Skip to content
Prev 4363 / 7420 Next

problems regarding varpart function in r

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
-------------- next part --------------
[1] "C:/Documents and Settings/Rajendra/Desktop"
+ "VM","VN","VO","VP","VQ","VR","VS","VT","VU","VV","VW","VX","VY","VZ","WA","WB","WC","WD","WE","WF","WG","WH","WI","WJ","WK","WL","WM","WN","WO","WP","WQ","WR","WS","WT","WU","WV","WW","WX","WY","WZ","XA","XB","XC","XD","XE","XF","XG","XH","XI","XJ","XK","XL","XM","XN","XO","XP","XQ","XR","XS","XT","XU","XV","XW","XX","XY","XZ","YA","YB","YC","YD","YE","YF","YG","YH","YI","YJ","YK","YL","YM","YN","YO","YP","YQ","YR","YS","YT","YU","YV","YW","YX","YY","YZ","ZA","ZB","ZC","ZD","ZE","ZF","ZG","ZH","ZI","ZJ","ZK","ZL","ZM","ZN","ZO","ZP","ZQ","ZR","ZS","ZT","ZU","ZV","ZW","ZX","ZY","ZZ","AAA","AAB","AAC","AAD","AAE","AAF","AAG","AAH","AAI","AAJ","AAK","AAL","AAM","AAN","AAO","AAP","AAQ","AAR","AAS","AAT","AAU","AAV","AAW","AAX","AAY","AAZ","ABA","ABB","ABC","ABD","ABE","ABF","ABG","ABH","ABI","ABJ","ABK","ABL","ABM","ABN","ABO","ABP","ABQ","ABR","ABS","ABT","ABU","ABV","ABW","ABX","ABY","ABZ","ACA","ACB","ACC","ACD","ACE","ACF","ACG","ACH","ACI","ACJ","ACK","ACL","ACM","ACN","ACO","ACP","ACQ","ACR","ACS","ACT","ACU","ACV","ACW","ACX","ACY","ACZ","ADA","ADB","ADC","ADD","ADE","ADF","ADG","ADH","ADI","ADJ","ADK","ADL","ADM","ADN","ADO","ADP","ADQ","ADR","ADS","ADT","ADU","ADV","ADW","ADX","ADY","ADZ","AEA","AEB","AEC","AED","AEE","AEF","AEG","AEH","AEI","AEJ","AEK","AEL","AEM","AEN","AEO","AEP","AEQ","AER","AES","AET","AEU","AEV","AEW","AEX","AEY","AEZ","AFA","AFB","AFC","AFD","AFE","AFF","AFG","AFH","AFI","AFJ","AFK","AFL","AFM","AFN","AFO","AFP","AFQ","AFR","AFS","AFT","AFU","AFV","AFW","AFX","AFY","AFZ","AGA","AGB","AGC","AGD","AGE","AGF","AGG","AGH","AGI","AGJ","AGK","AGL","AGM","AGN","AGO","AGP","AGQ","AGR","AGS","AGT","AGU","AGV","AGW","AGX","AGY","AGZ","AHA","AHB","AHC","AHD","AHE","AHF","AHG","AHH","AHI","AHJ","AHK","AHL","AHM","AHN","AHO","AHP","AHQ","AHR","AHS","AHT","AHU","AHV","AHW","AHX","AHY","AHZ","AIA","AIB","AIC","AID","AIE","AIF","AIG","AIH","AII","AIJ","AIK","AIL","AIM","AIN","AIO","AIP","AIQ","AIR","AIS","AIT","AIU","AIV","AIW","AIX","AIY","AIZ","AJA","AJB","AJC","AJD","AJE","AJF","AJG","AJH","AJI","AJJ","AJK","AJL","AJM","AJN","AJO","AJP","AJQ","AJR","AJS","AJT","AJU","AJV","AJW","AJX","AJY","AJZ","AKA","AKB","AKC","AKD","AKE","AKF","AKG","AKH","AKI","AKJ","AKK","AKL","AKM","AKN","AKO","AKP","AKQ","AKR","AKS","AKT","AKU","AKV","AKW","AKX","AKY","AKZ","ALA","ALB","ALC","ALD","ALE","ALF","ALG","ALH","ALI","ALJ","ALK","ALL","ALM","ALN","ALO","ALP","ALQ","ALR","ALS","ALT","ALU","ALV","ALW","ALX","ALY","ALZ","AMA","AMB","AMC","AMD","AME","AMF","AMG","AMH","AMI","AMJ","AMK","AML","AMM","AMN","AMO","AMP","AMQ","AMR","AMS","AMT","AMU","AMV","AMW","AMX","AMY","AMZ","ANA","ANB","ANC","AND","ANE","ANF","ANG","ANH","ANI","ANJ","ANK","ANL","ANM","ANN","ANO","ANP","ANQ","ANR","ANS","ANT","ANU","ANV","ANW","ANX","ANY","ANZ","AOA","AOB","AOC","AOD","AOE","AOF","AOG","AOH","AOI","AOJ","AOK","AOL","AOM","AON","AOO","AOP","AOQ","AOR","AOS","AOT","AOU","AOV","AOW","AOX","AOY","AOZ","APA","APB","APC","APD","APE","APF","APG","APH","API","APJ","APK","APL","APM","APN","APO","APP","APQ","APR","APS","APT","APU","APV","APW",
+ "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")
This is vegan 2.0-10
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
Error: unexpected '=' in "rda.vasc.0 <- rda (SPHL ~1, data = SAE, scale = TRUE, na.action = na.action ="
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
Error in formula.default(object, env = baseenv()) : invalid formula
Error in formula.default(object, env = baseenv()) : invalid formula
Error in formula.default(object, env = baseenv()) : invalid formula
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
Error in is.nan(SAE) : default method not implemented for type 'list'
Error in svd(Xbar, nu = 0, nv = 0) : infinite or missing values in 'x'
Error in model.frame.default(data = SAE, na.rm = TRUE, na.action = function (object,  : 
  variable lengths differ (found for '(na.rm)')
Error in qr.fitted(Q, Y) : NA/NaN/Inf in foreign function call (arg 5)
Error in as.vector(x, mode) : 
  cannot coerce type 'closure' to vector of type 'any'
Error in as.vector(x, mode) : 
  cannot coerce type 'closure' to vector of type 'any'
Error in model.frame(data = X, na.action = function (object, ...)  : 
  object 'X' not found
Error in as.vector(x, mode) : 
  cannot coerce type 'closure' to vector of type 'any'
Error in varpart(SPHL, ~Pptn + ~Temp + ~Moisture, data = SAE, scale = FALSE) : 
  needs 2 to 4 explanatory tables
Error in varpart(SPHL, ~Pptn + ~Temp + ~Moisture, data = SAE, scale = TRUE) : 
  needs 2 to 4 explanatory tables
Error in varpart(SPHL, ~Pptn + ~Temp + ~Moisture, data = SAE, scale = TRUE) : 
  needs 2 to 4 explanatory tables
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
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
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
Error in SAE$Pptn : $ operator is invalid for atomic vectors
Error in varpart(SA, SAE, transfo = "hell") : 
  needs 2 to 4 explanatory tables
Error in SAE[~Pptn, ~Temp, ~Moisture] : incorrect number of dimensions
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed
Error in if (any(x < 0, na.rm = na.rm)) { : 
  missing value where TRUE/FALSE needed