548",
"549", "55", "550", "551", "552", "553", "554", "555", "556",
"557", "558", "559", "56", "560", "561", "562", "563", "564",
"565", "566", "567", "568", "569", "57", "570", "571", "572",
"573", "574", "575", "576", "577", "578", "579", "58", "580",
"581", "582", "583", "584", "585", "586", "587", "588", "589",
"59", "590", "591", "592", "593", "594", "595", "596", "597",
"598", "599", "6", "60", "600", "601", "602", "603", "604", "605",
"606", "607", "608", "609", "61", "610", "611", "612", "613",
"614", "615", "616", "617", "618", "619", "62", "620", "621",
"622", "623", "624", "625", "626", "627", "628", "629", "63",
"630", "631", "632", "633", "634", "635", "636", "637", "638",
"639", "64", "640", "641", "642", "643", "644", "645", "646",
"647", "648", "649", "65", "650", "651", "652", "653", "654",
"655", "656", "657", "658", "659", "66", "660", "661", "662",
"663", "664", "665", "666", "667", "668", "669", "67", "670",
"671", "672", "673", "674", "675", "676", "677", "678", "679",
"68", "680", "681", "682", "683", "684", "685", "686", "687",
"688", "689", "69", "690", "691", "692", "693", "694", "695",
"696", "697", "698", "699", "7", "70", "700", "701", "702", "703",
"704", "705", "706", "707", "708", "709", "71", "710", "711",
"712", "713", "714", "715", "716", "717", "718", "719", "72",
"720", "721", "722", "723", "724", "725", "726", "727", "728",
"729", "73", "730", "731", "732", "733", "734", "735", "736",
"737", "738", "739", "74", "740", "741", "742", "743", "744",
"745", "746", "747", "748", "749", "75", "750", "751", "752",
"753", "754", "755", "756", "757", "758", "759", "76", "760",
"761", "762", "763", "764", "765", "766", "767", "768", "769",
"77", "770", "771", "772", "773", "774", "775", "776", "777",
"778", "779", "78", "780", "781", "782", "783", "784", "785",
"786", "787", "788", "789", "79", "790", "791", "792", "793",
"794", "795", "796", "797", "798", "799", "8", "80", "800", "801",
"802", "803", "804", "805", "806", "807", "808", "809", "81",
"810", "811", "812", "813", "814", "815", "816", "817", "818",
"819", "82", "820", "821", "822", "823", "824", "825", "826",
"827", "828", "829", "83", "830", "831", "832", "833", "834",
"835", "836", "837", "838", "839", "84", "840", "841", "842",
"843", "844", "845", "846", "847", "848", "849", "85", "850",
"851", "852", "853", "854", "855", "856", "857", "858", "859",
"86", "860", "861", "862", "863", "864", "865", "866", "867",
"868", "869", "87", "870", "871", "872", "873", "874", "875",
"876", "877", "878", "879", "88", "880", "881", "882", "883",
"884", "885", "886", "887", "888", "889", "89", "890", "891",
"892", "893", "894", "895", "896", "897", "898", "899", "9",
"90", "900", "901", "902", "903", "904", "905", "906", "907",
"908", "909", "91", "910", "911", "912", "913", "914", "915",
"916", "917", "918", "919", "92", "920", "921", "922", "923",
"924", "925", "926", "927", "928", "929", "93", "930", "931",
"932", "933", "934", "935", "936", "937", "938", "939", "94",
"940", "941", "942", "943", "944", "945", "946", "947", "948",
"949", "95", "950", "951", "952", "953", "954", "955", "956",
"957", "958", "959", "96", "960", "961", "962", "963", "964",
"965", "966", "967", "968", "969", "97", "970", "971", "972",
"973", "974", "975", "976", "977", "978", "979", "98", "980",
"981", "982", "983", "984", "985", "986", "987", "988", "989",
"99", "990", "991", "992", "993", "994", "995", "996", "997",
"998", "999"), class = "factor"), ER_Groups = c(2, 2, 2, 3, 5,
6), Er_Count = c(60, 75, 14, 12, 8, 26), Mn_Count = c(30, 9, 6, 33,
7, 12), Bp_Groups = c(1, 2, 1, 1, 0, 1), Bp_Count = c(3, 3, 2,
5, 0, 6), Mn_Groups = c(1, 1, 3, 1, 0, 0), Month = c(10L, 6L,
12L, 4L, 2L, 4L), Year = c(2000L, 2001L, 2009L, 2004L, 2002L,
2001L), SurveyID = structure(c(16L, 24L, 93L, 56L, 34L, 22L), .Label = c("199708HS",
"199808HS", "199908HS", "199909SSLQ", "199910SSL", "199911SSL",
"200001SSLQ", "200002SSL", "200003SSLQ", "200004SSLQ", "200005SSL",
"200006SSL", "200007SSL", "200008HS", "200008SSL", "200009SSL",
"200010SSL", "200011SSL", "200101SSL", "200102SSL", "200103SSL",
"200104SSL", "200105SSL", "200106SSL", "200107SSL", "200108HS",
"200108SSL", "200109SSL", "200110SSL", "200111SSL", "200112SSL",
"200201SSL", "200202SSL", "200203SSL", "200204SSL", "200205SSL",
"200206SSL", "200207SSL", "200208HS", "200208SSL", "200210SSL",
"200211SSL", "200212SSL", "200301SSL", "200302SSL", "200303SSL",
"200304SSL", "200305SSL", "200306SSL", "200307SSL", "200309SSL",
"200310SSL", "200311SSL", "200312SSL", "200403SSL", "200404SSL",
"200405SSL", "200406SSL", "200407SSL", "200408HS", "200408SSL",
"200409SSL", "200505SSL", "200506SSL", "200507SSL", "200510SSL",
"200512SSL", "200603SSL", "200609SSL", "200612SSL", "200709GAP07",
"200710GAP07", "200712GAP07", "200802GAP07", "200803GAP07", "200804GAP07",
"200805GAP07", "200806GAP07", "200807GAP07", "200808GAP07", "200809GAP08",
"200810GAP08", "200812GAP08", "200901GAP08", "200903GAP08", "200904GAP08",
"200905GAP08", "200906GAP08", "200907GAP08", "200908GAP08", "200909GAP08",
"200910GAP09", "200912GAP09", "201001GAP09", "201002GAP09", "201003GAP09",
"201004GAP09", "201005GAP09", "201006GAP09", "201007GAP09", "201008GAP09",
"201009GAP09", "201010GAP09", "201011GAP09", "201101GAP09", "201102GAP09",
"201103GAP09", "201104GAP09", "201106GAP09", "201108GAP09", "201109GAP09",
"201111GAP09", "201201GAP09", "201203GAP09", "201205GAP09", "201207GAP09",
"201208GAP09", "201211GAP09", "201301GAP09", "201303GAP09", "201305GAP09",
"201307GAP09", "201309GAP09", "201311GAP09"), class = "factor"),
Er_Group_Density = c(4, 9, 12, 4, 1, 0), Mn_Group_Density = c(3,
1, 1, 1, 0, 2), Bp_Group_Density = c(1, 2, 1, 0, 1, 0), Er_Count_Density = c(50,
14, 12, 9, 6, 4), Mn_Count_Density = c(9, 5, 2, 3, 2, 0), Bp_Count_Density = c(2,
3, 0, 4, 1, 0)), .Names = c("Grid_ID", "ER_Groups", "Er_Count",
"Mn_Count", "Bp_Groups", "Bp_Count", "Mn_Groups", "Month", "Year",
"SurveyID", "Er_Group_Density", "Mn_Group_Density", "Bp_Group_Density",
"Er_Count_Density", "Mn_Count_Density", "Bp_Count_Density"), row.names = c(2770L,
4421L, 17348L, 11263L, 6736L, 3974L), class = "data.frame")

There are a number of ways to get statistics by group. I'll assume you have a bias for plyr, since your example uses it.
Remember that dlply() splits the data into smaller dataframes by the grouping variables, then it applies the requested function to each of the smaller dataframes. Therefore the function you pass should operate on a whole dataframe. sum() does not do this. You can write your own function, though.
Based on your description, what you want is something like this
myfun <- function(x) colSums(x[, c("Er_Count", "Mn_Count", "Bp_Count")])
dlply(Effort_All, c("Month", "Year", "Grid_ID", "SurveyID"), myfun)
Remember that the second argument to dlply() is the set of variables used for grouping. Not sure why you want the output as a list. Would it be easier to read if you used ddply (with the same arguments)?
Other approaches include using sqldf() or something like lapply().
=============== EDIT: Other approaches =============
sqldf is always very easy to read and understand:
output <- sqldf('select Month,Year,Grid_ID,SurveyID,
sum(Er_Count) as ercount,
sum(Mn_Count) as mncount,
sum(Bp_Count) as bpcount
from Effort_All
group by Month, Year, Grid_ID, SurveyID')
lapply works pretty much the same way as dlply. Just different arguments.

Also, you could use colwise from plyr
dlply(Effort_All, .(Month, Year, Grid_ID, SurveyID), colwise(sum, .(Er_Count, Mn_Count, Bp_Count)))
Or summarise_each from dplyr
library(dplyr)
Effort_All%>%
group_by(Month, Year, Grid_ID, SurveyID) %>%
summarise_each(funs(sum), Er_Count, Mn_Count, Bp_Count)
#Source: local data frame [6 x 7]
#Groups: Month, Year, Grid_ID
# Month Year Grid_ID SurveyID Er_Count Mn_Count Bp_Count
# 1 2 2002 884 200203SSL 8 7 0
# 2 4 2001 126 200104SSL 26 12 6
# 3 4 2004 399 200404SSL 12 33 5
# 4 6 2001 125 200106SSL 75 9 3
# 5 10 2000 517 200009SSL 60 30 3
# 6 12 2009 340 200912GAP09 14 6 2

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