[R-sig-eco] problems regarding varpart function in r

[Rajendra Mohan panda]

Dear members

I get immense help from this forum. Therefore I put my problems to this
forum without hesitation. I also thank you all for quick and valuable
responses. This time I face problems with *varpart function* and *forward
selection* while using vegan. I herewith attach my codes I have run in a
separate file so also a sample data structure for your kind reference. Look
forward to your valuable guidance and advice.

I have arranged the whole data into to tables in name SA (with sites and
species) and SAE containing only environmental variables (here I have
considered three).

I will be grateful for your help and response.

With best Regards
Rajendra M Panda
School of Water Resources,
Indian Institute of Technology Kharagpur
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>  getwd()
[1] "C:/Documents and Settings/Rajendra/Desktop"
> SA<-read.csv("SASP.csv",header = TRUE,stringsAsFactors = FALSE)
> colnames(SA)<-c("Sites", "Species")
>  Species<-c("A","B","C","D","E","F","G","H","I","J","K","L","M","N","O","P","Q","R","S","T","U", "V","W","X","Y","Z","AA","AB","AC","AD","AE","AF","AG","AH","AI","AJ","AK","AL","AM","AN","AO","AP","AQ","AR","AS","AT","AU","AV","AW","AX","AY","AZ","BA","BB","BC","BD","BE","BF","BG","BH","BI","BJ","BK","BL","BM","BN","BO","BP","BQ","BR","BS","BT","BU","BV","BW","BX","BY","BZ","CA","CB","CC","CD","CE","CF","CG","CH","CI","CJ","CK","CL","CM","CN","CO","CP","CQ","CR","CS","CT","CU","CV","CW","CX","CY","CZ","DA","DB","DC","DD","DE","DF","DG","DH","DI","DJ","DK","DL","DM","DN","DO","DP","DQ","DR","DS","DT","DU","DV","DW","DX","DY","DZ","EA","EB","EC","ED","EE","EF","EG","EH","EI","EJ","EK","EL","EM","EN","EO","EP","EQ","ER","ES","ET","EU","EV","EW","EX","EY","EZ","DA","DB","DC","DD","DE","DF","DG","DH","DI","DJ","DK","DL","DM","DN","DO","DP","DQ","DR","DS","DT","DU","DV","DW","DX","DY","DZ","EA","EB","EC","ED","EE","EF","EG","EH","EI","EJ","EK","EL","EM","EN","EO","EP","EQ","ER","ES","ET","EU","EV","EW","EX","EY","EZ","FA","FB","FC","FD","FE","FF","FG","FH","FI","FJ","FK","FL","FM","FN","FO","FP","FQ","FR","FS","FT","FU","FV","FW","FX","FY","FZ","GA","GB","GC","GD","GE","GF","GG","GH","GI","GJ","GK","GL","GM","GN","GO","GP","GQ","GR","GS","GT","GU","GV","GW","GX","GY","GZ","HA","HB","HC","HD","HE","HF","HG","HH","HI","HJ","HK","HL","HM","HN","HO","HP","HQ","HR","HS","HT","HU","HV","HW","HX","HY","HZ","IA","IB","IC","ID","IE","IF","IG","IH","II","IJ","IK","IL","IM","IN","IO","IP","IQ","IR","IS","IT","IU","IV","IW","IX","IY","IZ","JA","JB","JC","JD","JE","JF","JG","JH","JI","JJ","JK","JL","JM","JN","JO","JP","JQ","JR","JS","JT","JU","JV","JW","JX","JY","JZ","KA","KB","KC","KD","KE","KF","KG","KH","KI","KJ","KK","KL","KM","KN","KO","KP","KQ","KR","KS","KT","KU","KV","KW","KX","KY","KZ","LA","LB","LC","LD","LE","LF","LG","LH","LI","LJ","LK","LL","LM","LN","LO","LP","LQ","LR","LS","LT","LU","LV","LW","LX","LY","LZ","MA","MB","MC","MD","ME","MF","MG","MH","MI","MJ","MK","ML","MM","MN","MO","MP","MQ","MR","MS","MT","MU","MV","MW","MX","MY","MZ","NA","NB","NC","ND","NE","NF","NG","NH","NI","NJ","NK","NL","NM","NN","NO","NP","NQ","NR","NS","NT","NU","NV","NW","NX","NY","NZ","OA","OB","OC","OD","OE","OF","OG","OH","OI","OJ","OK","OL","OM","ON","OO","OP","OQ","OR","OS","OT","OU","OV","OW","OX","OY","OZ","PA","PB","PC","PD","PE","PF","PG","PH","PI","PJ","PK","PL","PM","PN","PO","PP","PQ","PR","PS","PT","PU","PV","PW","PX","PY","PZ","QA","QB","QC","QD","QE","QF","QG","QH","QI","QJ","QK","QL","QM","QN","QO","QP","QQ","QR","QS","QT","QU","QV","QW","QX","QY","QZ","RA","RB","RC","RD","RE","RF","RG","RH","RI","RJ","RK","RL","RM","RN","RO","RP","RQ","RR","RS","RT","RU","RV","RW","RX","RY","RZ","SA","SB","SC","SD","SE","SF","SG","SH","SI","SJ","SK","SL","SM","SN","SO","SP","SQ","SR","SS","ST","SU","SV","SW","SX","SY","SZ","TA","TB","TC","TD","TE","TF","TG","TH","TI","TJ","TK","TL","TM","TN","TO","TP","TQ","TR","TS","TT","TU","TV","TW","TX","TY","TZ","UA","UB","UC","UD","UE","UF","UG","UH","UI","UJ","UK","UL","UM","UN","UO","UP","UQ","UR","US","UT","UU","UV","UW","UX","UY","UZ","VA","VB","VC","VD","VE","VF","VG","VH","VI","VJ","VK","VL",
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+ "APX","APY","APZ","AQA","AQB","AQC","AQD","AQE","AQF","AQG","AQH","AQI","AQJ","AQK","AQL","AQM","AQN","AQO","AQP","AQQ","AQR","AQS","AQT","AQU","AQV","AQW","AQX","AQY","AQZ","ARA","ARB","ARC","ARD","ARE","ARF","ARG","ARH","ARI","ARJ","ARK","ARL","ARM","ARN","ARO","ARP","ARQ","ARR","ARS","ART","ARU","ARV","ARW","ARX","ARY","ARZ","ASA","ASB","ASC","ASD","ASE","ASF","ASG","ASH","ASI","ASJ","ASK","ASL","ASM","ASN","ASO","ASP","ASQ","ASR","ASS","AST","ASU","ASV","ASW","ASX","ASY","ASZ","ATA","ATB","ATC","ATD","ATE","ATF","ATG","ATH","ATI","ATJ","ATK","ATL","ATM","ATN","ATO","ATP","ATQ","ATR","ATS","ATT","ATU","ATV","ATW","ATX","ATY","ATZ","AUA","AUB","AUC","AUD","AUE","AUF","AUG","AUH","AUI","AUJ","AUK","AUL","AUM","AUN","AUO","AUP","AUQ","AUR","AUS","AUT","AUU","AUV","AUW","AUX","AUY","AUZ","AVA","AVB","AVC","AVD","AVE","AVF","AVG","AVH","AVI","AVJ","AVK","AVL","AVM","AVN","AVO","AVP","AVQ","AVR","AVS","AVT","AVU","AVV","AVW","AVX","AVY","AVZ","AWA","AWB","AWC","AWD","AWE","AWF","AWG","AWH","AWI","AWJ","AWK","AWL","AWM","AWN","AWO","AWP","AWQ","AWR","AWS","AWT","AWU","AWV","AWW","AWX","AWY","AWZ","AXA","AXB","AXC","AXD","AXE","AXF","AXG","AXH","AXI","AXJ","AXK","AXL","AXM","AXN","AXO","AXP","AXQ","AXR","AXS","AXT","AXU","AXV","AXW","AXX","AXY","AXZ","AYA","AYB","AYC","AYD","AYE","AYF","AYG","AYH","AYI","AYJ","AYK","AYL","AYM","AYN","AYO","AYP","AYQ","AYR","AYS","AYT","AYU","AYV","AYW","AYX","AYY","AYZ","AZA","AZB","AZC","AZD","AZE","AZF","AZG","AZH","AZI","AZJ","AZK","AZL","AZM","AZN","AZO","AZP","AZQ","AZR","AZS","AZT","AZU","AZV","AZW","AZX","AZY","AZZ","BAA","BAB","BAC","BAD","BAE","BAF","BAG","BAH","BAI","BAJ","BAK","BAL","BAM","BAN","BAO","BAP","BAQ","BAR","BAS","BAT","BAU","BAV","BAW","BAX","BAY","BAZ","BBA","BBB","BBC","BBD","BBE","BBF","BBG","BBH","BBI","BBJ","BBK","BBL","BBM","BBN","BBO","BBP","BBQ","BBR","BBS","BBT","BBU","BBV","BBW","BBX","BBY","BBZ","BCA","BCB","BCC","BCD","BCE","BCF","BCG","BCH","BCI","BCJ","BCK","BCL","BCM","BCN","BCO","BCP","BCQ","BCR","BCS","BCT","BCU","BCV","BCW","BCX","BCY")
> Sites<-c(1:434)
> Sites<-SA[2:435,1]
>  Species<-SA[2:435,2:1508]
> SAE<-read.csv("SAE.csv",header = TRUE,stringsAsFactors = FALSE)
> colnames(SAE)<- c( "Pptn", "Temp", "Moisture")
> Pptn<-c(0,1386,1774,2063,2145,2201,2237,2249,2295,2471,2483,2494,2575,2624,2637,2699,2703,2724,2824,2881,2923,2951,2960,3062,3063,3084,3103,3119,3125,3137,3161,3163,3195,3240,3255,3286,3290,3297,3344,3392,3401,3523,3531,3534,3563,3567,3578,3590,3614,3655,3706,3718,3724,3730,3731,3732,3756,3773,3815,3834,3835,3863,3881,3904,3935,3982,4032,4049,4081,4089,4120,4127,4191,4192,4241,4295,4299,4303,4323,4386,4400,4429,4480,4485,4533,4549,4632,4684,4686,4761,4778,4916,4960,4970,4990,5009,5066,5083,5092,5193,5208,5286,5338,5351,5400,5411,5488,5540,5589,5598,5612,5627,5630,5733,5749,6155,6210,6232,6243,6295)
>  Temp<-c(270,271,272,273,274,275,276,277,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296)
> Moisture<-c(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,46,47,48,49,50,51,53)
>  Temp<-SAE[2:435,2]
>    Pptn<-SAE[2:435,1]
>  Moisture<-SAE[2:435,3]
> library(permute)
> library(lattice)
>  library(vegan)
This is vegan 2.0-10
> SPHL<-decostand (SA, "hell", na.rm = TRUE)
> rda.vasc.0 <- rda (SPHL ~1, data = SAE, scale = FALSE, na.action = na.action.omit)
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
> rda.vasc.0 <- rda (SPHL ~1, data = SAE, scale = TRUE, na.action = na.action.omit)
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
> rda.vasc.0 <- rda (SPHL ~1, data = SAE, scale = TRUE, na.action = na.action = NULL)
Error: unexpected '=' in "rda.vasc.0 <- rda (SPHL ~1, data = SAE, scale = TRUE, na.action = na.action ="
> rda.vasc.0 <- rda (SPHL ~1, data = SAE, scale = TRUE, na.action = NULL)
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
> rda.vasc.0 <- rda (SPHL ~1, data = SAE, scale = FALSE)
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
> rda.vasc.0 <- rda (SPHL ~1, data = SAE)
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
> rda.vasc.0 <- rda (SPHL ~., data = SAE, scale = FALSE)
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
> rda.vasc.0 <- rda (SPHL ~., data = SAE, scale = FALSE, na.action = na.omit)
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
> rda.vasc.0 <- rda (SPHL ~., data = SAE, scale = TRUE, na.action = na.omit)
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
> SAE <- scale(SAE)
> SAE[is.nan(SAE)] <- 0 
> rda.vasc.All <- rda (SPHL ~., data = SAE, scale = TRUE, na.action = na.omit)
Error in formula.default(object, env = baseenv()) : invalid formula
> rda.vasc.All <- rda (SPHL ~., data = SAE, scale = FALSE, na.action = na.omit)
Error in formula.default(object, env = baseenv()) : invalid formula
> rda.vasc.All <- rda (SPHL ~ ., data = SAE, scale = FALSE, na.action = na.omit)
Error in formula.default(object, env = baseenv()) : invalid formula
> SAE<-read.csv("SAE.csv",header = TRUE,stringsAsFactors = FALSE)
> SPHL<-decostand (SA, "hell", na.rm = TRUE)
> rda.vasc.All <- rda (SPHL ~ ., data = SAE, scale = FALSE, na.action = na.omit)
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
> SAE[is.nan(SAE)] <- 0 
Error in is.nan(SAE) : default method not implemented for type 'list'
> rda.vasc.All <- rda (SPHL ~ ., SAE, scale = FALSE, na.action = na.omit)
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
> rda.vasc.All <- rda (SPHL ~ ., SAE, scale = FALSE, na.rm = TRUE)
Error in model.frame.default(data = SAE, na.rm = TRUE, na.action = function (object,  : 
  variable lengths differ (found for '(na.rm)')
> vp1 <- varpart (SPHL, ~Pptn, ~ Temp, ~Moisture, data = SAE)
Error in qr.fitted(Q, Y) : NA/NaN/Inf in foreign function call (arg 5)
> vp1 <- varpart (SPHL, ~Pptn, ~ Temp, ~Moisture, data = SAE, na.action = na.omit)
Error in as.vector(x, mode) : 
  cannot coerce type 'closure' to vector of type 'any'
> vp1 <- varpart (SPHL, ~Pptn, ~ Temp, ~Moisture, data = SAE, scale = FALSE, na.action = na.omit)
Error in as.vector(x, mode) : 
  cannot coerce type 'closure' to vector of type 'any'
> vp1<-rda(SPHL ~Pptn, data = X, scale = TRUE, na.action = na.fail)
Error in model.frame(data = X, na.action = function (object, ...)  : 
  object 'X' not found
> vp1 <- varpart (SPHL, ~Pptn + ~ Temp + ~Moisture, data = SAE, scale = FALSE, na.action = na.omit)
Error in as.vector(x, mode) : 
  cannot coerce type 'closure' to vector of type 'any'
> vp1 <- varpart (SPHL, ~Pptn + ~ Temp + ~Moisture, data = SAE, scale = FALSE)
Error in varpart(SPHL, ~Pptn + ~Temp + ~Moisture, data = SAE, scale = FALSE) : 
  needs 2 to 4 explanatory tables
> vp1 <- varpart (SPHL, ~Pptn + ~ Temp + ~Moisture, data = SAE, scale = TRUE)
Error in varpart(SPHL, ~Pptn + ~Temp + ~Moisture, data = SAE, scale = TRUE) : 
  needs 2 to 4 explanatory tables
> SAE <- scale(SAE)
> SAE[is.nan(SAE)] <- 0 
> vp1 <- varpart (SPHL, ~Pptn + ~ Temp + ~Moisture, data = SAE, scale = TRUE)
Error in varpart(SPHL, ~Pptn + ~Temp + ~Moisture, data = SAE, scale = TRUE) : 
  needs 2 to 4 explanatory tables
> vp1 <- varpart (SPHL, ~Pptn, ~ Temp, ~Moisture, data = SAE, scale = TRUE)
Error in model.frame.default(X[[i]], data, na.action = na.fail, drop.unused.levels = TRUE) : 
  'data' must be a data.frame, not a matrix or an array
> vp1 <- varpart (SPHL, ~Pptn, ~ Temp, ~Moisture, data = SAE, scale = TRUE, na.action = na.omit)
Error in model.frame.default(X[[i]], data, na.action = na.fail, drop.unused.levels = TRUE) : 
  'data' must be a data.frame, not a matrix or an array
> vp1 <- varpart (SPHL, ~Pptn, ~ Temp, data = SAE, scale = TRUE, na.action = na.omit)
Error in model.frame.default(X[[i]], data, na.action = na.fail, drop.unused.levels = TRUE) : 
  'data' must be a data.frame, not a matrix or an array
> varpart (SA, SAE$Pptn, SAE$Temp, SAE$Moisture, transfo = 'hell')
Error in SAE$Pptn : $ operator is invalid for atomic vectors
> varpart (SA, SAE, transfo = 'hell')
Error in varpart(SA, SAE, transfo = "hell") : 
  needs 2 to 4 explanatory tables
> varpart (SA, SAE [~Pptn, ~Temp, ~Moisture], transfo = 'hell')
Error in SAE[~Pptn, ~Temp, ~Moisture] : incorrect number of dimensions
> varpart (SA, ~Pptn, ~Temp, ~Moisture, data = SAE, transfo = "hell")
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
> varpart (SA, ~Pptn, ~Temp, ~Moisture, data = SAE, transfo = "hell", na.rm = TRUE)
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
> varpart (SA, ~Pptn, ~Temp, ~Moisture, data = SAE, transfo = "hell", scale = FALSE, na.rm = TRUE)
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
> varpart (SA, ~Pptn, ~Temp, ~Moisture, data = SAE, transfo = "hell", scale = TRUE, na.rm = TRUE)
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
> varpart (SA, ~Pptn, ~Temp, ~Moisture, data = SAE, transfo = "hell", na.rm = FALSE)
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
> varpart (SA, ~Pptn, ~Temp, ~Moisture, data = SAE, transfo = "hell", na.action = na.omit)
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
> varpart (SA, ~Pptn, ~Temp, ~Moisture, data = SAE, transfo = "hell", scale = FALSE, na.action = na.omit)
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
> varpart (SA, ~Pptn, ~Temp, ~Moisture, data = SAE, transfo = "hell", scale = TRUE, na.action = na.omit)
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
> SAE <- scale(SAE)
> SAE[is.nan(SAE)] <- 0 
> varpart (SA, ~Pptn, ~Temp, ~Moisture, data = SAE, transfo = "hell", scale = TRUE, na.action = na.omit)
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
> varpart (SA, ~Pptn, ~Temp, ~Moisture, data = SAE, transfo = "hell", scale = TRUE, na.rm = TRUE)
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
> varpart (SA, ~Pptn, ~Temp, ~Moisture, data = SAE, transfo = "hell", scale = TRUE, na.action = NULL)
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
> varpart (SA, ~Pptn, ~Temp, ~Moisture, data = SAE, transfo = "hell", scale = TRUE, na.action = na.exclude)
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
>